77 results on '"Temmam, S"'
Search Results
2. Immunological and virological profile of children with chilblain‐like lesions and SARS‐CoV‐2
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Fertitta, L., primary, Welfringer‐Morin, A., additional, Ouedrani, A., additional, Polivka, L., additional, Chhun, S., additional, Chatenoud, L., additional, Fourgeaud, J., additional, Hadj‐Rabia, S., additional, Temmam, S., additional, Eloit, M., additional, Sermet‐Gaudelus, I., additional, and Bodemer, C., additional
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- 2020
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3. Immunological and virological profile of children with chilblain‐like lesions and SARS‐CoV‐2.
- Author
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Fertitta, L., Welfringer‐Morin, A., Ouedrani, A., Polivka, L., Chhun, S., Chatenoud, L., Fourgeaud, J., Hadj‐Rabia, S., Temmam, S., Eloit, M., Sermet‐Gaudelus, I., and Bodemer, C.
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SARS-CoV-2 ,URTICARIA - Abstract
In 23/30 patients (77%) and 14/17 (82%) of chilblains patients, COVID-19 was suspected in at least one first-degree relative and confirmed in four including two with chilblains. A clinical, histopathological and laboratory study of 19 consecutive Italian paediatric patients with chilblain-like lesions: lights and shadows on the relationship with COVID-19 infection. Serology was positive in only 1/16 chilblains patient among the 26 patients tested. [Extracted from the article]
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- 2021
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4. Long PCR product sequencing (LoPPS) : a shotgun-based approach to sequence long PCR products
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Emonet, S. F., Grard, G., Brisbarre, N. M., Moureau, G. N., Temmam, S., Charrel, R. N., and de Lamballerie, Xavier
- Abstract
Here we describe a practical procedure for sequencing long PCR products. The method relies on ultrasonic shearing of PCR products, resulting in fragments 700 - 1,000 nt long. Termini are subsequently repaired to obtain blunt ends and 3' A-overhangs are added before TA cloning. A predetermined number of clones are sequenced using an insert-independent primer to obtain an overlapping contig covering the full length of the PCR product. This method is cost effective and enables the complete sequencing of any large PCR product in a high-throughput format. Processing of amplified DNA requires 3 h handling time prior to the ligation step, and the clone library is available 2 d later. The complete sequence information is obtained approximately 5 d after the PCR step, depending on the sequencing procedure adopted.
- Published
- 2007
5. Pathogenic Leptospira spp. in Bats, Madagascar and Union of the Comoros
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Lagadec, E, Gomard, Y, Guernier, Vanina, Dietrich, M, Pascalis, H, Temmam, S, Ramasindrazana, B, Goodman, SM, Tortosa, P, Dellagi, K, Lagadec, E, Gomard, Y, Guernier, Vanina, Dietrich, M, Pascalis, H, Temmam, S, Ramasindrazana, B, Goodman, SM, Tortosa, P, and Dellagi, K
- Published
- 2012
6. Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009
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Dellagi, K, Rollot, O, Temmam, S, Salez, N, Guernier, Vanina, Pascalis, H, Gerardin, P, Fianu, A, Lapidus, N, Naty, N, Tortosa, P, Boussaid, K, Jaffar-Banjee, M-C, Filleul, L, Flahault, A, Carrat, F, Favier, F, de Lamballerie, X, Dellagi, K, Rollot, O, Temmam, S, Salez, N, Guernier, Vanina, Pascalis, H, Gerardin, P, Fianu, A, Lapidus, N, Naty, N, Tortosa, P, Boussaid, K, Jaffar-Banjee, M-C, Filleul, L, Flahault, A, Carrat, F, Favier, F, and de Lamballerie, X
- Abstract
Background To date, there is little information that reflects the true extent of spread of the pH1N1/2009v influenza pandemic at the community level as infection often results in mild or no clinical symptoms. This study aimed at assessing through a prospective study, the attack rate of pH1N1/2009 virus in Reunion Island and risk factors of infection, during the 2009 season. Methodology/Principal Findings A serosurvey was conducted during the 2009 austral winter, in the frame of a prospective population study. Pairs of sera were collected from 1687 individuals belonging to 772 households, during and after passage of the pandemic wave. Antibodies to pH1N1/2009v were titered using the hemagglutination inhibition assay (HIA) with titers ≥1/40 being considered positive. Seroprevalence during the first two weeks of detection of pH1N1/2009v in Reunion Island was 29.8% in people under 20 years of age, 35.6% in adults (20–59 years) and 73.3% in the elderly (≥60 years) (P<0.0001). Baseline corrected cumulative incidence rates, were 42.9%, 13.9% and 0% in these age groups respectively (P<0.0001). A significant decline in antibody titers occurred soon after the passage of the epidemic wave. Seroconversion rates to pH1N1/2009 correlated negatively with age: 63.2%, 39.4% and 16.7%, in each age group respectively (P<0.0001). Seroconversion occurred in 65.2% of individuals who were seronegative at inclusion compared to 6.8% in those who were initially seropositive. Conclusions Seroincidence of pH1N1/2009v infection was three times that estimated from clinical surveillance, indicating that almost two thirds of infections occurring at the community level have escaped medical detection. People under 20 years of age were the most affected group. Pre-epidemic titers ≥1/40 prevented seroconversion and are likely protective against infection. A concern was raised about the long term stability of the antibody
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- 2011
7. A Real-Time RT-PCR Method for the Universal Detection and Identification of Flaviviruses
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Moureau, G., primary, Temmam, S., additional, Gonzalez, J.P., additional, Charrel, R.N., additional, Grard, G., additional, and de Lamballerie, X., additional
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- 2007
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8. Influenza A(H1N1)pdm09 virus in pigs, Réunion Island.
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Cardinale E, Pascalis H, Temmam S, Hervé S, Saulnier A, Turpin M, Barbier N, Hoarau J, Quéguiner S, Gorin S, Foray C, Roger M, Porphyre V, André P, Thomas T, de Lamballerie X, Dellagi K, Simon G, Cardinale, Eric, and Pascalis, Hervé
- Abstract
During 2009, pandemic influenza A(H1N1)pdm09 virus affected humans on Réunion Island. Since then, the virus has sustained circulation among local swine herds, raising concerns about the potential for genetic evolution of the virus and possible retransmission back to humans of variants with increased virulence. Continuous surveillance of A(H1N1)pdm09 infection in pigs is recommended. [ABSTRACT FROM AUTHOR]
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- 2012
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9. Insights into the virome of Hyalomma marginatum in the Danube Delta: a major vector of Crimean-Congo hemorrhagic fever virus in Eastern Europe.
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Bratuleanu BE, Chretien D, Bigot T, Regnault B, Pérot P, Savuta G, Eloit M, and Temmam S
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- Animals, Birds virology, Arachnid Vectors virology, Europe, Eastern epidemiology, Phylogeny, Female, Hemorrhagic Fever Virus, Crimean-Congo genetics, Hemorrhagic Fever Virus, Crimean-Congo isolation & purification, Hemorrhagic Fever Virus, Crimean-Congo classification, Virome genetics, Ixodidae virology, Hemorrhagic Fever, Crimean virology, Hemorrhagic Fever, Crimean epidemiology, Hemorrhagic Fever, Crimean transmission, Wetlands
- Abstract
Background: Ticks are significant vectors of pathogens, including viruses, bacteria, and protozoa. With approximately 900 tick species worldwide, many are expanding their geographical range due to changing socioeconomic and climate factors. The Danube Delta, one of Europe's largest wetlands, is an ecosystem that, despite its ecological importance, remains understudied concerning the risk of introducing new tick-borne viruses. This region serves as a critical habitat for migratory birds, which can carry ticks over long distances, potentially introducing exotic tick species and their pathogens into the local ecosystem. Hyalomma marginatum ticks, the primary vector of Crimean-Congo hemorrhagic fever virus (CCHFV), are of particular concern due to their expanding presence in Europe and potential to spread other arboviruses. In addition to being the primary vector for CCHFV, Hyalomma sp. ticks are capable of transmitting other pathogens of medical and veterinary importance, including Dugbe virus, West Nile virus, African horse sickness virus, and Kyasanur forest disease virus. Therefore, it is essential to monitor the presence of Hyalomma sp. ticks while simultaneously surveilling arbovirus circulation in tick populations to mitigate the risk of arboviral outbreaks., Methods: In this work, we used an RNA sequencing technique to analyze the virome of H. marginatum ticks collected from the Danube Delta Biosphere Reserve, Romania, one of the major bird migration hubs from Africa to Europe., Results: Among the viral taxa detected in H. marginatum ticks, sequences belonging to Volzhskoe tick virus (VTV), Balambala tick virus (BMTV) and Bole tick virus 4 (BTV4) were identified. In addition, we report the first identification of a novel Rhabdoviridae-related virus, Hyalomma marginatum rhabdovirus (HMRV). No CCHFV or any CCHFV-related nairovirus were detected in this study., Conclusions: To summarize, detecting new viruses is essential for monitoring potential viral outbreaks. Our research expands the understanding of virus diversity in Eastern Europe, including the identification of novel viruses. This insight is crucial for monitoring viruses that may pose risks to both animal and human health, such as CCHFV., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)
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- 2024
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10. Preschool-age children maintain a distinct memory CD4 + T cell and memory B cell response after SARS-CoV-2 infection.
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Manfroi B, Cuc BT, Sokal A, Vandenberghe A, Temmam S, Attia M, El Behi M, Camaglia F, Nguyen NT, Pohar J, Salem-Wehbe L, Pottez-Jouatte V, Borzakian S, Elenga N, Galeotti C, Morelle G, de Truchis de Lays C, Semeraro M, Romain AS, Aubart M, Ouldali N, Mahuteau-Betzer F, Beauvineau C, Amouyal E, Berthaud R, Crétolle C, Arnould MD, Faye A, Lorrot M, Benoist G, Briand N, Courbebaisse M, Martin R, Van Endert P, Hulot JS, Blanchard A, Tartour E, Leite-de-Moraes M, Lezmi G, Ménager M, Luka M, Reynaud CA, Weill JC, Languille L, Michel M, Chappert P, Mora T, Walczak AM, Eloit M, Bacher P, Scheffold A, Mahévas M, Sermet-Gaudelus I, and Fillatreau S
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- Humans, Child, Preschool, Adult, Child, Memory T Cells immunology, Male, Immunologic Memory, Female, Antibodies, Viral immunology, Antibodies, Viral blood, Middle Aged, Antibodies, Neutralizing immunology, Antibodies, Neutralizing blood, Young Adult, COVID-19 immunology, COVID-19 virology, SARS-CoV-2 immunology, CD4-Positive T-Lymphocytes immunology, Memory B Cells immunology
- Abstract
The development of the human immune system lasts for several years after birth. The impact of this maturation phase on the quality of adaptive immunity and the acquisition of immunological memory after infection at a young age remains incompletely defined. Here, using an antigen-reactive T cell (ARTE) assay and multidimensional flow cytometry, we profiled circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-reactive CD3
+ CD4+ CD154+ T cells in children and adults before infection, during infection, and 11 months after infection, stratifying children into separate age groups and adults according to disease severity. During SARS-CoV-2 infection, children younger than 5 years old displayed a lower antiviral CD4+ T cell response, whereas children older than 5 years and adults with mild disease had, quantitatively and phenotypically, comparable virus-reactive CD4+ T cell responses. Adults with severe disease mounted a response characterized by higher frequencies of virus-reactive proinflammatory and cytotoxic T cells. After SARS-CoV-2 infection, preschool-age children not only maintained neutralizing SARS-CoV-2-reactive antibodies postinfection comparable to adults but also had phenotypically distinct memory T cells displaying high inflammatory features and properties associated with migration toward inflamed sites. Moreover, preschool-age children had markedly fewer circulating virus-reactive memory B cells compared with the other cohorts. Collectively, our results reveal unique facets of antiviral immunity in humans at a young age and indicate that the maturation of adaptive responses against SARS-CoV-2 toward an adult-like profile occurs in a progressive manner.- Published
- 2024
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11. Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236.
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Fujita S, Plianchaisuk A, Deguchi S, Ito H, Nao N, Wang L, Nasser H, Tamura T, Kimura I, Kashima Y, Suzuki R, Suzuki S, Kida I, Tsuda M, Oda Y, Hashimoto R, Watanabe Y, Uriu K, Yamasoba D, Guo Z, Hinay AA Jr, Kosugi Y, Chen L, Pan L, Kaku Y, Chu H, Donati F, Temmam S, Eloit M, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Suzuki Y, Ito J, Ikeda T, Tanaka S, Matsuno K, Fukuhara T, Takayama K, and Sato K
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- Animals, Humans, Spike Glycoprotein, Coronavirus metabolism, Spike Glycoprotein, Coronavirus genetics, Organoids virology, Organoids metabolism, Induced Pluripotent Stem Cells metabolism, Induced Pluripotent Stem Cells cytology, Induced Pluripotent Stem Cells virology, Cricetinae, Furin metabolism, Epithelial Cells virology, Vero Cells, Chlorocebus aethiops, SARS-CoV-2 genetics, SARS-CoV-2 physiology, COVID-19 virology, Chiroptera virology
- Abstract
Background: Although several SARS-CoV-2-related coronaviruses (SC2r-CoVs) were discovered in bats and pangolins, the differences in virological characteristics between SARS-CoV-2 and SC2r-CoVs remain poorly understood. Recently, BANAL-20-236 (B236) was isolated from a rectal swab of Malayan horseshoe bat and was found to lack a furin cleavage site (FCS) in the spike (S) protein. The comparison of its virological characteristics with FCS-deleted SARS-CoV-2 (SC2ΔFCS) has not been conducted yet., Methods: We prepared human induced pluripotent stem cell (iPSC)-derived airway and lung epithelial cells and colon organoids as human organ-relevant models. B236, SARS-CoV-2, and artificially generated SC2ΔFCS were used for viral experiments. To investigate the pathogenicity of B236 in vivo, we conducted intranasal infection experiments in hamsters., Findings: In human iPSC-derived airway epithelial cells, the growth of B236 was significantly lower than that of the SC2ΔFCS. A fusion assay showed that the B236 and SC2ΔFCS S proteins were less fusogenic than the SARS-CoV-2 S protein. The infection experiment in hamsters showed that B236 was less pathogenic than SARS-CoV-2 and even SC2ΔFCS. Interestingly, in human colon organoids, the growth of B236 was significantly greater than that of SARS-CoV-2., Interpretation: Compared to SARS-CoV-2, we demonstrated that B236 exhibited a tropism toward intestinal cells rather than respiratory cells. Our results are consistent with a previous report showing that B236 is enterotropic in macaques. Altogether, our report strengthens the assumption that SC2r-CoVs in horseshoe bats replicate primarily in the intestinal tissues rather than respiratory tissues., Funding: This study was supported in part by AMED ASPIRE (JP23jf0126002, to Keita Matsuno, Kazuo Takayama, and Kei Sato); AMED SCARDA Japan Initiative for World-leading Vaccine Research and Development Centers "UTOPIA" (JP223fa627001, to Kei Sato), AMED SCARDA Program on R&D of new generation vaccine including new modality application (JP223fa727002, to Kei Sato); AMED SCARDA Hokkaido University Institute for Vaccine Research and Development (HU-IVReD) (JP223fa627005h0001, to Takasuke Fukuhara, and Keita Matsuno); AMED Research Program on Emerging and Re-emerging Infectious Diseases (JP21fk0108574, to Hesham Nasser; JP21fk0108493, to Takasuke Fukuhara; JP22fk0108617 to Takasuke Fukuhara; JP22fk0108146, to Kei Sato; JP21fk0108494 to G2P-Japan Consortium, Keita Matsuno, Shinya Tanaka, Terumasa Ikeda, Takasuke Fukuhara, and Kei Sato; JP21fk0108425, to Kazuo Takayama and Kei Sato; JP21fk0108432, to Kazuo Takayama, Takasuke Fukuhara and Kei Sato; JP22fk0108534, Terumasa Ikeda, and Kei Sato; JP22fk0108511, to Yuki Yamamoto, Terumasa Ikeda, Keita Matsuno, Shinya Tanaka, Kazuo Takayama, Takasuke Fukuhara, and Kei Sato; JP22fk0108506, to Kazuo Takayama and Kei Sato); AMED Research Program on HIV/AIDS (JP22fk0410055, to Terumasa Ikeda; and JP22fk0410039, to Kei Sato); AMED Japan Program for Infectious Diseases Research and Infrastructure (JP22wm0125008 to Keita Matsuno); AMED CREST (JP21gm1610005, to Kazuo Takayama; JP22gm1610008, to Takasuke Fukuhara; JST PRESTO (JPMJPR22R1, to Jumpei Ito); JST CREST (JPMJCR20H4, to Kei Sato); JSPS KAKENHI Fund for the Promotion of Joint International Research (International Leading Research) (JP23K20041, to G2P-Japan Consortium, Keita Matsuno, Takasuke Fukuhara and Kei Sato); JST SPRING (JPMJSP2108 to Shigeru Fujita); JSPS KAKENHI Grant-in-Aid for Scientific Research C (22K07103, to Terumasa Ikeda); JSPS KAKENHI Grant-in-Aid for Scientific Research B (21H02736, to Takasuke Fukuhara); JSPS KAKENHI Grant-in-Aid for Early-Career Scientists (22K16375, to Hesham Nasser; 20K15767, to Jumpei Ito); JSPS Core-to-Core Program (A. Advanced Research Networks) (JPJSCCA20190008, to Kei Sato); JSPS Research Fellow DC2 (22J11578, to Keiya Uriu); JSPS Research Fellow DC1 (23KJ0710, to Yusuke Kosugi); JSPS Leading Initiative for Excellent Young Researchers (LEADER) (to Terumasa Ikeda); World-leading Innovative and Smart Education (WISE) Program 1801 from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (to Naganori Nao); Ministry of Health, Labour and Welfare (MHLW) under grant 23HA2010 (to Naganori Nao and Keita Matsuno); The Cooperative Research Program (Joint Usage/Research Center program) of Institute for Life and Medical Sciences, Kyoto University (to Kei Sato); International Joint Research Project of the Institute of Medical Science, the University of Tokyo (to Terumasa Ikeda and Takasuke Fukuhara); The Tokyo Biochemical Research Foundation (to Kei Sato); Takeda Science Foundation (to Terumasa Ikeda and Takasuke Fukuhara); Mochida Memorial Foundation for Medical and Pharmaceutical Research (to Terumasa Ikeda); The Naito Foundation (to Terumasa Ikeda); Hokuto Foundation for Bioscience (to Tomokazu Tamura); Hirose Foundation (to Tomokazu Tamura); and Mitsubishi Foundation (to Kei Sato)., Competing Interests: Declaration of interests Yuki Yamamoto and Tetsuharu Nagamoto are founders and shareholders of HiLung, Inc. Yuki Yamamoto is a co-inventor of patents (PCT/JP2016/057254; "Method for inducing differentiation of alveolar epithelial cells", PCT/JP2016/059786, "Method of producing airway epithelial cells"). Jumpei Ito has consulting fees and honoraria for lectures from Takeda Pharmaceutical Co. Ltd. Kei Sato has consulting fees from Moderna Japan Co., Ltd. and Takeda Pharmaceutical Co. Ltd. and honoraria for lectures from Gilead Sciences, Inc., Moderna Japan Co., Ltd., and Shionogi & Co., Ltd. The other authors declare that no competing interests exist., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)
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- 2024
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12. Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence.
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Temmam S, Tu TC, Regnault B, Bonomi M, Chrétien D, Vendramini L, Duong TN, Phong TV, Yen NT, Anh HN, Son TH, Anh PT, Amara F, Bigot T, Munier S, Thong VD, van der Werf S, Nam VS, and Eloit M
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- Humans, Animals, Vietnam epidemiology, Phylogeny, Genotype, Phenotype, Pandemics, Coronavirus genetics, Chiroptera, Severe acute respiratory syndrome-related coronavirus, Coronavirus Infections epidemiology, Coronavirus Infections veterinary
- Abstract
Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.
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- 2023
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13. Comprehensive Characterization of Viral Diversity of Female Mosquitoes in Madagascar.
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Bennouna A, Tantely ML, Raharinosy V, Andriamandimby SF, Bigot T, Chrétien D, Jacquemet E, Volant S, Temmam S, Dussart P, Lacoste V, Girod R, and Eloit M
- Abstract
The diversity and circulation of arboviruses are not much studied in Madagascar. The fact is that arboviral emergences are rarely detected. The existing surveillance system primarily relies on serological detection and records only a few human infections annually. The city of Mahajanga, however, experienced a confirmed dengue fever epidemic in 2020 and 2021. This study aimed to characterize and analyze the virome of mosquitoes collected in Mahajanga, near patients with dengue-like syndromes to detect known and unknown viruses as well as investigate the factors contributing to the relative low circulation of arboviruses in the area. A total of 4280 mosquitoes representing at least 12 species from the Aedes , Anopheles , and Culex genera were collected during the dry and the rainy seasons from three sites, following an urbanization gradient. The virome analysis of 2192 female mosquitoes identified a diverse range of viral families and genera and revealed different patterns that are signatures of the influence of the mosquito genus or the season of collection on the composition and abundance of the virome. Despite the absence of known human or veterinary arboviruses, the identification and characterization of viral families, genera, and species in the mosquito virome contribute to our understanding of viral ecology and diversity within mosquito populations in Madagascar. This study serves as a foundation for ongoing surveillance efforts and provides a basis for the development of preventive strategies against various mosquito-borne viral diseases, including known arboviruses.
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- 2023
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14. Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia.
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Mohamed Ali S, Rakotonirina A, Heng K, Jacquemet E, Volant S, Temmam S, Boyer S, and Eloit M
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- Humans, Animals, Cambodia epidemiology, Longitudinal Studies, Mosquito Vectors, Birnaviridae, Culicidae
- Abstract
Arthropod-borne viruses (arboviruses) pose a significant global health threat and are primarily transmitted by mosquitoes. In Cambodia, there are currently 290 recorded mosquito species, with at least 17 of them considered potential vectors of arboviruses to humans. Effective surveillance of virome profiles in mosquitoes from Cambodia is vital, as it could help prevent and control arbovirus diseases in a country where epidemics occur frequently. The objective of this study was to identify and characterize the viral diversity in mosquitoes collected during a one-year longitudinal study conducted in various habitats across Cambodia. For this purpose, we used a metatranscriptomics approach and detected the presence of chikungunya virus in the collected mosquitoes. Additionally, we identified viruses categorized into 26 taxa, including those known to harbor arboviruses such as Flaviviridae and Orthomyxoviridae , along with a group of viruses not yet taxonomically identified and provisionally named "unclassified viruses". Interestingly, the taxa detected varied in abundance and composition depending on the mosquito genus, with no significant influence of the collection season. Furthermore, most of the identified viruses were either closely related to viruses found exclusively in insects or represented new viruses belonging to the Rhabdoviridae and Birnaviridae families. The transmission capabilities of these novel viruses to vertebrates remain unknown., Competing Interests: The authors declare no conflict of interest.
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- 2023
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15. Acute tubulointerstitial nephritis with or without uveitis: a novel form of post-acute COVID-19 syndrome in children.
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Avramescu M, Isnard P, Temmam S, Chevalier A, Bastard P, Attia M, Berthaud R, Fila M, Dossier C, Hogan J, Ulinski T, Leguevaques D, Louillet F, Casado EM, Halimi JM, Cloarec S, Zaloszyc A, Faudeux C, Rousset-Rouvière C, Clavé S, Harambat J, Rollot E, Simon T, Nallet-Amate M, Ranchin B, Bacchetta J, Porcheret F, Bernard J, Ryckewaert A, Jamet A, Fourgeaud J, Da Rocha N, Pérot P, Kuperwasser N, Bouazza N, Rabant M, Duong Van Huyen JP, Robert MP, Zuber J, Casanova JL, Eloit M, Sermet-Gaudelus I, and Boyer O
- Subjects
- Child, Humans, Post-Acute COVID-19 Syndrome, COVID-19 complications, Nephritis, Interstitial diagnosis, Nephritis, Interstitial drug therapy, Uveitis diagnosis, Uveitis drug therapy, Uveitis etiology
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- 2023
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16. Virus Pop-Expanding Viral Databases by Protein Sequence Simulation.
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Kende J, Bonomi M, Temmam S, Regnault B, Pérot P, Eloit M, and Bigot T
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- Humans, Phylogeny, Computer Simulation, Databases, Factual, Metagenomics methods, Computational Biology methods, Viruses genetics
- Abstract
The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with datasets derived from biological samples or in silico spiked samples containing known viral sequences present in public databases, resulting in the inability to evaluate the capacity of these tools to detect novel or distant viruses. Simulating realistic evolutionary directions is therefore key to benchmark and improve these tools. Additionally, expanding current databases with realistic simulated sequences can improve the capacity of alignment-based searching strategies for finding distant viruses, which could lead to a better characterization of the "dark matter" of metagenomics data. Here, we present Virus Pop, a novel pipeline for simulating realistic protein sequences and adding new branches to a protein phylogenetic tree. The tool generates simulated sequences with substitution rate variations that are dependent on protein domains and inferred from the input dataset, allowing for a realistic representation of protein evolution. The pipeline also infers ancestral sequences corresponding to multiple internal nodes of the input data phylogenetic tree, enabling new sequences to be inserted at various points of interest in the group studied. We demonstrated that Virus Pop produces simulated sequences that closely match the structural and functional characteristics of real protein sequences, taking as an example the spike protein of sarbecoviruses . Virus Pop also succeeded at creating sequences that resemble real sequences not included in the databases, which facilitated the identification of a novel pathogenic human circovirus not included in the input database. In conclusion, Virus Pop is helpful for challenging taxonomic assignation tools and could help improve databases to better detect distant viruses.
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- 2023
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17. SARS-CoV-2-related bat virus behavior in human-relevant models sheds light on the origin of COVID-19.
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Temmam S, Montagutelli X, Herate C, Donati F, Regnault B, Attia M, Baquero Salazar E, Chretien D, Conquet L, Jouvion G, Pipoli Da Fonseca J, Cokelaer T, Amara F, Relouzat F, Naninck T, Lemaitre J, Derreudre-Bosquet N, Pascal Q, Bonomi M, Bigot T, Munier S, Rey FA, Le Grand R, van der Werf S, and Eloit M
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- Humans, Animals, Mice, SARS-CoV-2, Furin genetics, Furin metabolism, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus metabolism, Mutation, COVID-19
- Abstract
Bat sarbecovirus BANAL-236 is highly related to SARS-CoV-2 and infects human cells, albeit lacking the furin cleavage site in its spike protein. BANAL-236 replicates efficiently and pauci-symptomatically in humanized mice and in macaques, where its tropism is enteric, strongly differing from that of SARS-CoV-2. BANAL-236 infection leads to protection against superinfection by a virulent strain. We find no evidence of antibodies recognizing bat sarbecoviruses in populations in close contact with bats in which the virus was identified, indicating that such spillover infections, if they occur, are rare. Six passages in humanized mice or in human intestinal cells, mimicking putative early spillover events, select adaptive mutations without appearance of a furin cleavage site and no change in virulence. Therefore, acquisition of a furin site in the spike protein is likely a pre-spillover event that did not occur upon replication of a SARS-CoV-2-like bat virus in humans or other animals. Other hypotheses regarding the origin of the SARS-CoV-2 should therefore be evaluated, including the presence of sarbecoviruses carrying a spike with a furin cleavage site in bats., (© 2023 The Authors.)
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- 2023
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18. A Search for Tick-Associated, Bronnoya-like Virus Spillover into Sheep.
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Bratuleanu BE, Raileanu C, Chrétien D, Guardado-Calvo P, Bigot T, Savuta G, Temmam S, and Eloit M
- Abstract
Tick-borne diseases are responsible for many vector-borne diseases within Europe. Recently, novel viruses belonging to a new viral family of the order Bunyavirales were discovered in numerous tick species. In this study, we used metatranscriptomics to detect the virome, including novel viruses, associated with Ixodes ricinus collected from Romania and France. A bunyavirus-like virus related to the Bronnoya virus was identified for the first time in these regions. It presents a high level of amino-acid conservation with Bronnoya-related viruses identified in I. ricinus ticks from Norway and Croatia and with the Ixodes scapularis bunyavirus isolated from a tick cell line in Japan in 2014. Phylogenetic analyses revealed that the Bronnoya viruses' sub-clade is distinct from several Bunyavirales families, suggesting that it could constitute a novel family within the order. To determine if Bronnoya viruses could constitute novel tick-borne arboviruses, a Luciferase immunoprecipitation assay for detecting antibodies in the viral glycoprotein of the Romanian Bronnoya virus was used to screen sera from small ruminants exposed to tick bites. No positive serum was detected, suggesting that this virus is probably not able to infect small ruminants. This study represents the first serological investigation of mammalian infections with a Bronnoya-like virus and an initial step in the identification of potential new emergences of tick-borne arboviruses.
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- 2023
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19. Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery.
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Pérot P, Bigot T, Temmam S, Regnault B, and Eloit M
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- High-Throughput Nucleotide Sequencing methods, Humans, Metagenome, Viral Proteins genetics, Metagenomics methods, Viruses genetics
- Abstract
We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake Neopneumovirus viral sequences generated with variable evolutionary distances from known members of the Pneumoviridae family, were used. Results were compared to Chan Zuckerberg ID (CZ ID), a reference cloud-based mNGS pipeline. We show that Microseek reliably identifies known viral sequences and performs well for the detection of distant pseudoviral sequences, especially in complex samples such as in human plasma, while minimizing non-relevant hits.
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- 2022
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20. Author Correction: Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.
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Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, and Eloit M
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- 2022
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21. Seroprevalence of Crimean-Congo Hemorrhagic Fever Among Small Ruminants from Southern Romania.
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Bratuleanu B, Anita A, Temmam S, Dascalu A, Crivei L, Cozma A, Pourquier P, Savuta G, Eloit M, and Anita D
- Subjects
- Animals, Antibodies, Viral, Humans, Romania epidemiology, Ruminants, Seroepidemiologic Studies, Sheep, Goat Diseases epidemiology, Hemorrhagic Fever Virus, Crimean-Congo genetics, Hemorrhagic Fever, Crimean epidemiology, Hemorrhagic Fever, Crimean veterinary, Sheep Diseases epidemiology, Ticks
- Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease that can be contracted by direct contact with viremic animals or humans. Domestic animals are accidental hosts and contribute to the spread and amplification of the virus. The main objective of this study was to provide updated information related to CCHF virus (CCHFV) infection in Southern Romania by assessing the seroprevalence of CCHF in small ruminants (sheep and goats) using a double-antigen sandwich enzyme-linked immunosorbent assay and by detection of CCHFV in engorged ticks and serum samples using real-time RT-PCR. The overall seroprevalence of CCHF in small ruminants was 37.7% (95% CI 31.7 to 43.7). No statistical seroprevalence difference was observed between the two species of ruminants ( p = 0.76), but a significant difference was established between the locations ( p < 0.01). No CCHFV RNA was detected in tick pools and small ruminant's sera tested by real-time RT-PCR, although the high seroprevalence to CCHFV among ruminants indicates that CCHV or a closely related virus circulates in Southern Romania.
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- 2022
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22. The virome of Rhipicephalus, Dermacentor and Haemaphysalis ticks from Eastern Romania includes novel viruses with potential relevance for public health.
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Bratuleanu BE, Temmam S, Chrétien D, Regnault B, Pérot P, Bouchier C, Bigot T, Savuța G, and Eloit M
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- Animals, Humans, Mammals, Phylogeny, Public Health, Romania epidemiology, Virome, Dermacentor, Ixodidae, RNA Viruses, Rhipicephalus, Viruses
- Abstract
Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for the health of humans and livestock. The composition of viral communities in ticks and their interactions with pathogens, is poorly understood, particularly in Eastern Europe, an area that represents a major hub for animal-arthropod vectors exchanges (e.g., via bird migrations). The aim of this study was to describe the virome of Dermacentor sp., Rhipicephalus sp. and Haemaphysalis sp. ticks collected from relatively little studied regions of Romania (Iasi and Tulcea counties) located at the intersection of various biotopes, countries and routes of migrations. We also focused the study on viruses that could potentially have relevance for human and animal health. In 2019, more than 500 ticks were collected from the vegetation and from small ruminants and analysed by high-throughput transcriptome sequencing. Among the viral communities infecting Romanian ticks, viruses belonging to the Flaviviridae, Phenuiviridae and Nairoviridae families were identified and full genomes were derived. Phylogenetic analyses placed them in clades where mammalian isolates are found, suggesting that these viruses could constitute novel arboviruses. The characterization of these communities increase the knowledge of the diversity of viruses in Eastern Europe and provides a basis for further studies about the interrelationship between ticks and tick-borne viruses., (© 2021 Wiley-VCH GmbH.)
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- 2022
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23. Detection of Phenuiviridae, Chuviridae Members, and a Novel Quaranjavirus in Hard Ticks From Danube Delta.
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Bratuleanu BE, Temmam S, Munier S, Chrétien D, Bigot T, van der Werf S, Savuta G, and Eloit M
- Abstract
Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for the health of humans and livestock. The members of the Quaranjavirus genus are mainly associated with argas ticks but recent studies demonstrated the presence of novel quaranjaviruses-like in ixodid ticks. In 2020, 169 Rhipicephalus sanguineus ticks were collected in Southern Romania from small ruminants and analyzed by high-throughput transcriptome sequencing. Among the viral families that infect Romanian ticks, we have identified sequences from Phenuiviridae (Brown dog tick phlebovirus 1 [BDTPV1] and Brown dog tick phlebovirus 2 [BDTPV2]) and Chuviridae families (Cataloi mivirus [CTMV]), and numerous sequences from a new quaranjavirus-like, tentatively named Cataloi tick quaranjavirus (CTQV). Phylogenetic analyses performed on the five segments show that CTQV is phylogenetically positioned within a clade that encompasses Ixodidae -borne viruses associated with iguanas, small ruminants, seabirds, and penguins distributed across different geographical areas. Furthermore, CTQV is positioned differently depending on the segment considered. This is the first report on the detection of a quaranjavirus-like in Eastern Europe. Further investigations are needed to discern its infectivity and pathogenicity against vertebrates., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bratuleanu, Temmam, Munier, Chrétien, Bigot, van der Werf, Savuta and Eloit.)
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- 2022
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24. Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.
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Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, and Eloit M
- Subjects
- Angiotensin-Converting Enzyme 2, Animals, Asia, Caves, Disease Reservoirs, Humans, Protein Binding, SARS-CoV-2, Spike Glycoprotein, Coronavirus chemistry, COVID-19, Chiroptera virology
- Abstract
The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related viruses in Asian Rhinolophus bats
1-4 , including the closest virus from R. affinis, RaTG13 (refs.5,6 ), and pangolins7-9 . SARS-CoV-2 has a mosaic genome, to which different progenitors contribute. The spike sequence determines the binding affinity and accessibility of its receptor-binding domain to the cellular angiotensin-converting enzyme 2 (ACE2) receptor and is responsible for host range10-12 . SARS-CoV-2 progenitor bat viruses genetically close to SARS-CoV-2 and able to enter human cells through a human ACE2 (hACE2) pathway have not yet been identified, although they would be key in understanding the origin of the epidemic. Here we show that such viruses circulate in cave bats living in the limestone karstic terrain in northern Laos, in the Indochinese peninsula. We found that the receptor-binding domains of these viruses differ from that of SARS-CoV-2 by only one or two residues at the interface with ACE2, bind more efficiently to the hACE2 protein than that of the SARS-CoV-2 strain isolated in Wuhan from early human cases, and mediate hACE2-dependent entry and replication in human cells, which is inhibited by antibodies that neutralize SARS-CoV-2. None of these bat viruses contains a furin cleavage site in the spike protein. Our findings therefore indicate that bat-borne SARS-CoV-2-like viruses that are potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)- Published
- 2022
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25. Low seroprevalence of COVID-19 in Lao PDR, late 2020.
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Virachith S, Pommelet V, Calvez E, Khounvisith V, Sayasone S, Kounnavong S, Maxay M, Xangsayarath P, Temmam S, Eloit M, Escriou N, Rose T, Vongphayloth K, Hübschen JM, Lacoste V, Somlor S, Phonekeo D, Brey PT, and Black AP
- Abstract
Background: In 2020 Lao PDR had low reported COVID-19 cases but it was unclear whether this masked silent transmission. A seroprevalence study was done August - September 2020 to determine SARS-CoV-2 exposure., Methods: Participants were from the general community (n=2433) or healthcare workers (n=666) in five provinces and bat/wildlife contacts (n=74) were from Vientiane province. ELISAs detected anti- SARS-CoV-2 Nucleoprotein (N; n=3173 tested) and Spike (S; n=1417 tested) antibodies. Double-positive samples were checked by IgM/IgG rapid tests. Controls were confirmed COVID-19 cases (n=15) and pre-COVID-19 samples (n=265). Seroprevalence for the general community was weighted to account for complex survey sample design, age and sex., Findings: In pre-COVID-19 samples, 5·3%, [95% CI=3·1-8·7%] were anti-N antibody single-positive and 1·1% [0·3-3·5%] were anti-S antibody single positive. None were double positive. Anti-N and anti-S antibodies were detected in 5·2% [4·2-6·5%] and 2·1% [1·1-3·9%] of the general community, 2·0% [1·1-3·3%] and 1·4% [0·5-3·7%] of healthcare workers and 20·3% [12·6-31·0%] and 6·8% [2·8-15·3%] of bat/wildlife contacts. 0·1% [0·02-0·3%] were double positive for anti-N and anti-S antibodies (rapid test negative)., Interpretation: We find no evidence for significant SARS-CoV-2 circulation in Lao PDR before September 2020. This likely results from early decisive measures taken by the government, social behavior, and low population density. High anti-N /low anti-S seroprevalence in bat/wildlife contacts may indicate exposure to cross-reactive animal coronaviruses with threat of emerging novel viruses., Funding: Agence Française de Développement. Additional; Institut Pasteur du Laos, Institute Pasteur, Paris and Luxembourg Ministry of Foreign and European Affairs ("PaReCIDS II")., Competing Interests: The authors have no conflict of interest to declare., (© 2021 The Author(s). Published by Elsevier Ltd.)
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- 2021
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26. Identification of Umbre Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 French Patients with Hypogammaglobulinemia.
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Pérot P, Bielle F, Bigot T, Foulongne V, Bolloré K, Chrétien D, Gil P, Gutiérrez S, L'Ambert G, Mokhtari K, Hellert J, Flamand M, Tamietti C, Coulpier M, Huard de Verneuil A, Temmam S, Couderc T, De Sousa Cunha E, Boluda S, Plu I, Delisle MB, Bonneville F, Brassat D, Fieschi C, Malphettes M, Duyckaerts C, Mathon B, Demeret S, Seilhean D, and Eloit M
- Subjects
- Animals, Europe, France epidemiology, Humans, Agammaglobulinemia, Encephalitis, Orthobunyavirus genetics, Viruses
- Abstract
Background: Human encephalitis represents a medical challenge from a diagnostic and therapeutic point of view. We investigated the cause of 2 fatal cases of encephalitis of unknown origin in immunocompromised patients., Methods: Untargeted metatranscriptomics was applied on the brain tissue of 2 patients to search for pathogens (viruses, bacteria, fungi, or protozoans) without a prior hypothesis., Results: Umbre arbovirus, an orthobunyavirus never previously identified in humans, was found in 2 patients. In situ hybridization and reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) showed that Umbre virus infected neurons and replicated at high titers. The virus was not detected in cerebrospinal fluid by RT-qPCR. Viral sequences related to Koongol virus, another orthobunyavirus close to Umbre virus, were found in Culex pipiens mosquitoes captured in the south of France where the patients had spent some time before the onset of symptoms, demonstrating the presence of the same clade of arboviruses in Europe and their potential public health impact. A serological survey conducted in the same area did not identify individuals positive for Umbre virus. The absence of seropositivity in the population may not reflect the actual risk of disease transmission in immunocompromised individuals., Conclusions: Umbre arbovirus can cause encephalitis in immunocompromised humans and is present in Europe., (© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)
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- 2021
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27. Arterial abnormalities identified in kidneys transplanted into children during the COVID-19 pandemic.
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Berteloot L, Berthaud R, Temmam S, Lozach C, Zanelli E, Blanc T, Heloury Y, Capito C, Chardot C, Sarnacki S, Garcelon N, Lacaille F, Charbit M, Pastural M, Rabant M, Boddaert N, Leruez-Ville M, Eloit M, Sermet-Gaudelus I, Dehoux L, and Boyer O
- Subjects
- Adolescent, Child, Constriction, Pathologic pathology, Female, Humans, Male, Retrospective Studies, Arteries pathology, COVID-19 complications, Kidney blood supply, Kidney Transplantation, Pandemics
- Abstract
Graft artery stenosis can have a significant short- and long-term negative impact on renal graft function. From the beginning of the COVID-19 pandemic, we noticed an unusual number of graft arterial anomalies following kidney transplant (KTx) in children. Nine children received a KTx at our center between February and July 2020, eight boys and one girl, of median age of 10 years. Seven presented Doppler features suggesting arterial stenosis, with an unusual extensive pattern. For comparison, over the previous 5-year period, persistent spectral Doppler arterial anomalies (focal anastomotic stenoses) following KTx were seen in 5% of children at our center. We retrospectively evidenced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in five of seven children with arterial stenosis. The remaining two patients had received a graft from a deceased adolescent donor with a positive serology at D0. These data led us to suspect immune postviral graft vasculitis, triggered by SARS-CoV-2. Because the diagnosis of COVID-19 is challenging in children, we recommend pretransplant monitoring of graft recipients and their parents by monthly RT-PCR and serology. We suggest balancing the risk of postviral graft vasculitis against the risk of prolonged dialysis when considering transplantation in a child during the pandemic., (© 2020 The American Society of Transplantation and the American Society of Transplant Surgeons.)
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- 2021
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28. SARS-CoV-2 infection in schools in a northern French city: a retrospective serological cohort study in an area of high transmission, France, January to April 2020.
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Fontanet A, Tondeur L, Grant R, Temmam S, Madec Y, Bigot T, Grzelak L, Cailleau I, Besombes C, Ungeheuer MN, Renaudat C, Perlaza BL, Arowas L, Jolly N, Pellerin SF, Kuhmel L, Staropoli I, Huon C, Chen KY, Crescenzo-Chaigne B, Munier S, Charneau P, Demeret C, Bruel T, Eloit M, Schwartz O, and Hoen B
- Subjects
- Child, Cohort Studies, France epidemiology, Humans, Retrospective Studies, SARS-CoV-2, Schools, COVID-19
- Abstract
BackgroundChildren's role in SARS-CoV-2 epidemiology remains unclear. We investigated an initially unnoticed SARS-CoV-2 outbreak linked to schools in northern France, beginning as early as mid-January 2020.AimsThis retrospective observational study documents the extent of SARS-CoV-2 transmission, linked to an affected high school (n = 664 participants) and primary schools (n = 1,340 study participants), in the context of unsuspected SARS-CoV-2 circulation and limited control measures.MethodsBetween 30 March and 30 April 2020, all school staff, as well as pupils and their parents and relatives were invited for SARS-CoV-2 antibody testing and to complete a questionnaire covering symptom history since 13 January 2020.ResultsIn the high school, infection attack rates were 38.1% (91/239), 43.4% (23/53), and 59.3% (16/27), in pupils, teachers, and non-teaching staff respectively vs 10.1% (23/228) and 12.0% (14/117) in the pupils' parents and relatives (p < 0.001). Among the six primary schools, three children attending separate schools at the outbreak start, while symptomatic, might have introduced SARS-CoV-2 there, but symptomatic secondary cases related to them could not be definitely identified. In the primary schools overall, antibody prevalence in pupils sharing classes with symptomatic cases was higher than in pupils from other classes: 15/65 (23.1%) vs 30/445 (6.7%) (p < 0.001). Among 46 SARS-CoV-2 seropositive pupils < 12 years old, 20 were asymptomatic. Whether past HKU1 and OC43 seasonal coronavirus infection protected against SARS-CoV-2 infection in 6-11 year olds could not be inferred.ConclusionsViral circulation can occur in high and primary schools so keeping them open requires consideration of appropriate control measures and enhanced surveillance.
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- 2021
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29. Prior infection by seasonal coronaviruses, as assessed by serology, does not prevent SARS-CoV-2 infection and disease in children, France, April to June 2020.
- Author
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Sermet-Gaudelus I, Temmam S, Huon C, Behillil S, Gajdos V, Bigot T, Lurier T, Chrétien D, Backovic M, Delaunay-Moisan A, Donati F, Albert M, Foucaud E, Mesplées B, Benoist G, Faye A, Duval-Arnould M, Cretolle C, Charbit M, Aubart M, Auriau J, Lorrot M, Kariyawasam D, Fertitta L, Orliaguet G, Pigneur B, Bader-Meunier B, Briand C, Enouf V, Toubiana J, Guilleminot T, van der Werf S, Leruez-Ville M, and Eloit M
- Subjects
- Adolescent, Antibodies, Viral blood, COVID-19 blood, COVID-19 diagnosis, Child, Child, Preschool, Cross-Sectional Studies, Female, France epidemiology, Humans, Infant, Infant, Newborn, Male, Paris, Seasons, Serologic Tests methods, Spike Glycoprotein, Coronavirus, Antibodies, Viral immunology, COVID-19 immunology, Coronavirus OC43, Human, SARS-CoV-2 immunology, Systemic Inflammatory Response Syndrome
- Abstract
BackgroundChildren have a low rate of COVID-19 and secondary severe multisystem inflammatory syndrome (MIS) but present a high prevalence of symptomatic seasonal coronavirus infections.AimWe tested if prior infections by seasonal coronaviruses (HCoV) NL63, HKU1, 229E or OC43 as assessed by serology, provide cross-protective immunity against SARS-CoV-2 infection.MethodsWe set a cross-sectional observational multicentric study in pauci- or asymptomatic children hospitalised in Paris during the first wave for reasons other than COVID (hospitalised children (HOS), n = 739) plus children presenting with MIS (n = 36). SARS-CoV-2 antibodies directed against the nucleoprotein (N) and S1 and S2 domains of the spike (S) proteins were monitored by an in-house luciferase immunoprecipitation system assay. We randomly selected 69 SARS-CoV-2-seropositive patients (including 15 with MIS) and 115 matched SARS-CoV-2-seronegative patients (controls (CTL)). We measured antibodies against SARS-CoV-2 and HCoV as evidence for prior corresponding infections and assessed if SARS-CoV-2 prevalence of infection and levels of antibody responses were shaped by prior seasonal coronavirus infections.ResultsPrevalence of HCoV infections were similar in HOS, MIS and CTL groups. Antibody levels against HCoV were not significantly different in the three groups and were not related to the level of SARS-CoV-2 antibodies in the HOS and MIS groups. SARS-CoV-2 antibody profiles were different between HOS and MIS children.ConclusionPrior infection by seasonal coronaviruses, as assessed by serology, does not interfere with SARS-CoV-2 infection and related MIS in children.
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- 2021
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30. Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results.
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Regnault B, Bigot T, Ma L, Pérot P, Temmam S, and Eloit M
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- Genomic Library, Humans, Limit of Detection, Viruses genetics, Genome, Viral genetics, Metagenomics methods, Nucleic Acid Amplification Techniques methods, Viruses isolation & purification
- Abstract
Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit is the low pathogen load compared to the high background of host nucleic acids. To overcome this issue, several solutions exist, such as applying a very high depth of sequencing, or performing a relative enrichment of viral genomes associated with capsids. At the end, the quantity of total nucleic acids is often below the concentrations recommended by the manufacturers of library kits, which necessitates to random amplify nucleic acids. Using a pool of 26 viruses representative of viral diversity, we observed a deep impact of the nature of sample (total nucleic acids versus RNA only), the reverse transcription, the random amplification and library construction method on virus recovery. We further optimized the two most promising methods and assessed their performance with fully characterized reference virus stocks. Good genome coverage and limit of detection lower than 100 or 1000 genome copies per mL of plasma, depending on the genome viral type, were obtained from a three million reads dataset. Our study reveals that optimized random amplification is a technique of choice when insufficient amounts of nucleic acid are available for direct libraries constructions.
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- 2021
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31. Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus.
- Author
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Temmam S, Barbarino A, Maso D, Behillil S, Enouf V, Huon C, Jaraud A, Chevallier L, Backovic M, Pérot P, Verwaerde P, Tiret L, van der Werf S, and Eloit M
- Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China, in 2019, is responsible for the COVID-19 pandemic. It is now accepted that the wild fauna, probably bats, constitute the initial reservoir of the virus, but little is known about the role pets can play in the spread of the disease in human communities, knowing the ability of SARS-CoV-2 to infect some domestic animals. In this cross-sectional study, we tested the antibody response in a cluster of 21 domestic pets (9 cats and 12 dogs) living in close contact with their owners (belonging to a veterinary community of 20 students) in which two students tested positive for COVID-19 and several others ( n = 11/18) consecutively showed clinical signs (fever, cough, anosmia, etc. ) compatible with COVID-19 infection. Although a few pets presented many clinical signs indicative for a coronavirus infection, no antibodies against SARS-CoV-2 were detectable in their blood one month after the index case was reported, using an immunoprecipitation assay. These original data can serve a better evaluation of the host range of SARS-CoV-2 in natural environment exposure conditions., (© 2020 Published by Elsevier B.V.)
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- 2020
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32. A comparison of four serological assays for detecting anti-SARS-CoV-2 antibodies in human serum samples from different populations.
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Grzelak L, Temmam S, Planchais C, Demeret C, Tondeur L, Huon C, Guivel-Benhassine F, Staropoli I, Chazal M, Dufloo J, Planas D, Buchrieser J, Rajah MM, Robinot R, Porrot F, Albert M, Chen KY, Crescenzo-Chaigne B, Donati F, Anna F, Souque P, Gransagne M, Bellalou J, Nowakowski M, Backovic M, Bouadma L, Le Fevre L, Le Hingrat Q, Descamps D, Pourbaix A, Laouénan C, Ghosn J, Yazdanpanah Y, Besombes C, Jolly N, Pellerin-Fernandes S, Cheny O, Ungeheuer MN, Mellon G, Morel P, Rolland S, Rey FA, Behillil S, Enouf V, Lemaitre A, Créach MA, Petres S, Escriou N, Charneau P, Fontanet A, Hoen B, Bruel T, Eloit M, Mouquet H, Schwartz O, and van der Werf S
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, COVID-19, COVID-19 Testing, Cohort Studies, Coronavirus Infections epidemiology, Coronavirus Infections immunology, Enzyme-Linked Immunosorbent Assay methods, Female, Flow Cytometry methods, France epidemiology, Healthy Volunteers, Humans, Immunoprecipitation methods, Luciferases, Male, Middle Aged, Neutralization Tests, Pandemics, Pneumonia, Viral epidemiology, Pneumonia, Viral immunology, SARS-CoV-2, Seroepidemiologic Studies, Spike Glycoprotein, Coronavirus immunology, Translational Research, Biomedical, Young Adult, Antibodies, Viral blood, Betacoronavirus immunology, Clinical Laboratory Techniques methods, Coronavirus Infections diagnosis, Pneumonia, Viral diagnosis, Serologic Tests methods
- Abstract
It is of paramount importance to evaluate the prevalence of both asymptomatic and symptomatic cases of SARS-CoV-2 infection and their differing antibody response profiles. Here, we performed a pilot study of four serological assays to assess the amounts of anti-SARS-CoV-2 antibodies in serum samples obtained from 491 healthy individuals before the SARS-CoV-2 pandemic, 51 individuals hospitalized with COVID-19, 209 suspected cases of COVID-19 with mild symptoms, and 200 healthy blood donors. We used two ELISA assays that recognized the full-length nucleoprotein (N) or trimeric spike (S) protein ectodomain of SARS-CoV-2. In addition, we developed the S-Flow assay that recognized the S protein expressed at the cell surface using flow cytometry, and the luciferase immunoprecipitation system (LIPS) assay that recognized diverse SARS-CoV-2 antigens including the S1 domain and the carboxyl-terminal domain of N by immunoprecipitation. We obtained similar results with the four serological assays. Differences in sensitivity were attributed to the technique and the antigen used. High anti-SARS-CoV-2 antibody titers were associated with neutralization activity, which was assessed using infectious SARS-CoV-2 or lentiviral-S pseudotype virus. In hospitalized patients with COVID-19, seroconversion and virus neutralization occurred between 5 and 14 days after symptom onset, confirming previous studies. Seropositivity was detected in 32% of mildly symptomatic individuals within 15 days of symptom onset and in 3% of healthy blood donors. The four antibody assays that we used enabled a broad evaluation of SARS-CoV-2 seroprevalence and antibody profiling in different subpopulations within one region., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
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- 2020
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33. Whole genome sequencing and phylogenetic characterization of a novel bat-associated picornavirus-like virus with an unusual genome organization.
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Temmam S, Hul V, Bigot T, Bessaud M, Chrétien D, Hoem T, Gorman C, Duong V, Dussart P, Cappelle J, and Eloit M
- Subjects
- 3' Untranslated Regions, Animals, Cambodia, Capsid Proteins genetics, Open Reading Frames, Picornaviridae isolation & purification, RNA, Viral chemistry, Rectum virology, Whole Genome Sequencing, Chiroptera virology, Genome, Viral, Phylogeny, Picornaviridae genetics
- Abstract
The order Picornavirales is one of the most important viral orders in terms of virus diversity and genome organizations, ranging from a mono- or bi-cistronic expression strategies to the recently described poly-cistronic Polycipiviridae viruses. We report here the description and characterization of a novel picorna-like virus identified in rectal swabs of frugivorous bats in Cambodia that presents an unusual genome organization. Kandabadicivirus presents a unique genome architecture and distant phylogenetic relationship to the proposed Badiciviridae family. These findings highlight a high mosaicism of genome organizations among the Picornavirales., Competing Interests: Declaration of Competing Interest None., (Copyright © 2019 Elsevier B.V. All rights reserved.)
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- 2020
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34. Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes.
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Birnberg L, Temmam S, Aranda C, Correa-Fiz F, Talavera S, Bigot T, Eloit M, and Busquets N
- Subjects
- Animals, Genome, Viral, High-Throughput Nucleotide Sequencing, Mosquito Vectors virology, Phylogeny, Polymerase Chain Reaction, RNA, Viral, Sequence Analysis, DNA, Spain, Virus Diseases transmission, Viruses classification, Viruses genetics, Culicidae virology, Environmental Microbiology, Honey, Metagenomics methods, Virome
- Abstract
Worldwide, emerging and re-emerging infectious diseases (EIDs) are a major burden on public and animal health. Arthropod vectors, with mosquitoes being the main contributors of global disease, transmit more than 70% of the recognized EIDs. To assess new alternatives for arthropod-borne viral diseases surveillance, and for the detection of new viruses, honey-baited Flinders Technology Associates (FTA) cards were used as sugar bait in mosquito traps during entomological surveys at the Llobregat River Delta (Catalonia, Spain). Next generation sequencing (NGS) metagenomics analysis was applied on honey-baited FTA cards, which had been exposed to field-captured mosquitoes to characterize their associated virome. Arthropod- and plant-infecting viruses governed the virome profile on FTA cards. Twelve near-complete viral genomes were successfully obtained, suggesting good quality preservation of viral RNAs. Mosquito pools linked to the FTA cards were screened for the detection of mosquito-associated viruses by specific RT-PCRs to confirm the presence of these viruses. The circulation of viruses related to Alphamesonivirus , Quaranjavirus and unclassified Bunyavirales was detected in mosquitoes, and phylogenetic analyses revealed their similarities to viruses previously reported in other continents. To the best our knowledge, our findings constitute the first distribution record of these viruses in European mosquitoes and the first hint of insect-specific viruses in mosquitoes' saliva in field conditions, demonstrating the feasibility of this approach to monitor the transmissible fraction of the mosquitoes' virome. In conclusion, this pilot viromics study on honey-baited FTA cards was shown to be a valid approach for the detection of viruses circulating in mosquitoes, thereby setting up an alternative tool for arbovirus surveillance and control programs., Competing Interests: The authors declare no conflict of interest.
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- 2020
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35. RNA Viruses of Amblyomma variegatum and Rhipicephalus microplus and Cattle Susceptibility in the French Antilles.
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Gondard M, Temmam S, Devillers E, Pinarello V, Bigot T, Chrétien D, Aprelon R, Vayssier-Taussat M, Albina E, Eloit M, and Moutailler S
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- Animals, Antibodies, Viral blood, Cattle immunology, Disease Susceptibility, Flaviviridae genetics, Flaviviridae immunology, Genome, Viral, Martinique, Phylogeny, RNA Viruses genetics, RNA Viruses immunology, RNA, Viral analysis, RNA, Viral genetics, Seroepidemiologic Studies, Tick Infestations immunology, West Indies, Cattle Diseases immunology, Cattle Diseases parasitology, Flaviviridae isolation & purification, Ixodidae virology, RNA Viruses classification, RNA Viruses isolation & purification, Rhipicephalus virology, Tick Infestations veterinary
- Abstract
Ticks transmit a wide variety of pathogens including bacteria, parasites and viruses. Over the last decade, numerous novel viruses have been described in arthropods, including ticks, and their characterization has provided new insights into RNA virus diversity and evolution. However, little is known about their ability to infect vertebrates. As very few studies have described the diversity of viruses present in ticks from the Caribbean, we implemented an RNA-sequencing approach on Amblyomma variegatum and Rhipicephalus microplus ticks collected from cattle in Guadeloupe and Martinique. Among the viral communities infecting Caribbean ticks, we selected four viruses belonging to the Chuviridae , Phenuiviridae and Flaviviridae families for further characterization and designing antibody screening tests. While viral prevalence in individual tick samples revealed high infection rates, suggesting a high level of exposure of Caribbean cattle to these viruses, no seropositive animals were detected. These results suggest that the Chuviridae - and Phenuiviridae -related viruses identified in the present study are more likely tick endosymbionts, raising the question of the epidemiological significance of their occurrence in ticks, especially regarding their possible impact on tick biology and vector capacity. The characterization of these viruses might open the door to new ways of preventing and controlling tick-borne diseases., Competing Interests: The authors declare that they have no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
- Published
- 2020
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36. Six Nearly Complete Genome Segments of a Novel Reovirus Identified in Laotian Batflies.
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Temmam S, Vongphayloth K, Hertz JC, Sutherland I, Douangboubpha B, Grandadam M, Bigot T, Brey PT, and Eloit M
- Abstract
As part of the characterization of viral communities of Laotian batflies, we report here the sequencing of six nearly complete genome segments of a novel reovirus identified in Laotian batflies that is distantly related to reoviruses recently reported in various Diptera species., (Copyright © 2019 Temmam et al.)
- Published
- 2019
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37. Insights into the Host Range, Genetic Diversity, and Geographical Distribution of Jingmenviruses.
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Temmam S, Bigot T, Chrétien D, Gondard M, Pérot P, Pommelet V, Dufour E, Petres S, Devillers E, Hoem T, Pinarello V, Hul V, Vongphayloth K, Hertz JC, Loiseau I, Dumarest M, Duong V, Vayssier-Taussat M, Grandadam M, Albina E, Dussart P, Moutailler S, Cappelle J, Brey PT, and Eloit M
- Subjects
- Animals, Cattle, Chiroptera, Filoviridae Infections veterinary, Filoviridae Infections virology, Flaviviridae genetics, Flaviviridae growth & development, Global Health, Humans, Ticks, Flaviviridae classification, Flaviviridae isolation & purification, Genetic Variation, Host Specificity, Phylogeography
- Abstract
Jingmenvirus is a recently identified group of segmented RNA viruses phylogenetically linked with unsegmented Flaviviridae viruses. Primarily identified in various tick genera originating in China, Jingmenvirus geographical distribution has rapidly expanded to cover Africa, South America, Caribbean, and Europe. The identification of Jingmen-related viruses in various mammals, including febrile humans, opens the possibility that Jingmenviruses may be novel tick-borne arboviruses. In this study, we aimed at increasing knowledge of the host range, genetic diversity, and geographical distribution of Jingmenviruses by reporting for the first time the identification of Jingmenviruses associated with Rhipicephalus microplus ticks originating in the French Antilles (Guadeloupe and Martinique islands), with Amblyomma testudinarium ticks in Lao PDR, and with Ixodes ricinus ticks in metropolitan France, and from urine of Pteropus lylei bats in Cambodia. Analyses of the relationships between the different Jingmenvirus genomes resulted in the identification of three main phylogenic subclades, each of them containing both tick-borne and mammal-borne strains, reinforcing the idea that Jingmenviruses may be considered as tick-borne arboviruses. Finally, we estimated the prevalence of Jingmenvirus-like infection using luciferase immunoprecipitation assay screening (LIPS) of asymptomatic humans and cattle highly exposed to tick bites. Among 70 French human, 153 Laotian human, and 200 Caribbean cattle sera tested, only one French human serum was found (slightly) positive, suggesting that the prevalence of Jingmenvirus human and cattle infections in these areas is probably low. IMPORTANCE Several arboviruses emerging as new pathogens for humans and domestic animals have recently raised public health concern and increased interest in the study of their host range and in detection of spillover events. Recently, a new group of segmented Flaviviridae -related viruses, the Jingmenviruses, has been identified worldwide in many invertebrate and vertebrate hosts, pointing out the issue of whether they belong to the arbovirus group. The study presented here combined whole-genome sequencing of three tick-borne Jingmenviruses and one bat-borne Jingmenvirus with comprehensive phylogenetic analyses and high-throughput serological screening of human and cattle populations exposed to these viruses to contribute to the knowledge of Jingmenvirus host range, geographical distribution, and mammalian exposure., (Copyright © 2019 Temmam et al.)
- Published
- 2019
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38. Monitoring Silent Spillovers Before Emergence: A Pilot Study at the Tick/Human Interface in Thailand.
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Temmam S, Chrétien D, Bigot T, Dufour E, Petres S, Desquesnes M, Devillers E, Dumarest M, Yousfi L, Jittapalapong S, Karnchanabanthoeng A, Chaisiri K, Gagnieur L, Cosson JF, Vayssier-Taussat M, Morand S, Moutailler S, and Eloit M
- Abstract
Emerging zoonoses caused by previously unknown agents are one of the most important challenges for human health because of their inherent inability to be predictable, conversely to emergences caused by previously known agents that could be targeted by routine surveillance programs. Emerging zoonotic infections either originate from increasing contacts between wildlife and human populations, or from the geographical expansion of hematophagous arthropods that act as vectors, this latter being more capable to impact large-scale human populations. While characterizing the viral communities from candidate vectors in high-risk geographical areas is a necessary initial step, the need to identify which viruses are able to spill over and those restricted to their hosts has recently emerged. We hypothesized that currently unknown tick-borne arboviruses could silently circulate in specific biotopes where mammals are highly exposed to tick bites, and implemented a strategy that combined high-throughput sequencing with broad-range serological techniques to both identify novel arboviruses and tick-specific viruses in a ticks/mammals interface in Thailand. The virome of Thai ticks belonging to the Rhipicephalus, Amblyomma, Dermacentor, Hyalomma , and Haemaphysalis genera identified numerous viruses, among which several viruses could be candidates for future emergence as regards to their phylogenetic relatedness with known tick-borne arboviruses. Luciferase immunoprecipitation system targeting external viral proteins of viruses identified among the Orthomyxoviridae, Phenuiviridae, Flaviviridae, Rhabdoviridae , and Chuviridae families was used to screen human and cattle Thai populations highly exposed to tick bites. Although no positive serum was detected for any of the six viruses selected, suggesting that these viruses are not infecting these vertebrates, or at very low prevalence (upper estimate 0.017% and 0.047% in humans and cattle, respectively), the virome of Thai ticks presents an extremely rich viral diversity, among which novel tick-borne arboviruses are probably hidden and could pose a public health concern if they emerge. The strategy developed in this pilot study, starting from the inventory of viral communities of hematophagous arthropods to end by the identification of viruses able (or likely unable) to infect vertebrates, is the first step in the prediction of putative new emergences and could easily be transposed to other reservoirs/vectors/susceptible hosts interfaces., (Copyright © 2019 Temmam, Chrétien, Bigot, Dufour, Petres, Desquesnes, Devillers, Dumarest, Yousfi, Jittapalapong, Karnchanabanthoeng, Chaisiri, Gagnieur, Cosson, Vayssier-Taussat, Morand, Moutailler and Eloit.)
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- 2019
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39. RVDB-prot, a reference viral protein database and its HMM profiles.
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Bigot T, Temmam S, Pérot P, and Eloit M
- Abstract
We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Bigot T et al.)
- Published
- 2019
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40. A Novel Polycipiviridae Virus Identified in Pteropus lylei Stools.
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Temmam S, Hul V, Bigot T, Hoem T, Gorman C, Duong V, Dussart P, Cappelle J, and Eloit M
- Abstract
Polycipiviridae is a recently recognized viral family within the order Picornavirales with unusual genome organization and phylogenetic placement. Viruses belonging to this family were only reported from arthropod hosts. We describe here the first full genome of a distant polycipivirus-related virus identified in frugivorous bat stools in Cambodia., (Copyright © 2019 Temmam et al.)
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- 2019
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41. Protocol for Generating Infectious RNA Viromes from Complex Biological Samples.
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Monteil-Bouchard S, Temmam S, and Desnues C
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- Animals, Centrifugation, Density Gradient, Humans, RNA Virus Infections diagnosis, RNA Viruses isolation & purification, RNA, Viral genetics, RNA, Viral isolation & purification, Reagent Kits, Diagnostic, Virion genetics, Virion isolation & purification, Zoonoses diagnosis, Zoonoses virology, Metagenome, Metagenomics methods, RNA Virus Infections virology, RNA Viruses genetics
- Abstract
This chapter proposes a simple, standardized protocol for generating RNA viromes from complex host-associated biological samples of various origins. Compared to other existing protocols to generate RNA viromes, this protocol preserves the infectivity of viral particles and allows for downstream applications such as viral characterization and isolation tests.
- Published
- 2018
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42. Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport.
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Temmam S, Davoust B, Chaber AL, Lignereux Y, Michelle C, Monteil-Bouchard S, Raoult D, and Desnues C
- Subjects
- Africa, Airports, Animals, Bacteriophages genetics, Commerce, DNA, Viral analysis, France, Genome, Viral, Mass Screening, Metagenome, Microscopy, Fluorescence, RNA, Viral analysis, Bacteriophages isolation & purification, Food Microbiology, Haplorhini virology, Meat virology
- Abstract
Illegal bushmeat traffic is an important threat to biodiversity conservation of several endangered species and may contribute to the emergence and spread of infectious diseases in humans. The hunting, manipulation and consumption of wildlife-based products, especially those of primate origin, may be a threat to human health; however, few studies have investigated the role of bushmeat trade and consumption as a potential source of human infections to date. In this study, we report the screening of viral pathogens in African simian game seized by French customs at Toulouse Blagnac Airport. Epifluorescence microscopy revealed the presence of virus-like particles in the samples, and further metagenomic sequencing of the DNA and RNA viromes confirmed the presence of sequences related to the Siphoviridae, Myoviridae and Podoviridae bacteriophage families; some of them infecting bacterial hosts that could be potentially pathogenic for humans. To increase the sensitivity of detection, twelve pan-generic PCRs targeting several viral zoonoses were performed, but no positive signal was detected. A large-scale inventory of bacteria, viruses and parasites is urgently needed to globally assess the risk for human health of the trade, manipulation and consumption of wildlife-related bushmeat., (© 2016 Blackwell Verlag GmbH.)
- Published
- 2017
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43. A new asfarvirus infecting amoebas discovered in hematophagous arthropods and their vertebrate hosts.
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Temmam S, Khalil JB, La Scola B, and Desnues C
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- 2016
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44. Zoonotic viruses: how to monitor their emergence?
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Temmam S and Desnues C
- Abstract
Zoonoses are responsible of more than two thirds of human viral infections. In addition, with increasing contacts between humans and the wildlife and the domestic fauna, the emergence and reemergence of zoonotic viruses is accelerating. The development and democratization of high-throughput sequencing tools and their application in metagenomics allow inventorying the viral communities of various reservoirs and vectors in order to detect the emergence of viruses before their transmission to humans. The prediction of future emerging zoonotic viruses is very difficult, if not impossible. However, the characterization of viral communities present in the different actors of zoonotic transmission cycle is a first step to evaluate potential risks of transmission to humans. In this article, we report a brief summary of the concepts of emergence and zoonoses before reviewing the current tools available to monitor their emergence.
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- 2016
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45. Characterization of Viral Communities of Biting Midges and Identification of Novel Thogotovirus Species and Rhabdovirus Genus.
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Temmam S, Monteil-Bouchard S, Robert C, Baudoin JP, Sambou M, Aubadie-Ladrix M, Labas N, Raoult D, Mediannikov O, and Desnues C
- Subjects
- Animals, High-Throughput Nucleotide Sequencing, Senegal, Biota, Ceratopogonidae virology, Disease Vectors, RNA Viruses classification, RNA Viruses isolation & purification
- Abstract
More than two thirds of emerging viruses are of zoonotic origin, and among them RNA viruses represent the majority. Ceratopogonidae (genus Culicoides) are well-known vectors of several viruses responsible for epizooties (bluetongue, epizootic haemorrhagic disease, etc.). They are also vectors of the only known virus infecting humans: the Oropouche virus. Female midges usually feed on a variety of hosts, leading to possible transmission of emerging viruses from animals to humans. In this context, we report here the analysis of RNA viral communities of Senegalese biting midges using next-generation sequencing techniques as a preliminary step toward the identification of potential viral biohazards. Sequencing of the RNA virome of three pools of Culicoides revealed the presence of a significant diversity of viruses infecting plants, insects and mammals. Several novel viruses were detected, including a novel Thogotovirus species, related but genetically distant from previously described tick-borne thogotoviruses. Novel rhabdoviruses were also detected, possibly constituting a novel Rhabdoviridae genus, and putatively restricted to insects. Sequences related to the major viruses transmitted by Culicoides, i.e., African horse sickness, bluetongue and epizootic haemorrhagic disease viruses were also detected. This study highlights the interest in monitoring the emergence and circulation of zoonoses and epizooties using their arthropod vectors.
- Published
- 2016
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46. Faustovirus-Like Asfarvirus in Hematophagous Biting Midges and Their Vertebrate Hosts.
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Temmam S, Monteil-Bouchard S, Sambou M, Aubadie-Ladrix M, Azza S, Decloquement P, Khalil JY, Baudoin JP, Jardot P, Robert C, La Scola B, Mediannikov OY, Raoult D, and Desnues C
- Abstract
Faustovirus, a new Asfarviridae-related giant virus, was recently isolated in Vermamoeba vermiformis, a protist found in sewage water in various geographical locations and occasionally reported in human eye infection cases. As part of a global metagenomic analysis of viral communities existing in biting midges, we report here for the first time the identification and isolation of a Faustovirus-like virus in hematophagous arthropods and its detection in their animal hosts. The DNA virome analysis of three pools of Culicoides sp., engorged female Culicoides imicola and non-engorged male/female C. imicola biting midges collected in Senegal, revealed the presence of amoeba-infecting giant viruses and, among them, a majority of sequences related to Faustovirus. Phylogenetic analyses conducted on several structural genes of Faustovirus confirmed the clustering of the arthropod-borne Faustovirus with sewage-borne Faustoviruses, with a distinct geographical clustering of Senegalese Faustovirus strains. Transmission electron microscopy identified viral particles with morphologies and diameters which were compatible with Faustovirus. The presence of infectious arthropod-borne Faustovirus was finally confirmed by successful isolation on V. vermiformis amoeba. Global proteomic analysis of biting midges identified that arthropods' blood meal originating from cattle, rodents and humans. Further screening of cattle sera and rodent tissue resulted in prevalence of Faustovirus being estimated at 38% in rodents and 14% in cattle, suggesting a possible origin of Faustovirus presence in arthropods via the ingestion of contaminated blood meal. Viral loads were the highest in rodents' urine and kidney samples, suggesting a possible excretion of viral particles into the environment. Faustovirus DNA polymerase-related sequences were also detected in more than 9 and 11% of febrile patients and healthy Senegalese human sera, respectively. Our study thus, highlights the need to investigate the role of arthropods, wildlife, and domestic animals in the lifecycle of amoeba-infecting giant viruses and, in particular, the environmental cycle of Faustovirus.
- Published
- 2015
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47. Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes.
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Temmam S, Monteil-Bouchard S, Robert C, Pascalis H, Michelle C, Jardot P, Charrel R, Raoult D, and Desnues C
- Subjects
- Metagenomics, RNA, Viral genetics
- Abstract
Background: Metagenomic analyses have been widely used in the last decade to describe viral communities in various environments or to identify the etiology of human, animal, and plant pathologies. Here, we present a simple and standardized protocol that allows for the purification and sequencing of RNA viromes from complex biological samples with an important reduction of host DNA and RNA contaminants, while preserving the infectivity of viral particles., Principal Findings: We evaluated different viral purification steps, random reverse transcriptions and sequence-independent amplifications of a pool of representative RNA viruses. Viruses remained infectious after the purification process. We then validated the protocol by sequencing the RNA virome of human body lice engorged in vitro with artificially contaminated human blood. The full genomes of the most abundant viruses absorbed by the lice during the blood meal were successfully sequenced. Interestingly, random amplifications differed in the genome coverage of segmented RNA viruses. Moreover, the majority of reads were taxonomically identified, and only 7-15% of all reads were classified as "unknown", depending on the random amplification method., Conclusion: The protocol reported here could easily be applied to generate RNA viral metagenomes from complex biological samples of different origins. Our protocol allows further virological characterizations of the described viral communities because it preserves the infectivity of viral particles and allows for the isolation of viruses.
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- 2015
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48. First molecular detection of Rickettsia africae in ticks from the Union of the Comoros.
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Yssouf A, Socolovschi C, Kernif T, Temmam S, Lagadec E, Tortosa P, and Parola P
- Subjects
- Animals, Cattle, Cattle Diseases epidemiology, Cattle Diseases parasitology, Comoros, Goat Diseases epidemiology, Goat Diseases parasitology, Goats, Phylogeny, Rickettsia classification, Rickettsia genetics, Tick Infestations epidemiology, Tick Infestations parasitology, Tick Infestations veterinary, Rickettsia isolation & purification, Ticks microbiology
- Abstract
Background: Rickettsia africae is the agent of African tick bite fever, a disease transmitted by ticks in sub-Saharan Africa. In Union of the Comoros, a recent study reported the presence of a Rickettsia africae vector but no information has been provided on the circulation of the pathogenic agent in this country., Methods: To evaluate the possible circulation of Rickettsia spp. in Comorian cattle, genomic DNA was extracted from 512 ticks collected either in the Union of the Comoros or from animals imported from Tanzania and subsequently tested for Rickettsia infection by quantitative PCR., Results: Rickettsia africae was detected in 90% (60/67) of Amblyomma variegatum, 1% (1/92) of Rhipicephalus appendiculatus and 2.7% (8/296) of Rhipicephalus (Boophilus) microplus ticks collected in the Union of the Comoros, as well as in 77.14% (27/35) of Amblyomma variegatum ticks collected from imported cattle. Partial sequences of both bacterial gltA and ompA genes were used in a phylogenetic analysis revealing the presence of several haplotypes, all included within the Rickettsia africae clade., Conclusions: Our study reports the first evidence of Rickettsia africae in ticks collected from the Union of the Comoros. The data show a significant difference of infection rate of Rickettsia africae infected ticks between the Islands, with maximum rates measured in Grande Comore Island, sheltering the main entry port for live animal importation from Tanzania. The high infection levels reported herein indicate the need for an in-depth assessment of the burden of rickettsioses in the Union of the Comoros, especially among those at risk of infection, such as cattle herders.
- Published
- 2014
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49. Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection?
- Author
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Temmam S, Davoust B, Berenger JM, Raoult D, and Desnues C
- Subjects
- Animals, DNA Virus Infections etiology, DNA Virus Infections virology, High-Throughput Nucleotide Sequencing, Humans, RNA Virus Infections etiology, RNA Virus Infections virology, RNA Viruses genetics, Zoonoses pathology, Metagenomics, Zoonoses virology
- Abstract
Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite of a bloodsucking arthropod. If a virus is able to adapt and replicate in its new human host, human-to-human transmissions may occur, possibly resulting in an epidemic, such as the A/H1N1 flu pandemic in 2009. Thus, predicting emerging zoonotic infections is an important challenge for public health officials in the coming decades. The recent development of viral metagenomics, i.e., the characterization of the complete viral diversity isolated from an organism or an environment using high-throughput sequencing technologies, is promising for the surveillance of such diseases and can be accomplished by analyzing the viromes of selected animals and arthropods that are closely in contact with humans. In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases.
- Published
- 2014
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50. Development of real-time RT-PCR for the detection of low concentrations of Rift Valley fever virus.
- Author
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Maquart M, Temmam S, Héraud JM, Leparc-Goffart I, Cêtre-Sossah C, Dellagi K, Cardinale E, and Pascalis H
- Subjects
- Animals, Comoros, Madagascar, Polymerase Chain Reaction methods, Rift Valley Fever diagnosis, Rift Valley Fever virology, Ruminants, Sensitivity and Specificity, Real-Time Polymerase Chain Reaction methods, Reverse Transcriptase Polymerase Chain Reaction methods, Rift Valley Fever veterinary, Rift Valley fever virus isolation & purification, Veterinary Medicine methods, Virology methods
- Abstract
In recent years, Madagascar and the Comoros archipelago have been affected by epidemics of Rift Valley fever (RVF), however detection of Rift Valley fever virus (RVFV) in zebu, sheep and goats during the post epidemic periods was frequently unsuccessful. Thus, a highly sensitive real-time RT-PCR assay was developed for the detection of RVFV at low viral loads. A new RVF SYBR Green RT-PCR targeting the M segment was tested on serum from different RVF seronegative ruminant species collected from May 2010 to August 2011 in Madagascar and the Comoros archipelago and compared with a RVF specific quantitative real time RT-PCR technique, which is considered as the reference technique. The specificity was tested on a wide range of arboviruses or other viruses giving RVF similar clinical signs. A total of 38 out of 2756 serum samples tested positive with the new RT-PCR, whereas the reference technique only detected 5 out of the 2756. The described RT-PCR is an efficient diagnostic tool for the investigation of enzootic circulation of the RVF virus. It allows the detection of low viral RNA loads adapted for the investigations of reservoirs or specific epidemiological situations such as inter-epizootic periods., (Copyright © 2013 Elsevier B.V. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
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