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1. Prevalence and Genetic Diversity of Bat Hepatitis B Viruses in Bat Species Living in Gabon

Author

Danielle S. Koumba Mavoungou, Linda Bohou Kombila, Neil M. Longo Pendy, Schedy E. Koumba Moukouama, Sonia Etenna Lekana-Douki, Gaël D. Maganga, Eric M. Leroy, Avelin F. Aghokeng, and Nadine N’dilimabaka

Subjects
hepatitis B virus, genetic diversity, bat species, interspecies transmission, Gabon, Microbiology, QR1-502
Abstract

Hepatitis B virus (HBV) infection leads to around 800,000 deaths yearly and is considered to be a major public health problem worldwide. However, HBV origins remain poorly understood. Here, we looked for bat HBV (BtHBV) in different bat species in Gabon to investigate the role of these animals as carriers of ancestral hepadnaviruses because these viruses are much more diverse in bats than in other host species. DNA was extracted from 859 bat livers belonging to 11 species collected in caves and villages in the southeast of Gabon and analyzed using PCRs targeting the surface gene. Positive samples were sequenced using the Sanger method. BtHBV DNA was detected in 64 (7.4%) individuals belonging to eight species mainly collected in caves. Thirty-six (36) sequences among the 37 obtained after sequencing were phylogenetically close to the RBHBV strain recently isolated in Gabonese bats, while the remaining sequence was close to a rodent HBV strain isolated in America. The generalized linear mixed model showed that the variable species best explained the occurrence of BtHBV infection in bats. The discovery of a BtHBV strain homologous to a rodent strain in bats raises the possibility that these animals may be carriers of ancestral hepadnaviruses.

Published
2024
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2. HPV genotypes in high-grade cervical lesions and invasive cervical carcinoma detected in Gabonese women

Author

Pamela Moussavou-Boundzanga, Ismaël Hervé Koumakpayi, Corinne Engohan Aloghe, Junie K. Chansi, Rose Revignet, Eric M. Leroy, and Nicolas Berthet

Subjects
High-grade cervical lesions, Invasive cervical cancer, HPV, Gabon, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Cervical cancer is the third most common cancer among women worldwide, but particularly affects women living in sub-Saharan Africa. Screening and vaccination programs are two prevention approaches that can reduce cervical cancer incidence. However, effective vaccination campaigns require better knowledge of the prevalence of the main human papillomavirus (HPV) genotypes reported in high-grade neoplastic lesions and invasive carcinomas in women. Methods All samples collected in this study were processed using standard histopathological methods with haematoxylin and eosin staining of the sections. Areas with abnormal cells were then identified. The HPV genotype was determined on the DNA extracted from the same sections using nested PCR followed by amplicon sequencing and real-time PCR specific to five different HPV genotypes (16, 18, 33, 45 and 58). Results A total of 132 Gabonese patients with high-grade neoplastic lesions were included in this study; 81% were squamous cell carcinomas (SCC). At least one HPV was detected in 92.4% patients; HPV16 (75.4%) was the most frequent genotype, followed by HPV18, 58, 45, 33 and 35. Moreover, histological analysis showed that SCC samples had 50% and 58.2% stage III and IV tumor cells, respectively, according to the FIGO classification. Finally, 36.9% of these stage III and IV patients were less than 50 years old. Conclusions Our results confirm the high prevalence of HPV16 and 18 genotypes among high-grade lesions in Gabonese women. This study confirms the need for a national strategy for early screening of precancerous lesions associated with a broad national vaccination program among non-sexually active women to significantly reduce the long-term cancer burden.

Published
2023
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3. Absence of Coronavirus RNA in Faecal Samples from Wild Primates in Gabon, Central Africa

Author

Illich Manfred Mombo, Océane Rieu, Matthieu Fritz, Larson Boundenga, Telstar Ndong Mebaley, Clark Mbou-Boutambe, Léadisaelle Hosanna Lenguiya, Gael Darren Maganga, Virginie Rougeron, Franck Prugnolle, Fredéric Thomas, and Eric M. Leroy

Subjects
coronaviruses, chimpanzee, gorilla, mandrill, surveillance, zoonosis, Medicine
Abstract

Coronaviruses (CoVs, Coronaviridae) are a diverse group of viruses that infect mammals, birds, and fish. Seven CoVs infect humans, among which Severe Acute Respiratory Syndrome CoVs-1 and -2 and Middle East respiratory syndrome CoVs have shown how they can impact global health and the economy. Their spillover from bats-the natural reservoir-to humans has required intermediary hosts. Prevention requires that active surveillance be conducted on animals. Today, there is no data concerning the genetic diversity of CoVs naturally circulating in wild primates. This study aimed to screen wild great apes and mandrills in Gabon for CoVs. A total of 229 faecal samples of great apes and mandrills collected from 2009 to 2012 in forests and national parks were used for the detection of CoVs by nested PCR using primers targeting a conserved region of the RNA-dependent RNA polymerase. While all samples were negative, this lack of detection could be related to sample size, the transient nature of the infection, or because faecal samples are not suitable for detecting CoVs in primates. A longitudinal study should be performed and other non-invasive methods used to collect respiratory samples to better evaluate the circulation of CoVs in these primates.

Published
2023
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4. Detection of SARS‐CoV‐2 in two cats during the second wave of the COVID‐19 pandemic in France

Author

Matthieu Fritz, Nicolas Nesi, Solène Denolly, Bertrand Boson, Vincent Legros, Serge G. Rosolen, Alexandra Briend‐Marchal, Meriadeg Ar Gouilh, and Eric M. Leroy

Subjects
cats, mild‐respiratory clinical signs, NGS, One Health, SARS‐CoV‐2, serology, Veterinary medicine, SF600-1100
Abstract

Abstract Although there are several reports in the literature of SARS‐CoV‐2 infection in cats, few SARS‐CoV‐2 sequences from infected cats have been published. In this study, SARS‐CoV‐2 infection was evaluated in two cats by clinical observation, molecular biology (qPCR and NGS), and serology (microsphere immunoassay and seroneutralization). Following the observation of symptomatic SARS‐CoV‐2 infection in two cats, infection status was confirmed by RT‐qPCR and, in one cat, serological analysis for antibodies against N‐protein and S‐protein, as well as neutralizing antibodies. Comparative analysis of five SARS‐CoV‐2 sequence fragments obtained from one of the cats showed that this infection was not with one of the three recently emerged variants of SARS‐CoV‐2. This study provides additional information on the clinical, molecular, and serological aspects of SARS‐CoV‐2 infection in cats.

Published
2022
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5. Early Circulation of SARS-CoV-2, Congo, 2020

Author

Novy Charel Bobouaka Bonguili, Matthieu Fritz, Leadisaelle Hosanna Lenguiya, Pembe Issamou Mayengue, Félix Koukouikila-Koussounda, Louis Régis Dossou-Yovo, Cynthia Nkoua Badzi, Eric M. Leroy, and Fabien R. Niama

Subjects
COVID-19, 2019 novel coronavirus disease, coronavirus disease, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, viruses, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

To determine when severe acute respiratory syndrome coronavirus 2 arrived in Congo, we retrospectively antibody tested 937 blood samples collected during September 2019–February 2020. Seropositivity significantly increased from 1% in December 2019 to 5.3% in February 2020, before the first officially reported case in March 2020, suggesting unexpected early virus circulation.

Published
2022
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6. Molecular Identification of Enteric Viruses in Domestic Animals in Northeastern Gabon, Central Africa

Author

Linda Bohou Kombila, Nadine N’dilimabaka, Déborah Garcia, Océane Rieu, Jéordy Dimitri Engone Ondo, Telstar Ndong Mebaley, Larson Boundenga, Matthieu Fritz, Léadisaelle Hosanna Lenguiya, Gael Darren Maganga, Eric M. Leroy, Pierre Becquart, and Illich Manfred Mombo

Subjects
astroviruses, enteroviruses, caliciviruses, vesivirus, small ruminants, dogs, Veterinary medicine, SF600-1100, Zoology, QL1-991
Abstract

Astroviruses (AstVs), enteroviruses (EVs), and caliciviruses (CaVs) infect several vertebrate taxa. Transmitted through the fecal–oral route, these enteric viruses are highly resistant and can survive in the environment, thereby increasing their zoonotic potential. Here, we screened for AstVs, EVs, and CaVs to investigate the role of domestic animals in the emergence of zoonoses, because they are situated at the human/wildlife interface, particularly in rural forested areas in Central Africa. Rectal swabs were obtained from 123 goats, 41 sheep, and 76 dogs in 10 villages located in northeastern Gabon. Extracted RNA reverse-transcribed into cDNA was used to detect AstVs, EVs, and CaVs by amplification of the RNA-dependent RNA polymerase (RdRp), or capsid protein (VP1) gene using PCR. A total of 23 samples tested positive, including 17 goats for AstVs, 2 goats, 2 sheep, 1 dog for EVs, and 1 dog for CaVs. Phylogenetic analyses revealed that AstV RdRp sequences clustered with sheep-, goat-, or bovine-related AstVs. In addition, one goat and two sheep VP1 sequences clustered with caprine/ovine-related Evs within the Enterovirus G species, and the CaV was a canine vesivirus. However, human-pathogenic Evs, EV-B80 and EV-C99, were detected in goats and dogs, raising questions on the maintenance of viruses able to infect humans.

Published
2023
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7. Whole-Genome Characterization of SARS-CoV-2 Reveals Simultaneous Circulation of Three Variants and a Putative Recombination (20B/20H) in Pets, Brazzaville, Republic of the Congo

Author

Léadisaelle Hosanna Lenguiya, Matthieu Fritz, Daphné de Riols De Fonclare, Sandrine Corbet, Pierre Becquart, Christophe Mbou, Ruben Junias Nguie, Wivine Salva Mouellet, Jordy Exaucé Lyelet Demboux, N’kaya-Tobi, Pembe Issamou Mayengue, Félix Koukouikila-Koussounda, Meriadeg Ar Gouilh, Eric M. Leroy, and Fabien Roch Niama

Subjects
SARS-CoV-2, pets, cats, dogs, RT-qPCR, serology, Microbiology, QR1-502
Abstract

Following the emergence of SARS-CoV-2, cases of pets infected with variants circulating among humans were reported. In order to evaluate the occurrence of SARS-CoV-2 circulation among pets in the Republic of the Congo, we conducted a ten-month study of dogs and cats living in COVID-19-positive households in Brazzaville and neighboring localities. Real-time PCR and the Luminex platform were used to detect SARS-CoV-2 RNA and antibodies to SARS-CoV-2 RBD and S proteins, respectively. Our results show for the first time the simultaneous circulation of several variants of SARS-CoV-2, including viruses from clades 20A and 20H and a putative recombinant variant between viruses from clades 20B and 20H. We found a high seroprevalence of 38.6%, with 14% of tested pets positive for SARS-CoV-2 RNA. Thirty-four percent of infected pets developed mild clinical signs, including respiratory and digestive signs, and shed the virus for about one day to two weeks. These results highlight the potential risk of SARS-CoV-2 interspecies transmission and the benefits of a “One Health” approach that includes SARS-CoV-2 diagnosis and surveillance of viral diversity in pets. This approach aims to prevent transmission to surrounding wildlife as well as spillback to humans.

Published
2023
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8. Potential Association between Zika Infection and Microcephaly during 2007 Fever Outbreak, Gabon

Author

Claudine A. Kombila Koumavor, Eric Elguero, and Eric M. Leroy

Subjects
Aedes albopictus, Africa, febrile illnesses, Gabon, high-risk pregnancy, microcephaly, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Although Zika virus (ZIKV) circulates in sub-Saharan Africa, no case of ZIKV-associated microcephaly has thus far been reported. Here, we report evidence of a possible association between a 2007 outbreak of febrile illness and an increase in microcephaly and possibly ZIKV infection in Gabon.

Published
2021
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9. At Least Seven Distinct Rotavirus Genotype Constellations in Bats with Evidence of Reassortment and Zoonotic Transmissions

Author

Ceren Simsek, Victor Max Corman, Hermann Ulrich Everling, Alexander N. Lukashev, Andrea Rasche, Gael Darren Maganga, Tabea Binger, Daan Jansen, Leen Beller, Ward Deboutte, Florian Gloza-Rausch, Antje Seebens-Hoyer, Stoian Yordanov, Augustina Sylverken, Samuel Oppong, Yaw Adu Sarkodie, Peter Vallo, Eric M. Leroy, Mathieu Bourgarel, Kwe Claude Yinda, Marc Van Ranst, Christian Drosten, Jan Felix Drexler, and Jelle Matthijnssens

Subjects
Microbiology, QR1-502
Abstract

The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens.

Published
2021
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10. High prevalence of SARS-CoV-2 antibodies in pets from COVID-19+ households

Author

Matthieu Fritz, Béatrice Rosolen, Emilie Krafft, Pierre Becquart, Eric Elguero, Oxana Vratskikh, Solène Denolly, Bertrand Boson, Jessica Vanhomwegen, Meriadeg Ar Gouilh, Angeli Kodjo, Catherine Chirouze, Serge G. Rosolen, Vincent Legros, and Eric M. Leroy

Subjects
SARS-CoV-2, COVID-19, Pets, Seroprevalence, One health, Luminex, Medicine (General), R5-920
Abstract

In a survey of household cats and dogs of laboratory-confirmed COVID-19 patients, we found a high seroprevalence of SARS-CoV-2 antibodies, ranging from 21% to 53%, depending on the positivity criteria chosen. Seropositivity was significantly greater among pets from COVID-19+ households compared to those with owners of unknown status. Our results highlight the potential role of pets in the spread of the epidemic.

Published
2020
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12. First Evidence of Natural SARS-CoV-2 Infection in Domestic Rabbits

Author

Matthieu Fritz, Daphné de Riols de Fonclare, Déborah Garcia, Stéphanie Beurlet, Pierre Becquart, Serge G. Rosolen, Alexandra Briend-Marchal, and Eric M. Leroy

Subjects
SARS-CoV-2, COVID-19, rabbits, pet rabbit, France, Luminex, Veterinary medicine, SF600-1100
Abstract

We tested 144 pet rabbits sampled in France between November 2020 and June 2021 for antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by microsphere immunoassay. We reported the first evidence of a natural SARS-CoV-2 infection in rabbits with a low observed seroprevalence between 0.7% and 1.4%.

Published
2022
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13. Detection of human bocavirus-1 in both nasal and stool specimens from children under 5 years old with influenza-like illnesses or diarrhea in Gabon

Author

Sonia Etenna Lekana-Douki, Sylvie Behillil, Vincent Enouf, Eric M. Leroy, and Nicolas Berthet

Subjects
HBoV-1, Influenza-like illness, Diarrhea, Children, Gabon, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Objective Human bocavirus (HBoV) is a viral pathogen which causes respiratory tract diseases and acute gastroenteritis worldwide. This virus mainly affected children under 5 years old. There is little information on HBoV in Gabon. Two first studies was conducted to determine the prevalence of respiratory and enteric viruses in children under 5 years old who visited health centers for influenza-like illness (ILI) or diarrhea in Gabon from March 2010 to June 2011. However, HBoV was not included in the screening. The aim of this retrospective study was to evaluate the prevalence and the HBoV genotype in children under 5 years old with ILI or diarrhea in Gabon. Results A total of 810 nasal swabs and 317 feces samples collected during the two first study were analyzed among which 32 (4.4%) and 7 (2.2%) were positive for HBoV respectively. While there were no significant differences in prevalence between age groups in children with ILI, all children with diarrhea were under 12 months of age. Moreover, 84.4 and 42.8% were diagnosed in co-infections with at least one other respiratory virus, or enteric viruses respectively. Finally, HBoV subtype 1 has been detected in both respiratory and gastrointestinal tracts with very low variability.

Published
2018
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14. Re-emergence of chikungunya in the Republic of the Congo in 2019 associated with a possible vector-host switch

Author

Matthieu Fritz, Raphaël Taty Taty, Chantale Portella, Christ Guimbi, Michel Mankou, Eric M. Leroy, and Pierre Becquart

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

In January 2019, an outbreak of chikungunya virus fever was reported in a rural region near Pointe-Noire, Republic of the Congo. Molecular and phylogenetic analysis of this new CHIKV strain demonstrated the presence of the A226V substitution and a surprisingly close relation with Aedes aegypti-associated Central Africa chikungunya strains. These results, combined with the preponderance of Aedes albopictus in the outbreak area, suggest a recent vector-host switch facilitated by the emergence and spread of the A226V mutation from a related CHIKV strain previously circulating in Aedes aegypti. The proximity of this outbreak to the large city of Pointe-Noire alerts us to a possibly devastating future outbreak in the absence of measures limiting the proliferation of Ae. albopictus mosquitoes. Keywords: Chikungunya, Virus, Outbreak, Republic of the Congo, Central Africa, Aedes albopictus

Published
2019
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15. Human papillomavirus detection using the Abbott RealTime high-risk HPV tests compared with conventional nested PCR coupled to high-throughput sequencing of amplification products in cervical smear specimens from a Gabonese female population

Author

Pamela Moussavou-Boundzanga, Ismaël Hervé Koumakpayi, Ingrid Labouba, Eric M. Leroy, Ernest Belembaogo, and Nicolas Berthet

Subjects
Abbott RealTime high-risk HPV, Conventional PCR, Human papillomavirus, Screening, Cervical cancer, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Cervical cancer is the fourth most common malignancy in women worldwide. However, screening with human papillomavirus (HPV) molecular tests holds promise for reducing cervical cancer incidence and mortality in low- and middle-income countries. The performance of the Abbott RealTime High-Risk HPV test (AbRT) was evaluated in 83 cervical smear specimens and compared with a conventional nested PCR coupled to high-throughput sequencing (HTS) to identify the amplicons. Results The AbRT assay detected at least one HPV genotype in 44.57% of women regardless of the grade of cervical abnormalities. Except for one case, good concordance was observed for the genotypes detected with the AbRT assay in the high-risk HPV category determined with HTS of the amplicon generated by conventional nested PCR. Conclusions The AbRT test is an easy and reliable molecular tool and was as sensitive as conventional nested PCR in cervical smear specimens for detection HPVs associated with high-grade lesions. Moreover, sequencing amplicons using an HTS approach effectively identified the genotype of the hrHPV identified with the AbRT test.

Published
2017
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16. Report of One-Year Prospective Surveillance of SARS-CoV-2 in Dogs and Cats in France with Various Exposure Risks: Confirmation of a Low Prevalence of Shedding, Detection and Complete Sequencing of an Alpha Variant in a Cat

Author

Emilie Krafft, Solène Denolly, Bertrand Boson, Sophie Angelloz-Pessey, Sophie Levaltier, Nicolas Nesi, Sandrine Corbet, Bryce Leterrier, Matthieu Fritz, Eric M. Leroy, Meriadeg Ar Gouilh, François-Loïc Cosset, Angeli Kodjo, and Vincent Legros

Subjects
SARS-CoV-2, variants, prevalence, sequencing, zoonosis, Microbiology, QR1-502
Abstract

Despite the probable zoonotic origin of SARS-CoV-2, only limited research efforts have been made to understand the role of companion animals in SARS-CoV-2 epidemiology. According to recent serological prevalence studies, human-to-companion animal transmission is quite frequent, which led us to consider that the risk of SARS-CoV-2 transmission from animal to human, albeit negligible in the present context, may have been underestimated. In this study, we provide the results of a prospective survey that was conducted to evaluate the SARS-CoV-2 isolation rate by qRT-PCR in dogs and cats with different exposure risks and clinical statuses. From April 2020 to April 2021, we analyzed 367 samples and investigated the presence of SARS-CoV-2 RNA using qRT-PCR. Only four animals tested positive, all of them being cats. Three cats were asymptomatic and one presented a coryza-like syndrome. We describe in detail the infection in two cats and the associated clinical characteristics. Importantly, we obtained SARS-CoV-2 genomes from one infected animal and characterized them as Alpha variants. This represents the first identification of the SARS-CoV-2 Alpha variant in an infected animal in France.

Published
2021
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17. Herpes Infections in Suspected Cases of Yellow Fever in the Democratic Republic of the Congo

Author

Sheila Makiala-Mandanda, Jessica L. Abbate, Elisabeth Pukuta-Simbu, Steve Ahuka-Mundeke, Jean-Jacques Muyembe-Tamfum, Eric M. Leroy, and Pierre Becquart

Subjects
herpes, yellow fever, Democratic Republic of the Congo, Medicine (General), R5-920
Abstract

In the battle to quickly identify potential yellow fever arbovirus outbreaks in the Democratic Republic of the Congo, active syndromic surveillance of acute febrile jaundice patients across the country is a powerful tool. However, patients who test negative for yellow fever virus infection are too often left without a diagnosis. By retroactively screening samples for other potential viral infections, we can both try to find sources of patient disease and gain information on how commonly they may occur and co-occur. Several human arboviruses have previously been identified, but there remain many other viral families that could be responsible for acute febrile jaundice. Here, we assessed the prevalence of human herpes viruses (HHVs) in these acute febrile jaundice disease samples. Total viral DNA was extracted from serum of 451 patients with acute febrile jaundice. We used real-time quantitative PCR to test all specimens for cytomegalovirus (CMV), herpes simplex virus (HSV), human herpes virus type 6 (HHV-6) and varicella-zoster virus (VZV). We found 21.3% had active HHV replication (13.1%, 2.4%, 6.2% and 2.4% were positive for CMV, HSV, HHV-6 and VZV, respectively), and that nearly half (45.8%) of these infections were characterized by co-infection either among HHVs or between HHVs and other viral infection, sometimes associated with acute febrile jaundice previously identified. Our results show that the role of HHV primary infection or reactivation in contributing to acute febrile jaundice disease identified through the yellow fever surveillance program should be routinely considered in diagnosing these patients.

Published
2021
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18. Detection of Ebola Virus Antibodies in Fecal Samples of Great Apes in Gabon

Author

Illich M. Mombo, Matthieu Fritz, Pierre Becquart, Florian Liegeois, Eric Elguero, Larson Boundenga, Telstar N. Mebaley, Franck Prugnolle, Gael D. Maganga, and Eric M. Leroy

Subjects
great ape, Ebola, Africa, Luminex, Microbiology, QR1-502
Abstract

Based on a large study conducted on wild great ape fecal samples collected in regions of Gabon where previous human outbreaks of Ebola virus disease have occurred between 1994 and 2002, we provide evidence for prevalence of Zaire ebolavirus (EBOV)-specific antibodies of 3.9% (immunoglobulin G (IgG)) and 3.5% (immunoglobulin M (IgM)) in chimpanzees and 8.8% (IgG) and 2.4% (IgM) in gorillas. Importantly, we observed a high local prevalence (31.2%) of anti-EBOV IgG antibodies in gorilla samples. This high local rate of positivity among wild great apes raises the question of a spatially and temporally localized increase in EBOV exposure risk and the role that can be played by these animals as sentinels of the virus’s spread or reemergence in a given area.

Published
2020
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19. Molecular epidemiology of enteric viruses and genotyping of rotavirus A, adenovirus and astrovirus among children under 5 years old in Gabon

Author

Sonia Etenna Lekana-Douki, Claudine Kombila-Koumavor, Dieudonné Nkoghe, Christian Drosten, Jan Felix Drexler, and Eric M. Leroy

Subjects
Gabon, gastroenteritis, virus, strain, Infectious and parasitic diseases, RC109-216
Abstract

Objectives: This study aimed to determine the prevalence of enteric viruses causing gastroenteritis, and the circulating stains, in Gabonese children under five years old who visited health centers between March 2010 and June 2011. Methods: Stool specimens were collected and sent for analysis to CIRMF (Centre International de Recherches Médicales de Franceville). Stools were screened for six enteric viruses (rotavirus, adenovirus, norovirus I and II, sapovirus, human astrovirus) by means of a multiplex real-time reverse transcription polymerase chain reaction, and Rotavirus A, Adenovirus and Astrovirus were genotyped. Results: Among the 317 specimens analyzed, 193 (60.9%) were positive for at least one enteric virus. Rotavirus A (RVA) (27.1%) was the most frequently detected virus, followed by human Adenovirus (HAdV) (19.6%), Norovirus II (NoVs-II) (13.9%), Norovirus I (NoVs-I) (9.1%), Sapovirus (SaV) (9.5%) and human Astrovirus (HAstV) (6.3%). One-third of the 193 positive samples contained more than one virus. The most common Rotavirus A genotype was G6P[6]. Various HAdV serotypes were found. HAstV-1 was identified. Conclusions: These findings improve our knowledge of circulating enteric viruses in Gabon. The emergence of unusual G6P[6] strain of rotavirus A, predominant, suggested a particular epidemiological surveillance of circulating rotavirus strains during the introduction of vaccination in Gabon.

Published
2015
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20. Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014

Author

Jens H. Kuhn, Kristian G. Andersen, Sylvain Baize, Yīmíng Bào, Sina Bavari, Nicolas Berthet, Olga Blinkova, J. Rodney Brister, Anna N. Clawson, Joseph Fair, Martin Gabriel, Robert F. Garry, Stephen K. Gire, Augustine Goba, Jean-Paul Gonzalez, Stephan Günther, Christian T. Happi, Peter B. Jahrling, Jimmy Kapetshi, Gary Kobinger, Jeffrey R. Kugelman, Eric M. Leroy, Gael Darren Maganga, Placide K. Mbala, Lina M. Moses, Jean-Jacques Muyembe-Tamfum, Magassouba N'Faly, Stuart T. Nichol, Sunday A. Omilabu, Gustavo Palacios, Daniel J. Park, Janusz T. Paweska, Sheli R. Radoshitzky, Cynthia A. Rossi, Pardis C. Sabeti, John S. Schieffelin, Randal J. Schoepp, Rachel Sealfon, Robert Swanepoel, Jonathan S. Towner, Jiro Wada, Nadia Wauquier, Nathan L. Yozwiak, and Pierre Formenty

Subjects
Ebola, Ebola virus, ebolavirus, filovirid, Filoviridae, filovirus, genome annotation, Lomela, Lokolia, Makona, mononegavirad, Mononegavirales, mononegavirus, virus classification, virus isolate, virus nomenclature, virus strain, virus taxonomy, virus variant, Microbiology, QR1-502
Abstract

In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: “Makona”, Middle Africa: “Lomela”) and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures.

Published
2014
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21. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

Author

Jens H. Kuhn, Kristian G. Andersen, Yīmíng Bào, Sina Bavari, Stephan Becker, Richard S. Bennett, Nicholas H. Bergman, Olga Blinkova, Steven Bradfute, J. Rodney Brister, Alexander Bukreyev, Kartik Chandran, Alexander A. Chepurnov, Robert A. Davey, Ralf G. Dietzgen, Norman A. Doggett, Olga Dolnik, John M. Dye, Sven Enterlein, Paul W. Fenimore, Pierre Formenty, Alexander N. Freiberg, Robert F. Garry, Nicole L. Garza, Stephen K. Gire, Jean-Paul Gonzalez, Anthony Griffiths, Christian T. Happi, Lisa E. Hensley, Andrew S. Herbert, Michael C. Hevey, Thomas Hoenen, Anna N. Honko, Georgy M. Ignatyev, Peter B. Jahrling, Joshua C. Johnson, Karl M. Johnson, Jason Kindrachuk, Hans-Dieter Klenk, Gary Kobinger, Tadeusz J. Kochel, Matthew G. Lackemeyer, Daniel F. Lackner, Eric M. Leroy, Mark S. Lever, Elke Mühlberger, Sergey V. Netesov, Gene G. Olinger, Sunday A. Omilabu, Gustavo Palacios, Rekha G. Panchal, Daniel J. Park, Jean L. Patterson, Janusz T. Paweska, Clarence J. Peters, James Pettitt, Louise Pitt, Sheli R. Radoshitzky, Elena I. Ryabchikova, Erica Ollmann Saphire, Pardis C. Sabeti, Rachel Sealfon, Aleksandr M. Shestopalov, Sophie J. Smither, Nancy J. Sullivan, Robert Swanepoel, Ayato Takada, Jonathan S. Towner, Guido van der Groen, Viktor E. Volchkov, Valentina A. Volchkova, Victoria Wahl-Jensen, Travis K. Warren, Kelly L. Warfield, Manfred Weidmann, and Stuart T. Nichol

Subjects
Bundibugyo virus, cDNA clone, cuevavirus, Ebola, Ebola virus, ebolavirus, filovirid, Filoviridae, filovirus, genome annotation, ICTV, International Committee on Taxonomy of Viruses, Lloviu virus, Marburg virus, marburgvirus, mononegavirad, Mononegavirales, mononegavirus, Ravn virus, RefSeq, Reston virus, reverse genetics, Sudan virus, Taï Forest virus, virus classification, virus isolate, virus nomenclature, virus strain, virus taxonomy, virus variant, Microbiology, QR1-502
Abstract

Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.

Published
2014
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22. Early Introduction and Delayed Dissemination of Pandemic Influenza, Gabon

Author

Sonia Etenna Lekana-Douki, Augustin Mouinga-Ondémé, Dieudonné Nkoghe, Christian Drosten, Jan Felix Drexler, Mirdad Kazanji, and Eric M. Leroy

Subjects
Gabon, surveillance network, influenza, pH1N1, circulation, pandemic, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Active surveillance in health care centers in Gabon during 2009–2011 detected 72 clinical cases of pandemic (H1N1) 2009 (pH1N1). We found that pH1N1 virus was introduced in mid-2009 but spread throughout the country in 2010. Thus, Gabon was also affected by pH1N1.

Published
2013
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23. Ebola Virus Antibody Prevalence in Dogs and Human Risk

Author

Loïs Allela, Olivier Bourry, Régis Pouillot, André Délicat, Philippe Yaba, Brice Kumulungui, Pierre Rouquet, Jean-Paul Gonzalez, and Eric M. Leroy

Subjects
research, Ebola virus, dogs, antibody, human, prevention, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

During the 2001–2002 outbreak in Gabon, we observed that several dogs were highly exposed to Ebola virus by eating infected dead animals. To examine whether these animals became infected with Ebola virus, we sampled 439 dogs and screened them by Ebola virus–specific immunoglobulin (Ig) G assay, antigen detection, and viral polymerase chain reaction amplification. Seven (8.9%) of 79 samples from the 2 main towns, 15 (15.2%) of 14 the 99 samples from Mekambo, and 40 (25.2%) of 159 samples from villages in the Ebola virus–epidemic area had detectable Ebola virus–IgG, compared to only 2 (2%) of 102 samples from France. Among dogs from villages with both infected animal carcasses and human cases, seroprevalence was 31.8%. A significant positive direct association existed between seroprevalence and the distances to the Ebola virus–epidemic area. This study suggests that dogs can be infected by Ebola virus and that the putative infection is asymptomatic.

Published
2005
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24. Wild Animal Mortality Monitoring and Human Ebola Outbreaks, Gabon and Republic of Congo, 2001–2003

Author

Pierre Rouquet, Jean-Marc Froment, Magdalena Bermejo, Annelisa Kilbourne, William B. Karesh, Patricia Reed, Brice Kumulungui, Philippe Yaba, André Délicat, Pierre E. Rollin, and Eric M. Leroy

Subjects
Ebola virus, wildlife, great apes, Duiker, outbreak, Gabon, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

All human Ebola virus outbreaks during 2001–2003 in the forest zone between Gabon and Republic of Congo resulted from handling infected wild animal carcasses. After the first outbreak, we created an Animal Mortality Monitoring Network in collaboration with the Gabonese and Congolese Ministries of Forestry and Environment and wildlife organizations (Wildlife Conservation Society and Programme de Conservation et Utilisation Rationnelle des Ecosystèmes Forestiers en Afrique Centrale) to predict and possibly prevent human Ebola outbreaks. Since August 2001, 98 wild animal carcasses have been recovered by the network, including 65 great apes. Analysis of 21 carcasses found that 10 gorillas, 3 chimpanzees, and 1 duiker tested positive for Ebola virus. Wild animal outbreaks began before each of the 5 human Ebola outbreaks. Twice we alerted the health authorities to an imminent risk for human outbreaks, weeks before they occurred.

Published
2005
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25. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

Author

Yīmíng Bào, Gaya K. Amarasinghe, Christopher F. Basler, Sina Bavari, Alexander Bukreyev, Kartik Chandran, Olga Dolnik, John M. Dye, Hideki Ebihara, Pierre Formenty, Roger Hewson, Gary P. Kobinger, Eric M. Leroy, Elke Mühlberger, Sergey V. Netesov, Jean L. Patterson, Janusz T. Paweska, Sophie J. Smither, Ayato Takada, Jonathan S. Towner, Viktor E. Volchkov, Victoria Wahl-Jensen, and Jens H. Kuhn

Subjects
cuevavirus, Ebola, ebolavirus, Filoviridae, filovirus, marburgvirus, Mononegavirales, virus taxonomy, virus classification, ICTV, Microbiology, QR1-502
Abstract

The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55–58% sequence diversity threshold range for genera and at the 23–36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

Published
2017
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26. Concurrent Chikungunya and Dengue Virus Infections during Simultaneous Outbreaks, Gabon, 2007

Author

Eric M. Leroy, Dieudoné Nkoghe, Benjamin Ollomo, Chimène Nze-Nkogue, Pierre Becquart, Gilda Grard, Xavier Pourrut, Rémi N. Charrel, Grégory Moureau, Angélique Ndjoyi-Mbiguino, and Xavier de Lamballerie

Subjects
Vector-borne infections, viruses, chikungunya, dengue, Aedes albopictus, arbovirus, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

An outbreak of febrile illness occurred in Gabon in 2007, with 20,000 suspected cases. Chikungunya or dengue-2 virus infections were identified in 321 patients; 8 patients had documented co-infections. Aedes albopictus was identified as the principal vector for the transmission of both viruses.

Published
2009
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29. Santé humaine et santé animale

Author

J.-L. Angot, Jeanne Brugère-Picoux, S.G. Rosolen, and Eric M. Leroy

Subjects
medicine.medical_specialty, Encéphalopathie spongiforme bovine, medicine.disease_cause, Plague (disease), Vie de l’Académie, Zoonoses, Environmental health, Pandemic, medicine, Smallpox, One health, Transmission (medicine), Public health, Peste aviaire, General Medicine, medicine.disease, Influenza A virus subtype H5N1, Vaccinology, Geography, One Health, Bovine spongiform encephalopathy, Vaccinologie, Avian plague, Rabies, Covid-19, Une seule santé
Abstract

Le concept « une seule santé » lie étroitement la santé humaine et la santé animale car de nombreuses maladies sont des zoonoses. Les exemples historiques témoignant d’une collaboration efficace entre la médecine vétérinaire et la médecine humaine sont nombreux dans la mise au point des premiers vaccins utilisés dans le monde (variole, rage, tétanos, diphtérie, tuberculose, etc.). Mais lorsqu’une maladie nouvelle apparaît chez l’animal, le risque d’une transmission possible à l’Homme est difficile à estimer. Dans ce dernier cas, la perte de confiance du consommateur face aux incertitudes scientifiques peut provoquer une crise sanitaire (exemples de l’encéphalopathie spongiforme bovine et de la peste aviaire H5N1). Mais la plus grave crise que nous connaissons depuis le début de l’année 2020 est celle de la pandémie de Covid-19 qui confirme que la modification des écosystèmes de certaines espèces sauvages comme la chauve-souris fer à cheval peut avoir des conséquences importantes pour la santé publique. Les animaux ayant été malades de la Covid-19 ont été contaminés par l’Homme mais on ne peut pas exclure actuellement le risque de réservoir animal pour le SARS-CoV-2 qui a circulé dans le monde entier.

Published
2022

30. A large-scale serological survey in pets from October 2020 through June 2021 in France shows significantly higher exposure to SARS-CoV-2 in cats

Author

Matthieu Fritz, Eric Elguero, Pierre Becquart, Daphné de Riols de Fonclare, Déborah Garcia, Stephanie Beurlet, Solène Denolly, Bertrand Boson, Serge G. Rosolen, François-Loïc Cosset, Alexandra Briend-Marchal, Vincent Legros, and Eric M. Leroy

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect many animals, including pets such as dogs and cats. Many studies have documented infection in companion animals by bio-molecular and serological methods. However, only a few have compared seroprevalence in cats and dogs from the general population, and these studies were limited by small sample sizes and collections over short periods. Our goal was to obtain a more accurate evaluation of seroprevalence in companion animals in France and to determine whether cats and dogs differ in their exposure to SARS-CoV-2. For this purpose, we conducted an extensive SARS-CoV-2 serological survey of 2036 cats and 3577 dogs sampled by veterinarians during medical examinations in clinics throughout France. Sampling was carried out from October 2020 through June 2021, a period encompassing the second and third waves of SARS-CoV-2 infections in humans in the country. Using a microsphere immunoassay targeting receptor binding domain and trimeric spike protein, we found 7.1% seroprevalence in pets, in a subset of 308 seropositive samples, 26.3% had neutralizing antibodies. We found that cats were significantly more likely to test positive than dogs, with seropositivity rates of 9.3% and 5.9% in cats and dogs, respectively. Finally, data for both species showed that seroprevalence was lower in older animals and was not associated with the date of sampling or the sex of the animal. Our results show that cats are significantly more sensitive to SARS-CoV-2 than dogs, in line with experimental studies showing that cats are more susceptible than dogs. This study reinforces that pets are commonly infected or exposed to SARS-CoV-2, emphasizing the importance of a One-Health approach to the SARS-CoV-2 pandemic and raising the question of vaccination of companion animals in close contact with humans.

Published
2022

31. Detection of SARS‐CoV‐2 in two cats during the second wave of the COVID‐19 pandemic in France

Author

Nicolas Nesi, Meriadeg Ar Gouilh, Vincent Legros, Solène Denolly, Eric M. Leroy, Bertrand Boson, Alexandra Briend-Marchal, Serge G. Rosolen, Matthieu Fritz, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Virus enveloppés, vecteurs et immunothérapie – Enveloped viruses, Vectors and Immuno-therapy (EVIR), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Clinique Vétérinaire Voltaire, Vebiotel - Laboratoire de Biologie Vétérinaire, Service de Virologie [CHU Caen], CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), French National Agency for Research : ANR-RA-COVID-19 (Geographical and temporal serological investigation of companion animal infection with SARS-CoV-2 during the second wave of COVID-19 in France, CoVet), IDEXLYON project of Université de Lyon as part of the 'Programme Investissements d’Avenir'. Grant Number: ANR-16-IDEX-0005, WHO throught the SARS-CoV-2 EvoZoone project, OIE through the European Union EBO-SURSY project, ANR-16-IDEX-0005,IDEXLYON,IDEXLYON(2016), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique et évolution des maladies infectieuses (GEMI), Gestionnaire, HAL Sorbonne Université 5, and IDEXLYON - - IDEXLYON2016 - ANR-16-IDEX-0005 - IDEX - VALID

Subjects
Coronavirus disease 2019 (COVID-19), Veterinary medicine, viruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), serology, mild‐respiratory clinical signs, Cat Diseases, SARS‐CoV‐2, Microsphere, Serology, 03 medical and health sciences, SF600-1100, Pandemic, Animals, Medicine, One Health, skin and connective tissue diseases, Pandemics, mild-respiratory clinical signs, 030304 developmental biology, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, CATS, General Veterinary, biology, medicine.diagnostic_test, SARS-CoV-2, 030306 microbiology, business.industry, cats, fungi, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, COVID-19, Original Articles, Virology, respiratory tract diseases, 3. Good health, body regions, NGS, Immunoassay, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, Original Article, France, Antibody, business
Abstract

Although there are several reports in the literature of SARS‐CoV‐2 infection in cats, few SARS‐CoV‐2 sequences from infected cats have been published. In this study, SARS‐CoV‐2 infection was evaluated in two cats by clinical observation, molecular biology (qPCR and NGS), and serology (microsphere immunoassay and seroneutralization). Following the observation of symptomatic SARS‐CoV‐2 infection in two cats, infection status was confirmed by RT‐qPCR and, in one cat, serological analysis for antibodies against N‐protein and S‐protein, as well as neutralizing antibodies. Comparative analysis of five SARS‐CoV‐2 sequence fragments obtained from one of the cats showed that this infection was not with one of the three recently emerged variants of SARS‐CoV‐2. This study provides additional information on the clinical, molecular, and serological aspects of SARS‐CoV‐2 infection in cats., This study provides additional information on the clinical, molecular, and serological aspects of SARS‐CoV‐2 infection in cats.

Published
2021

32. Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon

Author

Anais Pinto, Jan Felix Drexler, Gael Darren Maganga, Christian Drosten, Meriadeg Ar Gouilh, Illich Manfred Mombo, Mankomra Madjitobaye, Larson Boundenga, Eric M. Leroy, Antoine Mitte Mbeang Beyeme, and Nadine N'Dilimabaka

Subjects
0301 basic medicine, Miniopterus inflatus, Primates, Range (biology), 030106 microbiology, lcsh:Medicine, Rodentia, Hipposideros, Alphacoronavirus, Microbiology, Article, 03 medical and health sciences, Betacoronavirus, Cave, Coronavirus 229E, Human, Chiroptera, Prevalence, Animals, Humans, Gabon, lcsh:Science, Phylogeny, Taxonomy, geography, Genetic diversity, Multidisciplinary, geography.geographical_feature_category, biology, Base Sequence, Ecology, Reverse Transcriptase Polymerase Chain Reaction, lcsh:R, Genetic Variation, virus diseases, Insectivore, Eulipotyphla, Biodiversity, Hipposideros gigas, biology.organism_classification, Caves, 030104 developmental biology, RNA, Viral, lcsh:Q, Seasons, Coronavirus Infections
Abstract

Little research on coronaviruses has been conducted on wild animals in Africa. Here, we screened a wide range of wild animals collected in six provinces and five caves of Gabon between 2009 and 2015. We collected a total of 1867 animal samples (cave-dwelling bats, rodents, non-human primates and other wild animals). We explored the diversity of CoVs and determined the factors driving the infection of CoVs in wild animals. Based on a nested reverse transcription-polymerase chain reaction, only bats, belonging to the Hipposideros gigas (4/156), Hipposideros cf. ruber (13/262) and Miniopterus inflatus (1/249) species, were found infected with CoVs. We identified alphacoronaviruses in H. gigas and H. cf. ruber and betacoronaviruses in H. gigas. All Alphacoronavirus sequences grouped with Human coronavirus 229E (HCoV-229E). Ecological analyses revealed that CoV infection was significantly found in July and October in H. gigas and in October and November in H. cf ruber. The prevalence in the Faucon cave was significantly higher. Our findings suggest that insectivorous bats harbor potentially zoonotic CoVs; highlight a probable seasonality of the infection in cave-dwelling bats from the North-East of Gabon and pointed to an association between the disturbance of the bats’ habitat by human activities and CoV infection.

Published
2020

33. Exposure to Ebola Virus and Risk for Infection with Malaria Parasites, Rural Gabon

Author

Pierre Becquart, Vanessa O. Ezenwa, Benjamin Roche, Jessica L. Abbate, and Eric M. Leroy

Subjects
Male, Rural Population, Plasmodium, viruses, lcsh:Medicine, Disease, medicine.disease_cause, pathogen-pathogen interactions, Ebola virus, 0302 clinical medicine, Risk Factors, Surveys and Questionnaires, Epidemiology, 030212 general & internal medicine, Malaria, Falciparum, education.field_of_study, biology, virus diseases, Middle Aged, Ebolavirus, Infectious Diseases, surveillance, epidemiology, Female, Antibody, ecology, Microbiology (medical), Adult, medicine.medical_specialty, Surveillance study, Adolescent, 030231 tropical medicine, Population, prevalence, Plasmodium falciparum, malaria, parasites, occurrence, lcsh:Infectious and parasitic diseases, Host-Parasite Interactions, 03 medical and health sciences, Young Adult, parasitic diseases, medicine, Humans, lcsh:RC109-216, Gabon, education, disease, Research, lcsh:R, populations at risk, Hemorrhagic Fever, Ebola, biology.organism_classification, medicine.disease, Virology, Exposure to Ebola Virus and Risk for Infection with Malaria Parasites, Gabon, biology.protein, Malaria
Abstract

An association between malaria and risk for death among patients with Ebola virus disease has suggested within-host interactions between Plasmodium falciparum parasites and Ebola virus. To determine whether such an interaction might also influence the probability of acquiring either infection, we used a large snapshot surveillance study from rural Gabon to test if past exposure to Ebola virus is associated with current infection with Plasmodium spp. during nonepidemic conditions. We found a strong positive association, on population and individual levels, between seropositivity for antibodies against Ebola virus and the presence of Plasmodium parasites in the blood. According to a multiple regression model accounting for other key variables, antibodies against Ebola virus emerged as the strongest individual-level risk factor for acquiring malaria. Our results suggest that within-host interactions between malaria parasites and Ebola virus may underlie epidemiologic associations.

Published
2020

34. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Amadou A. Sall, Christopher F. Basler, Gary P. Kobinger, Amy J. Lambert, Rodrigo Jardim, John V. da Graça, Yong-Zhen Zhang, Víctor Romanowski, Massimo Turina, John W. McCauley, Lin-Fa Wang, Paul A. Rota, Olga Dolnik, Juan Carlos de la Torre, Gabriele Neumann, Natalie J. Thornburg, Tomohide Natsuaki, Jin Won Song, Kartik Chandran, Carol D. Blair, Michael A. Drebot, Guohui Zhou, Rémi N. Charrel, Heather L. Wells, Ralf G. Dietzgen, Bernadett Pályi, Arnfinn Lodden Økland, Ian Crozier, Gael Kurath, Gilda B. Jonson, Robert R. Martin, Xuejie Yu, Anthony R. Fooks, Renato O. Resende, Ali Mirazimi, Bernadette G. van den Hoogen, Scott Adkins, Colin R. Parrish, Alexander Bukreyev, Anthony Griffiths, Timothy H. Hyndman, Peter Simmonds, Rachel Breyta, Zhìqiáng Wú, Ralf Dürrwald, Jorlan Fernandes, Biao Chen, Udo Hetzel, Alexandro Guterres, Jessica R. Spengler, Michael J. Buchmeier, Rayapati A. Naidu, Janusz T. Paweska, Keizō Tomonaga, Kamil Sarpkaya, Ivan V. Kuzmin, Jens H. Kuhn, Piet Maes, Marco Marklewitz, Masayuki Horie, Arvind Varsani, Shin-Yi Lee Marzano, Ursula J. Buchholz, Jean-Paul Gonzalez, Angelantonio Minafra, Daniela Alioto, Simon J. Anthony, Florian Pfaff, Brian H. Bird, Peter J. Walker, Robert A. Lamb, Noël Tordo, Rainer G. Ulrich, Sergio H. Marshall, Eric M. Leroy, Ayato Takada, Kirsten Spann, Xavier de Lamballerie, John M. Dye, Inmaculada Casas, Manuela Sironi, J. Christopher S. Clegg, Paul Brown, Dennis Rubbenstroth, Yan Liu, Márcio Roberto Teixeira Nunes, Tatjana Avšič-Županc, Martin Verbeek, Andrew J. Easton, Beatriz Navarro, Hideki Ebihara, Benhur Lee, Pierre Formenty, Qi Jin, Hideki Kondō, Eric Bergeron, Sébastien Massart, Daniel R. Perez, S. V. Alkhovsky, Charles H. Calisher, Anna Papa, Xīnglóu Yáng, José A. Navarro, Xifeng Wang, Taiyun Wei, Kim R. Blasdell, Lucie Dufkova, Renata Carvalho de Oliveira, Elba Regina Sampaio de Lemos, Nikos Vasilakis, Pedro Luis Ramos-González, Tong Zhang, Holly R. Hughes, Leonie Forth, Serpil Karadağ, F. Murilo Zerbini, Xueping Zhou, María Laura García, Tomáš Bartonička, Sandra Junglen, Aziz ul Rahman, Petra Straková, Karen E. Keller, William G. Dundon, Jiří Salát, Dexin Li, Jussi Hepojoki, Maria S. Salvato, Hui Wang, Justin Bahl, Bernd Hoffmann, Alberto M. R. Dávila, Jonathan S. Towner, Wénwén Liú, Mifang Liang, Yuri I. Wolf, Gaya K. Amarasinghe, Jianwei Wang, Alex Pauvolid-Corrêa, Anna Maria Vaira, Roy A. Hall, William Marciel de Souza, Thomas Briese, Felicity J. Burt, Valerian V. Dolja, Boris Klempa, Satu Hepojoki, Mengji Cao, Selma Gago-Zachert, Il-Ryong Choi, Rik L. de Swart, Jan Felix Drexler, Gabriel Robles Luna, Igor S. Lukashevich, Maria Minutolo, Amara Jambai, Nihal Buzkan, Steven B. Bradfute, Are Nylund, Ioannis E. Tzanetakis, Xiǎohóng Shí, Stephan Günther, Aura R. Garrison, Takahide Sasaya, Mart Krupovic, Victoria Wahl, Seiji Hongo, Matthew J. Ballinger, María A. Ayllón, Jonas Klingström, David M. Stone, Sead Sabanadzovic, Tracey Goldstein, George Fú Gāo, Aiah Gbakima, Norbert Nowotny, Vicente Pallás, Carina Andrea Reyes, W. Paul Duprex, Roger Hewson, Muhammad Zubair Shabbir, Sophie J. Smither, John V. Williams, Hans Peter Mühlbach, John Chamberlain, Yukio Shirako, Elke Mühlberger, Lies Laenen, Martin Beer, Jiànróng Lǐ, Giovanni P. Martelli, Gustavo Palacios, Sina Bavari, Natalya Yutin, Elena Dal Bó, Michele Digiaro, Jonathan A. Runstadler, John Hammond, Martin Schwemmle, Robert B. Tesh, Dirk Höper, Martin H. Groschup, Francesco Di Serio, Teemu Smura, Sheli R. Radoshitzky, Juliana Freitas-Astúa, Susan Payne, Dennis A. Bente, Anne Balkema-Buschmann, Adolfo García-Sastre, Eugene V. Koonin, Nicholas Di Paola, Bertus K. Rima, Mark D. Stenglein, Mohamed Hassan, Michela Chiumenti, Koray Ergünay, Patrick L. Di Bello, Ron A. M. Fouchier, Anna E. Whitfield, Toufic Elbeaino, Xin Yang, Nicole Mielke-Ehret, Jana Širmarová, Daniel Ruzek, Dàohóng Jiāng, Stanley L. Langevin, Sergey V. Netesov, Zhengli Shi, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Centre collaborateur de l'OMS Arbovirus et Fièvres Hémorragiques virales - Stratégies antivirales (CC-OMS), Institut Pasteur de Guinée, Les Mandinaux, 16450 Le Grand Madieu, This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This project has been funded in whole or in part with federal funds from the National Cancer Institute (NCI), National Institutes of Health (NIH), under Contract No. 75N91019D00024, Task Order No. 75N91019F00130 to I.C., who was supported by the Clinical Monitoring Research Program Directorate, Frederick National Lab for Cancer Research, sponsored by NCI. This work was also funded in part by Contract No. HSHQDC-15-C-00064 awarded by the US Department of Homeland Security (DHS) Science and Technology Directorate (S&T) for the management and operation of The National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center operated by the Battelle National Biodefense Institute (V.W.), and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges partial support from the Special Research Initiative of Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University, and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494., We thank W. Ian Lipkin and Rafal Tokarz (Columbia University Irving Medical Center, New York, New York, USA) for providing/approving new names for 'blacklegged tick phleboviruses 1 and 3' and Edward Holmes (University of Sydney, Australia) for providing/approving a new name for 'Norway phlebovirus'. Many authors are current members of 2017-2020 International Committee on Taxonomy of Viruses (ICTV) Study Groups: Arenaviridae (Jens H. Kuhn, Michael J. Buchmeier, Rémi N. Charrel, J. Christopher S. Clegg, Juan Carlos de la Torre, Jean-Paul J. Gonzalez, Stephan Günther, Mark D. Stenglein, Jussi Hepojoki, Manuela Sironi, Igor S. Lukashevich, Sheli R. Radoshitzky, Víctor Romanowski, Maria S. Salvato), Artoviridae (Jens H. Kuhn, Ralf G. Dietzgen, Dàohóng Jiāng, Nikos Vasilakis), Aspiviridae (John V. da Graça, Elena Dal Bó, Selma Gago-Zachert, María Laura García, John Hammond, Tomohide Natsuaki, José A. Navarro, Vicente Pallás, Carina A. Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis Tzanetakis, Anna Maria Vaira, Martin Verbeek), Bornaviridae (Jens H. Kuhn, Thomas Briese, Ralf Dürrwald, Masayuki Horie, Timothy H. Hyndman, Norbert Nowotny, Susan Payne, Dennis Rubbenstroth, Mark D. Stenglein, Keizō Tomonaga), Bunyavirales (Jens H. Kuhn, Scott Adkins, Juan Carlos de la Torre, Sandra Junglen, Amy J. Lambert, Piet Maes, Marco Marklewitz, Gustavo Palacios, Takahide Sasaya, Yong-Zhen Zhang), Filoviridae (Jens H. Kuhn, Gaya K. Amarasinghe, Christopher Basler, Sina Bavari, Alexander Bukreyev, Kartik Chandran, Ian Crozier, Olga Dolnik, John M. Dye, Pierre B. H. Formenty, Anthony Griffiths, Roger Hewson, Gary Kobinger, Eric M. Leroy, Elke Mühlberger, Sergey V. Netesov, Gustavo Palacios, Bernadett Pályi, Janusz T. Pawęska, Sophie Smither, Ayato Takada, Jonathan S. Towner, Victoria Wahl), Fimoviridae (Michele Digiaro, Toufic Elbeaino, Giovanni P. Martelli, Nicole Mielke-Ehret, Hans-Peter Mühlbach), Hantaviridae (Steven Bradfute, Charles H. Calisher, Boris Klempa, Jonas Klingström, Lies Laenen, Piet Maes, Jin-Won Song, Yong-Zhen Zhang), Jingchuvirales (Nicholas Di Paola), Monjiviricetes (Jens H. Kuhn, Ralf G. Dietzgen, W. Paul Duprex, Dàohóng Jiāng, Piet Maes, Janusz T. Pawęska, Bertus K. Rima, Dennis Rubbenstroth, Peter J. Walker, Yong-Zhen Zhang), Mymonaviridae (María A. Ayllón, Dàohóng Jiāng, Shin-Yi L. Marzano), Nairoviridae (Jens H. Kuhn, Sergey V. Alkhovsky, Tatjana Avšič-Županc, Dennis A. Bente, Éric Bergeron, Felicity Burt, Nicholas Di Paola, Koray Ergünay, Aura R. Garrison, Roger Hewson, Ali Mirazimi, Gustavo Palacios, Anna Papa, Amadou Alpha Sall, Jessica R. Spengler), Negarnaviricota (Jens H. Kuhn, Eugene V. Koonin, Mart Krupovic, Yuri I. Wolf), Nyamiviridae (Jens H. Kuhn, Ralf G. Dietzgen, Dàohóng Jiāng, Nikos Vasilakis), Orthomyxoviridae (Justin Bahl, Inmaculada Casas, Adolfo García-Sastre, Seiji Hongo, Sergio H. Marshall, John W. McCauley, Gabriele Neumann, Colin R. Parrish, Daniel R. Pérez, Jonathan A. Runstadler, Martin Schwemmle), Paramyxoviridae (Anne Balkema-Buschmann, William G. Dundon, W. Paul Duprex, Andrew J. Easton, Ron Fouchier, Gael Kurath, Benhur Lee, Bertus K. Rima, Paul Rota, Lin-Fa Wang, Robobert A. Lamb), Peribunyaviridae (Scott Adkins, Sergey V. Alkhovsky, Martin Beer, Carol D. Blair, Charles H. Calisher, Michael A. Drebot, Holly R. Hughes, Amy J. Lambert, William Marciel de Souza, Marco Marklewitz, Márcio R. T. Nunes, Xiǎohóng Shí), Phasmaviridae (Matthew J. Ballinger, Roy A. Hall, Sandra Junglen, Stanley L. Langevin, Alex Pauvolid-Corrêa), Phenuiviridae (Thomas Briese, Rémi N. Charrel, Xavier De Lamballerie, Hideki Ebihara, George Fú Gāo, Martin H. Groschup, Márcio R. T. Nunes, Gustavo Palacios, Takahide Sasaya, Jin-Won Song), Pneumoviridae (Paul A. Brown, Ursula J. Buchholz, Rik L. de Swart, Jan Felix Drexler, W. Paul Duprex, Andrew J. Easton, Jiànróng Lǐ, Kirsten Spann, Natalie J. Thornburg, Bernadette van den Hoogen, John V. Williams), Rhabdoviridae (Kim R. Blasdell, Rachel Breyta, Ralf G. Dietzgen, Anthony R. Fooks, Juliana Freitas-Astúa, Hideki Kondō, Gael Kurath, Ivan V. Kuzmin, David M. Stone, Robert B. Tesh, Noël Tordo, Nikos Vasilakis, Peter J. Walker, Anna E. Whitfield), Sunviridae (Timothy H. Hyndman, Gael Kurath), Tenuivirus (Il-Ryong Choi, Gilda B. Jonson, Takahide Sasaya, Yukio Shirako, Tàiyún Wèi, Xueping Zhou), and Tospoviridae (Scott Adkins, Amy J. Lambert, Rayapati Naidu, Renato O. Resende, Massimo Turina, Anna E. Whitfield), or are ICTV Executive Committee Members: the 2017–2020 ICTV Chair of the Fungal and Protist Viruses Subcommittee (Peter Simmonds), the 2018–2020 ICTV Proposal Secretary (Peter J. Walker), the 2017–2020 ICTV Chair of the Plant Viruses Subcommittee (F. Murilo Zerbini), the 2017–2020 ICTV Chair of the Animal dsRNA and ssRNA- Viruses Subcommittee (Jens H. Kuhn), and 2017–2020 Elected Members (Sead Sabanadzovic, Arvind Varsani). We would like to thank Anya Crane (NIH/NIAID/DCR/IRF-Frederick) for critically editing the manuscript., NIH - National Institute of Allergy and Infectious Diseases (NIAID) (Estados Unidos), NIH - National Cancer Institute (NCI) (Estados Unidos), United State Department of Homeland Security (Estados Unidos), National Biodefense Analysis and Countermeasures Center (NBACC) (Estados Unidos), Battelle National Biodefense Institute, Mississippi Agricultural and Forestry Experiment Station (MAFES) (Estados Unidos), Mississippi State University (Estados Unidos), United States Department of Agriculture. National Institute of Food and Agriculture, Institut Pasteur [Paris] (IP), Virology, H Kuhn, Jen, Adkins, Scott, Alioto, Daniela, V Alkhovsky, Sergey, K Amarasinghe, Gaya, J Anthony, Simon, Avšič-Županc, Tatjana, A Ayllón, María, Bahl, Justin, Balkema-Buschmann, Anne, J Ballinger, Matthew, Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, A Bente, Denni, Bergeron, Éric, H Bird, Brian, Blair, Carol, R Blasdell, Kim, B Bradfute, Steven, Breyta, Rachel, Briese, Thoma, A Brown, Paul, J Buchholz, Ursula, J Buchmeier, Michael, Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, H Calisher, Charle, Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, N Charrel, Rémi, Chen, Biao, Chiumenti, Michela, Choi, Il-Ryong, S Clegg, J Christopher, Crozier, Ian, V da Graça, John, Dal Bó, Elena, R Dávila, Alberto M, Carlos de la Torre, Juan, de Lamballerie, Xavier, L de Swart, Rik, L Di Bello, Patrick, Di Paola, Nichola, Di Serio, Francesco, G Dietzgen, Ralf, Digiaro, Michele, V Dolja, Valerian, Dolnik, Olga, A Drebot, Michael, Felix Drexler, Jan, Dürrwald, Ralf, Dufkova, Lucie, G Dundon, William, Paul Duprex, W, M Dye, John, J Easton, Andrew, Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, R Fooks, Anthony, H Formenty, Pierre B, F Forth, Leonie, M Fouchier, Ron A, Freitas-Astúa, Juliana, Gago-Zachert, Selma, Fú Gāo, George, Laura García, María, García-Sastre, Adolfo, R Garrison, Aura, Gbakima, Aiah, Goldstein, Tracey, J Gonzalez, Jean-Paul, Griffiths, Anthony, H Groschup, Martin, Günther, Stephan, Guterres, Alexandro, A Hall, Roy, Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, R Hughes, Holly, H Hyndman, Timothy, Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, B Jonson, Gilda, Junglen, Sandra, Karadağ, Serpil, E Keller, Karen, Klempa, Bori, Klingström, Jona, Kobinger, Gary, Kondō, Hideki, V Koonin, Eugene, Krupovic, Mart, Kurath, Gael, V Kuzmin, Ivan, Laenen, Lie, A Lamb, Robert, J Lambert, Amy, L Langevin, Stanley, Lee, Benhur, S Lemos, Elba R, M Leroy, Eric, Li, Dexin, Lǐ, Jiànróng, Liang, Mifang, Liú, Wénwén, Liú, Yàn, S Lukashevich, Igor, Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, H Marshall, Sergio, P Martelli, Giovanni, R Martin, Robert, L Marzano, Shin-Yi, Massart, Sébastien, W McCauley, John, Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, A Navarro, José, V Netesov, Sergey, Neumann, Gabriele, Nowotny, Norbert, T Nunes, Márcio R, Nylund, Are, L Økland, Arnfinn, C Oliveira, Renata, Palacios, Gustavo, Pallas, Vicente, Pályi, Bernadett, Papa, Anna, R Parrish, Colin, Pauvolid-Corrêa, Alex, T Pawęska, Janusz, Payne, Susan, R Pérez, Daniel, Pfaff, Florian, R Radoshitzky, Sheli, Rahman, Aziz-Ul, L Ramos-González, Pedro, O Resende, Renato, A Reyes, Carina, K Rima, Bertu, Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Denni, A Runstadler, Jonathan, Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Alpha Sall, Amadou, S Salvato, Maria, Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Z Shabbir, Muhammad, Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin-Won, M Spann, Kirsten, R Spengler, Jessica, D Stenglein, Mark, M Stone, David, Straková, Petra, Takada, Ayato, B Tesh, Robert, J Thornburg, Natalie, Tomonaga, Keizō, Tordo, Noël, S Towner, Jonathan, Turina, Massimo, Tzanetakis, Ioanni, G Ulrich, Rainer, Maria Vaira, Anna, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Niko, Verbeek, Martin, Wahl, Victoria, J Walker, Peter, Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, E Whitfield, Anna, V Williams, John, I Wolf, Yuri, Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Murilo Zerbini, F, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, and Zhou., Xueping

Subjects
Species complex, MESH: Terminology as Topic, Biología, VÍRUS DE RNA, Biology, Article, 03 medical and health sciences, Biointeractions and Plant Health, V?rus / classifica??o, MESH: Mononegavirales, Genus, Virology, Terminology as Topic, Life Science, Bunyavirales, Ciencias Exactas, Taxonomy, 030304 developmental biology, Order Mononegavirales, 0303 health sciences, 030306 microbiology, Phylum, General Medicine, 15. Life on land, Negarnaviricota, Filogenia, Taxon, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), Mononegavirales
Abstract

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Agrarias y Forestales, Centro de Investigaciones en Fitopatología, Facultad de Ciencias Exactas, Instituto de Biotecnologia y Biologia Molecular

Published
2020

35. Infection with SARS‐CoV‐2 variant B.1.1.7 detected in a group of dogs and cats with suspected myocarditis

Author

Sandrine Corbet, Vincent Legros, Meriadeg Ar Gouilh, H. Ferasin, Pierre Becquart, L. Ferasin, Matthieu Fritz, and Eric M. Leroy

Subjects
Myocarditis, CATS, General Veterinary, biology, Transmission (medicine), business.industry, SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Research, COVID-19, General Medicine, Disease, Myocardial Disorder, medicine.disease, Immunology, Mutation, Spike Glycoprotein, Coronavirus, medicine, biology.protein, Animals, Antibody, Respiratory system, business, Original Research
Abstract

Background Domestic pets can contract severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection; however, it is unknown whether the UK B.1.1.7 variant can more easily infect certain animal species or increase the possibility of human‐to‐animal transmission. Methods This is a descriptive case series reporting SARS‐CoV‐2 B.1.1.7 variant infections in a group of dogs and cats with suspected myocarditis. Results The study describes the infection of domestic cats and dogs by the B.1.1.7 variant. Two cats and one dog were positive to SARS‐CoV‐2 PCR on rectal swab, and two cats and one dog were found to have SARS‐CoV‐2 antibodies 2–6 weeks after they developed signs of cardiac disease. Many owners of these pets had developed respiratory symptoms 3–6 weeks before their pets became ill and had also tested positive for COVID‐19. Interestingly, all these pets were referred for acute onset of cardiac disease, including severe myocardial disorders of suspected inflammatory origin but without primary respiratory signs. Conclusions These findings demonstrate, for the first time, the ability for pets to be infected by the B.1.1.7 variant and question its possible pathogenicity in these animals.

Published
2021

36. Potential Association between Zika Infection and Microcephaly during 2007 Fever Outbreak, Gabon

Author

Eric Elguero, Claudine A. Kombila Koumavor, and Eric M. Leroy

Subjects
Microbiology (medical), Microcephaly, Aedes albopictus, Epidemiology, vector-borne infections, 030231 tropical medicine, lcsh:Medicine, high-risk pregnancy, Disease Outbreaks, Zika virus, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Zika, 0302 clinical medicine, Aedes, parasitic diseases, Research Letter, Potential Association between Zika Infection and Microcephaly during 2007 Fever Outbreak, Gabon, ZikV Infection, Animals, Medicine, viruses, lcsh:RC109-216, 030212 general & internal medicine, Gabon, microcephaly, biology, Zika Virus Infection, business.industry, lcsh:R, Outbreak, Febrile illness, febrile illnesses, Zika Virus, medicine.disease, biology.organism_classification, Virology, Infectious Diseases, outbreaks, Africa, business, High risk pregnancy
Abstract

Although Zika virus (ZIKV) circulates in sub-Saharan Africa, no case of ZIKV-associated microcephaly has thus far been reported. Here, we report evidence of a possible association between a 2007 outbreak of febrile illness and an increase in microcephaly and possibly ZIKV infection in Gabon.

Published
2021

38. New detection of SARS-CoV-2 in two cats height months after COVID-19 outbreak appearance in France

Author

Bertrand Boson, Nicolas Nesi, Alexandra Briend-Marchal, Eric M. Leroy, Matthieu Fritz, Solène Denolly, Serge G. Rosolen, Vincent Legros, and Meriadeg Ar Gouil

Subjects
CATS, biology, Coronavirus disease 2019 (COVID-19), medicine.diagnostic_test, business.industry, viruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), fungi, Outbreak, Virology, respiratory tract diseases, Serology, Microsphere, body regions, Immunoassay, biology.protein, medicine, Antibody, skin and connective tissue diseases, business
Abstract

Although there are several reports in the literature of SARS-CoV-2 infection in cats, few SARS-CoV-2 sequences from infected cats have been published. In this report, SARS-CoV-2 infection was evaluated in two cats by clinical observation, molecular biology (qPCR and NGS), and serology (Microsphere immunoassay and seroneutralization). Following the observation of symptomatic SARS-CoV-2-infection in two cats, infection status was confirmed by RT-qPCR and, in one cat, serological analysis for antibodies against N-protein and S-protein, as well as neutralizing antibodies. Comparative analysis of five SARS-CoV-2 sequence-fragments obtained from one of the cats showed that this infection was not with one of the three recently emerged variants of SARS-CoV-2. This study provides additional information on the clinical, molecular, and serological aspects of SARS-CoV-2 infection in cats.

Published
2021

39. Myocarditis in naturally infected pets with the British variant of COVID-19

Author

Matthieu Fritz, Eric M. Leroy, Vincent Legros, H. Ferasin, L. Ferasin, and Pierre Becquart

Subjects
Infectivity, Myocarditis, Coronavirus disease 2019 (COVID-19), Transmission (medicine), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Immunology, medicine, Outbreak, medicine.disease, Pathogenicity, business, Animal species
Abstract

Domestic pets can contract SARS-CoV-2 infection but, based on the limited information available to date, it is unknown whether the new British B.1.1.7 variant can more easily infect certain animal species or increase the possibility of human-to-animal transmission. In this study, we report the first cases of infection of domestic cats and dogs by the British B.1.1.7 variant of SARS-CoV-2 diagnosed at a specialist veterinary hospital in the South-East of England. Furthermore, we discovered that many owners and handlers of these pets had developed Covid-19 respiratory symptoms 3-6 weeks before their pets became ill and had also tested PCR positive for Covid-19. Interestingly, all these B.1.1.7 infected pets developed atypical clinical manifestations, including severe cardiac abnormalities secondary to myocarditis and a profound impairment of the general health status of the patient but without any primary respiratory signs. Together, our findings demonstrate for the first time the ability for companion animals to be infected by the B.1.1.7 variant of SARS-CoV-2 and raise questions regarding its pathogenicity in these animals. Moreover, given the enhanced infectivity and transmissibility of B.1.1.7 variant for humans, these findings also highlights more than ever the risk that companion animals may potentially play a significant role in SARS-CoV-2 outbreak dynamics than previously appreciated.

Published
2021

40. First investigation of pathogenic bacteria, protozoa and viruses in rodents and shrews in context of forest-savannah-urban areas interface in the city of Franceville (Gabon)

Author

Eric M. Leroy, Octavie Banga, Jean-Bernard Lekana-Douki, Mathieu Bourgarel, Joa Braïthe Mangombi, Oleg Mediannikov, Sydney Maghendji-Nzondo, Florence Fenollar, Nadine N'dilimabaka, Centre International de Recherches Médicales de Franceville (CIRMF), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), Université des sciences de la santé, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), AUF-Agence universitaire de la Francophonie., CDMATHINBIO 17872Association pour la recherche en infectiologie (APRI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université des Sciences et Techniques de Masuku (USTM), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Plasmodium, [SDV]Life Sciences [q-bio], Rickettsiales, Artificial Gene Amplification and Extension, Pathology and Laboratory Medicine, L73 - Maladies des animaux, medicine.disease_cause, Polymerase Chain Reaction, Rickettsiaceae, 0302 clinical medicine, Zoonoses, Medicine and Health Sciences, Kinetoplastida, Mammals, Protozoans, Multidisciplinary, biology, Eukaryota, Orientia, Musaraigne, Bacterial Pathogens, 3. Good health, Anaplasmataceae, Medical Microbiology, S50 - Santé humaine, Vertebrates, Viruses, Medicine, Pathogens, Bartonella, Toxoplasma, Coxiella Burnetii, Research Article, zoonose, Trypanosoma, Anaplasma, Science, 030231 tropical medicine, relation homme-faune, Rodentia, Research and Analysis Methods, Rodents, Microbiology, 03 medical and health sciences, Leptospira, Borrelia, parasitic diseases, medicine, Animals, Humans, Gabon, Cities, Protozoa, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, Disease Reservoirs, Bacteria, Shrews, Organisms, Biology and Life Sciences, Pathogenic bacteria, biology.organism_classification, Coxiella burnetii, bacterial infections and mycoses, Maladie bactérienne, Parasitic Protozoans, 030104 developmental biology, Amniotes, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Rongeur, Virus pathogène, Zoology
Abstract

Rodents are reservoirs of numerous zoonotic diseases caused by bacteria, protozoans, or viruses. In Gabon, the circulation and maintenance of rodent-borne zoonotic infectious agents are poorly studied and are often limited to one type of pathogen. Among the three existing studies on this topic, two are focused on a zoonotic virus, and the third is focused on rodentPlasmodium. In this study, we searched for a wide range of bacteria, protozoa and viruses in different organs of rodents from the town of Franceville in Gabon. Samples from one hundred and ninety-eight (198) small mammals captured, including two invasive rodent species, five native rodent species and 19 shrews belonging to theSoricidaefamily, were screened. The investigated pathogens were bacteria from theRickettsiaceaeandAnaplasmataceaefamilies,Mycoplasmaspp.,Bartonellaspp.,Borreliaspp.,Orientiaspp.,Occidentiaspp.,Leptospiraspp.,Streptobacillus moniliformis,Coxiella burnetii, andYersinia pestis;parasites from classKinetoplastidaspp. (Leishmaniaspp.,Trypanosomaspp.),Piroplasmidaespp., andToxoplasma gondii; and viruses fromParamyxoviridae,Hantaviridae,FlaviviridaeandMammarenavirusspp. We identified the following pathogenic bacteria:Anaplasmaspp. (8.1%; 16/198),Bartonellaspp. (6.6%; 13/198),Coxiellaspp. (5.1%; 10/198) andLeptospiraspp. (3.5%; 7/198); and protozoans:Piroplasmasp. (1%; 2/198),Toxoplasma gondii(0.5%; 1/198), andTrypanosomasp. (7%; 14/198). None of the targeted viral genes were detected. These pathogens were found in Gabonese rodents, mainlyLophuromyssp.,Lemniscomys striatusandPraomyssp. We also identified new genotypes:CandidatusBartonella gabonensis and UnculturedAnaplasmaspp. This study shows that rodents in Gabon harbor some human pathogenic bacteria and protozoans. It is necessary to determine whether the identified microorganisms are capable of undergoing zoonotic transmission from rodents to humans and if they may be responsible for human cases of febrile disease of unknown etiology in Gabon.

Published
2021

41. Impact of Surface Chemistry of Silicon Nanoparticles on the Structural and Electrochemical Properties of Si/Ni3.4Sn4 Composite Anode for Li-Ion Batteries

Author

Tahar Azib, Eric M. Leroy, Nicolas Marx, Christian Jordy, Michel Latroche, Claire Thaury, Fermin Cuevas, Institut de Chimie et des Matériaux Paris-Est (ICMPE), Institut de Chimie du CNRS (INC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Société des accumulateurs fixes et de traction (SAFT), and UMICORE

Subjects
General Chemical Engineering, Intermetallic, Nanoparticle, 02 engineering and technology, Azib, 7. Clean energy, 01 natural sciences, Chemical reaction, Thaury, lcsh:Chemistry, chemistry.chemical_compound, Coating, E, General Materials Science, intermetallics, nanomaterials, Condensed Matter - Materials Science, T, M. Impact of Surface Li-ion batteries, anodes, coating, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Jordy, Cuevas, Electrode, 0210 nano-technology, Materials science, Silicon, Oxide, chemistry.chemical_element, FOS: Physical sciences, Li-ion batteries, engineering.material, 010402 general chemistry, composites, C, Latroche, Materials Science (cond-mat.mtrl-sci), silicon, N, 0104 chemical sciences, Anode, lcsh:QD1-999, Chemical engineering, chemistry, F, Marx, Leroy, engineering, mechanochemistry
Abstract

Embedding silicon nanoparticles in an intermetallic matrix is a promising strategy to produce remarkable bulk anode materials for lithium-ion (Li-ion) batteries with low potential, high electrochemical capacity and good cycling stability. These composite materials can be synthetized at a large scale using mechanical milling. However, for Si-Ni3Sn4 composites, milling also induces a chemical reaction between the two components leading to the formation of free Sn and NiSi2, which is detrimental to the performance of the electrode. To prevent this reaction, a modification of the surface chemistry of the silicon has been undertaken. Si nanoparticles coated with a surface layer of either carbon or oxide were used instead of pure silicon. The influence of the coating on the composition, (micro)structure and electrochemical properties of Si-Ni3Sn4 composites is studied and compared with that of pure Si. Si coating strongly reduces the reaction between Si and Ni3Sn4 during milling. Moreover, contrary to pure silicon, Si-coated composites have a plate-like morphology in which the surface-modified silicon particles are surrounded by a nanostructured, Ni3Sn4-based matrix leading to smooth potential profiles during electrochemical cycling. The chemical homogeneity of the matrix is more uniform for carbon-coated than for oxygen-coated silicon. As a consequence, different electrochemical behaviors are obtained depending on the surface chemistry, with better lithiation properties for the carbon-covered silicon able to deliver over 500 mAh/g for at least 400 cycles.

Published
2021

42. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Martin Schwemmle, S. V. Alkhovsky, Mark D. Stenglein, Jinguo Zhang, Shaohua Wen, Víctor Romanowski, Massimo Turina, Peter J. Walker, Baldwyn Torto, Paul A. Rota, Xavier de Lamballerie, Stuart G. Siddell, Noël Tordo, John M. Dye, Inmaculada Casas, Andrew J. Easton, Yasuhiro Tomitaka, Eugene V. Koonin, J. Christopher S. Clegg, Judith K. Brown, Kartik Chandran, Carol D. Blair, Shinya Tsuda, Tony L. Goldberg, Andrew J. Bennett, Ralf G. Dietzgen, Koray Ergünay, Aura R. Garrison, Jiang Hong, Kim R. Blasdell, Matthew J. Ballinger, Zuokun Yang, Manuela Sironi, Florian Hüttner, Timothy H. Hyndman, D. A. Patterson, Roy A. Hall, Eric M. Leroy, Liying Qi, Risto Jalkanen, Gary P. Kobinger, Yanxiang Wang, Michael A. Drebot, Emiliano Di Cicco, Martin H. Groschup, Amy K. Teffer, Thomas S. Postler, Sophie J. Smither, Ni Hong, Sina Bavari, Jamie Bojko, Amy Tabata, Michael J. Buchmeier, Sébastien Massart, Daniel R. Perez, Hironobu Yanagisawa, Janice Uchida, Xiǎohóng Shí, Marina Ciuffo, Jean-Paul Gonzalez, Brian H. Bird, Alejandro Olmedo-Velarde, Justin Bahl, Tao Hu, J. Felix Drexler, Gaya K. Amarasinghe, Jens H. Kuhn, Shaorong Li, Taiyun Wei, Sandra Junglen, José A. Navarro, Sofia Paraskevopoulou, Hans Peter Mühlbach, Nicholas Di Paola, Toufic Elbeaino, Guoping Wang, Song Zhang, Tong Han, Yukio Shirako, Pierre Formenty, Anthony R. Fooks, Lifeng Zhai, Benhur Lee, María Laura García, Dag-Ragnar Blystad, Bertus K. Rima, William G. Dundon, Hideki Ebihara, Jiangxiang Wu, John S. Hu, Gabriel Robles Luna, Jana Fránová, Maria S. Salvato, Norbert Nowotny, Carina Andrea Reyes, Kristina M. Miller, Eric Bergeron, Renato O. Resende, Holly R. Hughes, Victoria Wahl, Changchun Tu, Anna Papa, Roger Hewson, Anna Maria Vaira, Nicolás Bejerman, Alex Pauvolid-Corrêa, Seiji Hongo, Igor S. Lukashevich, Michael Kawate, Bernard R. Agwanda, Sead Sabanadzovic, Gideon J. Mordecai, Piet Maes, Steven B. Bradfute, Stephan Günther, Michele Digiaro, Tomio Usugi, Zhe Zhang, Adam C. Park, Guy Smagghe, Shin-Yi Lee Marzano, Kenji Kubota, Ioannis E. Tzanetakis, Christopher F. Basler, Rik L. de Swart, Yong-Zhen Zhang, Felicity J. Burt, Curtis A. Suttle, Mart Krupovic, Jussi Hepojoki, John W. McCauley, Jonathan S. Towner, Charles H. Calisher, Lei Xu, George Fú Gāo, Jonathan A. Runstadler, David M. Stone, Karia H. Kaukinen, Rachel Breyta, Masayuki Horie, Gael Kurath, Carmen Büttner, Lin-Fa Wang, Jessica R. Spengler, Olga Dolnik, Yuya Chiaki, Nicole Mielke-Ehret, Robert B. Tesh, Gustavo Palacios, Marco Chiapello, Tatjana Avšič-Županc, Martin Verbeek, Qi Cheng, Scott Adkins, Elena Dal Bó, Fujio Kadono, Selma Gago-Zachert, Sergio H. Marshall, Marta Vallino, Gilda B. Jonson, Jingjing Fu, Rosemary Sang, Takahide Sasaya, Amy J. Lambert, Paul Brown, Dennis Rubbenstroth, Dennis A. Bente, Colin R. Parrish, Jin Won Song, María A. Ayllón, Shigeharu Takeuchi, Arvind Varsani, Dàohóng Jiāng, Natalie J. Thornburg, Michael J. Melzer, Stanley L. Langevin, Igor Koloniuk, Mang Shi, John Hammond, Vicente Pallás, Thomas Briese, Amadou A. Sall, Jari Sugano, Sergey V. Netesov, Zhengli Shi, M. Ilyas, Yoshifumi Shimomoto, Wayne B. Borth, Anna E. Whitfield, Ayato Takada, Kirsten Spann, W. Paul Duprex, Marco Forgia, Jiro Wada, Susanne von Bargen, Rim Al Kubrusli, Tobi J. Ming, Gabriele Neumann, Rémi N. Charrel, Caixia Yang, Rayapati A. Naidu, Ralf Dürrwald, David P. Tchouassi, Ursula J. Buchholz, Carlotta Peracchio, Tomohide Natsuaki, Anthony Griffiths, Sheli R. Radoshitzky, Márcio Roberto Teixeira Nunes, Juliana Freitas-Astúa, Janusz T. Paweska, Humberto Debat, Francesco Di Serio, Stephanie Fürl, Susan Payne, Hugh W. Ferguson, Juan Carlos de la Torre, Keizō Tomonaga, Muhammad Waqas, Longhui Li, Elke Mühlberger, Bernadett Pályi, Lies Laenen, Ian Crozier, Yuri I. Wolf, Bernadette G. van den Hoogen, Martin Beer, Jiànróng Lǐ, Thomas Gaskin, Mengji Cao, Ali Mirazimi, F. Murilo Zerbini, Peter Simmonds, Anne Balkema-Buschmann, Adolfo García-Sastre, Hideki Kondō, William Marciel de Souza, Huazhen Liu, John V. Williams, Marco Marklewitz, Alexander Bukreyev, Luisa Rubino, Angela D. Schulze, Nolwenn M. Dheilly, Xueping Zhou, Nikos Vasilakis, Elliot J. Lefkowitz, Boris Klempa, Il-Ryong Choi, Yaqin Wang, and Jonas Klingström

Subjects
Biointeractions and Plant Health, biology, Phylum, Virology, Life Science, Bunyavirales, General Medicine, Mononegavirales, biology.organism_classification, Virology & Molecular Biology, Virologie & Moleculaire Biologie
Abstract

Unfortunately, the inclusion of original names (in non-Latin script) of the following authors caused problems with author name indexing in PubMed. Therefore, these original names were removed from XML data to correct the PubMed record. Mengji Cao, Yuya Chiaki, Hideki Ebihara, Jingjing Fu, George Fú Gāo, Tong Han, Jiang Hong, Ni Hong, Seiji Hongo, Masayuki Horie, Dàohóng Jiāng, Fujio Kadono, Hideki Kondō, Kenji Kubota, Shaorong Li, Longhui Li, Jiànróng Lǐ, Huazhen Liu, Tomohide Natsuaki, Sergey V. Netesov, Anna Papa, Sofia Paraskevopoulou, Liying Qi, Takahide Sasaya, Mang Shi, Xiǎohóng Shí, Zhènglì Shí, Yoshifumi Shimomoto, Jin‑Won Song, Ayato Takada, Shigeharu Takeuchi, Yasuhiro Tomitaka, Keizō Tomonaga, Shinya Tsuda, Changchun Tu, Tomio Usugi, Nikos Vasilakis, Jiro Wada, Lin‑Fa Wang, Guoping Wang, Yanxiang Wang, Yaqin Wang, Tàiyún Wèi, Shaohua Wen, Jiangxiang Wu, Lei Xu, Hironobu Yanagisawa, Caixia Yang, Zuokun Yang, Lifeng Zhai, Yong‑Zhen Zhang, Song Zhang, Jinguo Zhang, Zhe Zhang, Xueping Zhou. In addition, the publication call-out in the supplementary material was updated from issue 11 to issue 12. The original article has been corrected.

Published
2021

43. Natural infection of free-ranging mandrills (Mandrillus sphinx) by enteroviruses and astroviruses in southern Gabon

Author

Barthélémy Ngoubangoye, Eric M. Leroy, Eloise Suquet, Illich M Mombo, Gael Darren Maganga, Virginie Rougeron, Marie J. E. Charpentier, Larson Boundenga, Centre International de Recherches Médicales de Franceville (CIRMF), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
0301 basic medicine, food.ingredient, viruses, [SDV]Life Sciences [q-bio], 030106 microbiology, Cross-species transmission, medicine.disease_cause, Microbiology, Enteroviruses, Astrovirus, 03 medical and health sciences, food, fluids and secretions, biology.animal, Astroviridae Infections, medicine, Animals, Gabon, Feces, Phylogeny, Enterovirus, Astroviruses, Phylogenetic tree, biology, Transmission (medicine), Mamastrovirus, virus diseases, biology.organism_classification, Mandrills, Virology, 3. Good health, Mandrillus sphinx, 030104 developmental biology, Infectious Diseases, Mandrillus
Abstract

International audience; Enteroviruses (Picornaviridae) and astroviruses (Astroviridae) cause various diseases in humans and animals, including in non-human primates (NHPs). Some enteroviruses and astroviruses detected in NHPs are genetically related to those infecting humans, indicating the occurrence of interspecies transmissions. In this study, we screened 200 fecal samples of 56 free-ranging mandrills (Mandrillus sphinx) by nested reverse transcription-PCR with primers targeting the VP1 and RdRp genes, to evaluate the diversity of enterovirus and astrovirus infection, respectively, and the associated zoonotic risk. Overall, ten samples from six mandrills were enterovirus-positive (5%), and three samples from three mandrills were astrovirus-positive (1.5%). This is the first evidence of astrovirus infection in mandrills. Phylogenetic analyses based on the VP1 sequences revealed that all ten enterovirus sequences were part of the species Enterovirus J, suggesting low zoonotic risk. Phylogenetic analysis of the three astrovirus sequences showed that they all belonged to the Mamastrovirus genus. Two astrovirus sequences were highly divergent from all human astrovirus sequences (63.4-73% nucleotide identity), while one sequence (AstV-5) suggested cross-species transmission from humans to mandrills. Additional studies are needed to better characterize the identified astroviruses and to confirm whether mandrills are host of astroviruses than can be transmitted to humans.

Published
2021

44. De l’origine encore incertaine de la Covid-19 au risque d’un réservoir animal du SARS-Cov2 ou de ses variants dans le futur : une revue

Author

J. BrugÃre-Picoux, J.-L. Angot, Serge G. Rosolen, Yves Buisson, and Eric M. Leroy

Subjects
medicine.medical_specialty, transmission, zoonoses, animal reservoir, Covid-19, SARS-CoV-2, General Veterinary, biology, Coronavirus disease 2019 (COVID-19), Transmission (medicine), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Public health, Zoology, Raccoon Dogs, réservoir animal, biology.animal, Epidemiology, Pandemic, medicine, Mink
Abstract

Although the emergence of Covid-19 in China has not been clearly elucidated, the hypothesis of an animal origin remains the most likely. It is supported by the presence of the horseshoe bat suspected to be the progenitor of SARS-CoV-2 and by the scarcity of pork, due to African swine fever, diverting consumers to exotic animals of breeding sold in the markets. During this pandemic, several animal species were affected by SARS-CoV-2. Sporadic cases were first reported in pets (dogs and cats) infected by their owners, then in large feline species and apes infected in zoos by their nurses. The most significant human-to-animal transmission has occurred in mink farms, especially in the Netherlands and Denmark, requiring the euthanasia of several million animals, with mink in turn having contaminated men and stray or nomadic cats. The study of natural or experimental transmissions of SARS-CoV-2 has made it possible to identify the most receptive animal species : American minks and raccoon dogs, and to a lesser extent stray or nomadic cats, which could become an animal reservoir due to their sensitivity to this virus and their extending prolificacy. The European Commission decided on May 17, 2021 to strengthen the surveillance of SARS-CoV-2 infections in minks and other mustelids, as well as in raccoon dogs, highlighting stressing that the epidemiological assessment of the risk presented by the he appearance of SARS-CoV-2 in these susceptible species was a public health priority., Bien que l’émergence de la Covid-19 en Chine n’ait pas été clairement élucidée, l’hypothèse d’une origine animale reste la plus probable. Elle est étayée par la présence de la chauve-souris fer à cheval suspectée d’être le progéniteur du SARS-CoV-2 et par la raréfaction de la viande de porc, due à la peste porcine africaine, détournant les consommateurs vers des animaux exotiques d’élevage vendus sur les marchés. Au cours de cette pandémie, plusieurs espèces animales ont été atteintes par le SARS-CoV-2. Des cas sporadiques ont d’abord été rapportés chez des animaux de compagnie (chiens et chats) contaminés par leurs propriétaires, puis des grands félins et des gorilles contaminés dans des zoos par leurs soigneurs. La transmission la plus importante de l’Homme à l’animal a eu lieu dans les élevages de visons, surtout aux Pays-Bas et au Danemark, nécessitant l’euthanasie de plusieurs millions d’animaux, les visons ayant, à leur tour, contaminé des hommes et des chats errants. L’étude des transmissions naturelles ou expérimentales du SARS-CoV-2 a permis d’identifier les espèces animales les plus réceptives : les visons d’Amérique et les chiens viverrins, et dans une moindre mesure les chats errants, qui pourraient devenir un réservoir animal en raison de leur sensibilité à ce virus et de leur prolificité. La Commission européenne a décidé le 17 mai 2021 de renforcer la surveillance des infections par le SARS-CoV-2 chez les visons et d’autres mustélidés, ainsi que chez des chiens viverrins, en soulignant que l’évaluation épidémiologique du risque que présente l’apparition du SARS-CoV-2 chez ces espèces sensibles était une priorité de santé publique., Brugères Jeanne, Leroy Éric, Rosolen Serge Georges, Angot Jean-Luc, Buisson Yves. De l’origine encore incertaine de la Covid-19 au risque d’un réservoir animal du SARS-Cov2 ou de ses variants dans le futur : une revue. In: Bulletin de l'Académie Vétérinaire de France tome 174, 2021. pp. 117-136.

Published
2021

45. The risk of SARS-CoV-2 transmission to pets and other wild and domestic animals strongly mandates a one-health strategy to control the COVID-19 pandemic

Author

Meriadeg Ar Gouilh, Jeanne Brugère-Picoux, and Eric M. Leroy

Subjects
Farm animals, Population, medicine.disease_cause, Disease cluster, Wild animals, Malayan tiger, Article, Environmental health, Pandemic, medicine, Dog, education, Coronavirus, education.field_of_study, lcsh:R5-920, biology, Transmission (medicine), Animal, SARS-CoV-2, Public Health, Environmental and Occupational Health, Outbreak, Bat, COVID-19, Cat, biology.organism_classification, Geography, One Health, Infectious Diseases, Pet, lcsh:Medicine (General)
Abstract

Infection with the new coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), termed coronavirus infectious disease 19 (COVID-19), came to the attention of health workers in December 2019 when a cluster of people who attended the seafood and animal market in Wuhan, Hubei Province, China presented with a severe respiratory illness [1,2]. The outbreak, first localized to Wuhan, quickly spread to neighbouring provinces and within three months was declared a pandemic, with cases reported in nearly 200 countries in all regions of the world. As of 8 April 2020, the pandemic has been resulted in over one million four hundred thousand confirmed cases and over 76, 000 deaths, including over 655,000 cases and 51, 000 deaths in Europe. While China has not registered new cases for several days, parts of western Europe have become the foci of the COVID-19 pandemic. The close association between humans and their pets has led to an examination of the potential risks of transmission. Viral RNA has been detected in two dogs and two cats, belonging to SARS-CoV-2 infected owners, in Hong Kong and Liege, Belgium. While pale in comparison with the scale of infection in the human population, these observations have nonetheless provoked many violent reactions towards dogs and cats. More recently, National Veterinary Services Laboratories (NVSL) of the US the Animal and Plant Health Inspection service (APHIS) in Ames, Iowa confirmed that a female Malayan Tiger at the Bronx zoo had positive RT-PCR for SARS-CoV2. Bronx Zoo veterinarians confirmed that the Malayan tiger, her sister, two Amur tigers, and three African Lions had developed a dray cough [3]. The objective of this note is to inventory the risks of SARS-CoV-2 contamination of pets, especially dogs and cats, by their owners, and the potential role of pets in the ongoing COVID-19 pandemic.

Published
2020

46. Towards a coordinated strategy for intercepting human disease emergence in Africa

Author

Angela L. Rasmussen, Krutika Kuppalli, Eric M. Leroy, Illich M Mombo, Alyson A. Kelvin, Tarja Sironen, Paul W. Webala, Julius Nziza, Colin J. Carlson, Joseph Ogola, Moses Masika, Roch Fabien Niama, Dufton Mwaengo, Olli Vapalahti, Brad S Pickering, Gael Darren Maganga, Omu Anzala, Kristian M. Forbes, and Jason Kindrachuk

Subjects
0106 biological sciences, Microbiology (medical), 0303 health sciences, Knowledge management, business.industry, Learning object, 010603 evolutionary biology, 01 natural sciences, Microbiology, 03 medical and health sciences, Infectious Diseases, Human disease, Geography, Virology, Africa, Humans, business, Pandemics, 030304 developmental biology
Published
2020

47. Bartonella gabonensis sp. nov., a new bartonella species from savannah rodent Lophuromys sp. in Franceville, Gabon

Author

Oleg Mediannikov, Florence Fenollar, S. Abdi, Jérôme Terras, Hacène Medkour, Eric M. Leroy, O.L. Banga, Nadine N'Dilimabaka, Mamadou Lamine Tall, Mathieu Bourgarel, Joa Braïthe Mangombi, M. Ben Khedher, Centre International de Recherches Médicales de Franceville (CIRMF), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Supported by Agence Universitaire de la Francophonie (AUF) through the doctoral college CDMATHINBIO, IHU Méditerranée Infection and Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF) and Afrique centrale et grands Lacs., Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université des Sciences et Techniques de Masuku (USTM), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Bartonella, zoonose, Rodent, [SDV]Life Sciences [q-bio], 030106 microbiology, Bartonella gabonensis sp. nov, L73 - Maladies des animaux, Microbiology, Genome, lcsh:Infectious and parasitic diseases, génomique, 03 medical and health sciences, biology.animal, lcsh:RC109-216, Gabon, genome, Génome, biology, Strain (biology), [SDV.BA]Life Sciences [q-bio]/Animal biology, Lophuromys sp, Central africa, L60 - Taxonomie et géographie animales, Taxonomie, biology.organism_classification, L10 - Génétique et amélioration des animaux, bacterial infections and mycoses, 030104 developmental biology, Infectious Diseases, rodents, Bactérie gram négatif, Rongeur, Lophuromys, Bartonella species, Taxonogenomics: Genome of a New Organism
Abstract

International audience; We describe a new strain named Bartonella gabonensis sp. nov. strain 669T (CSURB1083). The entire genome of this strain is described here. It was isolated from a savannah rodent, a brush-furred rat (Lophuromys sp.), trapped the city of Franceville in Gabon, in Central Africa. B. gabonensis is an aerobic, rod-shaped and Gram-negative bacterium. On the basis of the organism's features, and following a taxonogenomic approach, we propose the creation of the species Bartonella gabonensis sp. nov.

Published
2020

48. A Second Genome Sequence of an Enterovirus C99 Detected in a Healthy Chimpanzee

Author

Nicolas Berthet, Rebeca Atencia, Debby Cox, Eric M. Leroy, Gael Darren Maganga, Larson Boundenga, Christiane Bouchier, Virginie Rougeron, Illich Manfred Mombo, Centre International de Recherches Médicales de Franceville (CIRMF), Cellule d'Intervention Biologique d'Urgence (Centre National de Référence) - Laboratory for Urgent Response to Biological Threats (National Reference Center) (CIBU), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Tchimpounga Chimpanzee Rehabilitation Centre, The Jane Goodall Institute [Pointe-Noire, Republic of the Congo], The Jane Goodall Institute Global (JGIG), Institut National Supérieur d'Agronomie et de Biotechnologie (INSAB), Université des Sciences et Techniques de Masuku (USTM), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut Pasteur [Paris]-Institut Pasteur [Paris], Institut National Supérieur d'Agronomie et de Biotechnologie [Franceville, Gabon] (INSAB), Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), and Institut Pasteur [Paris]

Subjects
0301 basic medicine, Acute flaccid paralysis, Whole genome sequencing, Strain (biology), [SDV]Life Sciences [q-bio], Genome Sequences, Biology, medicine.disease_cause, Virology, 3. Good health, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Immunology and Microbiology (miscellaneous), Phylogenetics, 030220 oncology & carcinogenesis, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, medicine, Enterovirus, Molecular Biology
Abstract

We report the nearly complete genome sequence of an enterovirus 99 strain (Cpz-IJC08) detected in a healthy chimpanzee from the Tchimpounga Sanctuary, Republic of Congo. According to the phylogeny, Cpz-IJC08 clustered with Cpz-IJC04, a previously identified chimpanzee enterovirus from the same sanctuary, isolated in animals with signs of acute flaccid paralysis., We report the nearly complete genome sequence of an enterovirus 99 strain (Cpz-IJC08) detected in a healthy chimpanzee from the Tchimpounga Sanctuary in the Republic of Congo. According to the phylogeny, Cpz-IJC08 clustered with Cpz-IJC04, a previously identified chimpanzee enterovirus from the same sanctuary, isolated from an animal with signs of acute flaccid paralysis.

Published
2020

49. High prevalence of SARS-CoV-2 antibodies in pets from COVID-19+ households

Author

Eric M. Leroy, Vincent Legros, Pierre Becquart, Matthieu Fritz, Béatrice Rosolen, Meriadeg Ar Gouilh, Oxana Vratskikh, Solène Denolly, Eric Elguero, Emilie Krafft, Bertrand Boson, Angeli Kodjo, Catherine Chirouze, Jessica Vanhomwegen, and Serge G. Rosolen

Subjects
0303 health sciences, High prevalence, CATS, biology, Coronavirus disease 2019 (COVID-19), 040301 veterinary sciences, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 04 agricultural and veterinary sciences, 3. Good health, 0403 veterinary science, 03 medical and health sciences, Environmental health, biology.protein, Medicine, Seroprevalence, Antibody, business, 030304 developmental biology
Abstract

In a survey of household cats and dogs of laboratory-confirmed COVID-19 patients, we found a high seroprevalence of SARS-CoV-2 antibodies, ranging from 21% to 53%, depending on the positivity criteria chosen. Seropositivity was significantly greater among pets from COVID-19+ households compared to those with owners of unknown status. Our results highlight the potential role of pets in the spread of the epidemic.

Published
2020

50. Le chat est-il une victime collatérale de la pollution lumineuse ?

Author

Eric M. Leroy, Jeanne Brugère-Picoux, and Serge G. Rosolen

Subjects
2019-20 coronavirus outbreak, Covid-19, cat, light pollution, obesity, zoonotic risks, General Veterinary, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, Art, Humanities, pollution lumineuse, chat, risque zoonotique, obésité, media_common
Abstract

There are more than 75 million cats in Europe, a number that is constantly increasing. It is an animal that adapts very well to a reduced space and can live alone. However, it is also a predator, a behavior that requires frequent wandering away from its familiar environment. Along with the dog, it is the most medicalized animal species and whose life expectancy is increasing. Living in close contact with man, it shares its environment, and is thus subjected to the same environmental impacts such as light pollution : reduction of darkness in time and space and its replacement by artificial light. A recent study has shown that 45% of sedentary cats are overweight or even obese. We hypothesize that among the factors favouring obesity, the extension of domestic lighting would play an important role. In human, obesity is a risk factor for the development of type 2 diabetes, which is a public health problem. The same is true for obese cats. As a clinical expression of a homologous human disease, it is THE animal model of type 2 diabetes so much sought after by the scientific community. Light pollution presents another risk for the wandering cat : the probability of encountering wild animals (rodents, mustelids, birds, etc.) which, especially during the confinement period, are attracted by the space released by humans. This risk is important to consider because of the cat’s sensitivity to coronaviruses, in particular Sars-CoV-2, which it is likely to contract from with the wild animals that it may encounter. In the context of a pandemic situation, the question of unrestricted itinerancy of cats must be addressed. Cats should only be allowed to roam freely when they are vaccinated and undergo regular anti-parasite treatments., Il y a plus de 75 millions de chats en Europe et leur nombre ne cesse d’augmenter. C’est un animal qui s’accommode très bien d’un espace réduit, qui peut rester seul mais c’est aussi un chasseur qui peut demander à sortir fréquemment de son environnement familier. Avec le chien, c’est l’espèce animale de compagnie la plus médicalisée et dont l’espérance de vie augmente. Il vit étroitement au contact de l’homme, partage son environnement et est soumis aux mêmes impacts environnementaux que ce dernier, notamment la pollution lumineuse ; c’est à dire la réduction de la part d’obscurité en temps et en espace et son remplacement par des lumières artificielles. Une étude récente a montré que 45% des chats sédentaires sont en surpoids, voire obèses. Nous émettons l’hypothèse que, parmi les facteurs favorisant l’obésité, l’allongement de l’éclairage domestique jouerait un rôle important. Chez l’homme, l’obésité est un facteur de risque d’apparition du diabète (type 2) qui est un problème de santé publique. Chez le chat obèse, il en est de même. Exprimant cliniquement la maladie humaine homologue c’est LE modèle animal de diabète de type 2 tant recherché par la communauté scientifique. La pollution lumineuse fait courir un autre risque au chat qui se promène : la probabilité de rencontre avec la faune sauvage (rongeurs, mustélidés, oiseaux, etc.) qui, notamment en cas de confinement, est attirée par l’espace libéré par l’homme. Ce risque est d’autant plus à prendre en considération que le chat est une espèce sensible aux coronaviroses, notamment le Sars-CoV-2 qu’il pourrait contracter au contact de la faune sauvage. Dans un contexte de pandémie, la question de la libre circulation des chats doit se poser et ne devraient sortir librement que les animaux vaccinés et subissant régulièrement des traitements antiparasitaires., Rosolen Serge Georges, Brugère-Picoux Jeanne, Leroy Éric. Le chat est-il une victime collatérale de la pollution lumineuse ?. In: Bulletin de l'Académie Vétérinaire de France tome 173, 2020. pp. 180-184.

Published
2020

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