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Hepatitis E virus (HEV) is a prevalent pathogen responsible for acute viral hepatitis, HEV genotypes 3 and 4 infections causing zoonotic infections. Currently, the nucleotide similarity analysis between humans and pigs for HEV genotype 4 is limited. In this study, stool samples from an HEV‐infected patient who is a pig farmer and from pigs were collected to obtain the near full‐length genome of HEV, phylogenetic trees were constructed for genotyping, and similarity of HEV sequences was analyzed. The results showed that HEV‐RNA was detected in the stool samples from the patient and six pigs (6/30, 20.0%). Both HEV subtype in the patient and pigs was 4b. Additionally, similarity analysis showed that the range was 99.875%–99.944% between the patient and pigs at the nucleotide level. Four isolates of amino acid sequences (ORFs 1–3) from pigs were 100% identical to the patient. Phylogenetic tree and similarity analysis of an additional nine HEV sequences isolated from other patients in this region showed that the HEV sequence from the pig farmer had the closest relationship with the pigs from his farm rather than other sources of infection in this region. This study provides indirect evidences for HEV subtype 4b can be transmitted from pigs to humans at the nucleotide level. Further research is needed to explore the characteristics of different HEV subtypes. [ABSTRACT FROM AUTHOR]

Background: Food and mouth disease (FMD) is an endemic disease of cattle and other cloven hoofed animals. The objective of this study was to investigate the genetic characteristics and evolutionary relationships for the 2020 to 2021 field circulating Food and mouth disease virus (FMDV) obtained from reported outbreaks in different parts of Tanzania. Methods: The epithelial tissues were collected from lesions (oral, nasal, interdigital) of FMD suspect cases, stored and shipped to the laboratory for analysis. In the laboratory, the samples were prepared for nucleic acid extraction, FMDV detection, typing, sequencing, and phylogeny analysis. The construction of the phylogenetic trees was done by aligning current field strains nucleotide sequences with those from past studies stored in GenBank database. Results: The study identified three FMDV serotypes (A, O and, SAT1) to be circulating in the field as Africa Topotype G-I lineage, EA-2 Topotype, and Topotype I (NWZ) respectively. The identified field strains showed diverse scores of shared identity among current and past study strains. The generated nucleotide sequences from this study types O and SAT1 field strains were analysed categorically, and showed shared percent identities of 92.0-100.0% and 96.9-98.8% respectively. Conclusion: The sequencing and analysis of the VP1 coding region enhance FMDV knowledge on the genetic and evolutionary relationships existing among field strains, and commend for improved future strategies for effective national, regional and global FMD control measures. [ABSTRACT FROM AUTHOR]

Ilarviruses are a relatively understudied but important group of plant RNA viruses that includes a number of crop pathogens. Their genomes comprise three RNA segments encoding two replicase subunits, movement protein, coat protein (CP), and (in some ilarvirus subgroups) a protein that suppresses RNA silencing. Here we report that, in many ilarviruses, RNA3 encodes an additional protein (termed CP-RT) as a result of ribosomal readthrough of the CP stop codon into a short downstream readthrough (RT) ORF. Using asparagus virus 2 as a model, we find that CP-RT is expressed in planta where it functions as a weak suppressor of RNA silencing. CP-RT expression is essential for persistent systemic infection in leaves and shoot apical meristem. CP-RT function is dependent on a putative zinc-finger motif within RT. Replacing the asparagus virus 2 RT with the RT of an ilarvirus from a different subgroup restored the ability to establish persistent infection. These findings open up a new avenue for research on ilarvirus silencing suppression, persistent meristem invasion and vertical transmission. Author summary: Ilarviruses comprise a group of plant-infecting RNA viruses. Until now, ilarvirus genomes were thought to only encode two components of the viral replicase, a movement protein, the capsid protein, and the 2b suppressor of RNA silencing. Interestingly, whereas most plant viruses encode one or more proteins that suppress the host antiviral RNA silencing pathway, the gene encoding 2b is only present in some ilarviruses. Here, we identify an additional ilarvirus protein that is expressed via low efficiency ribosomal readthrough of the capsid protein (CP) stop codon. Readthrough ribosomes translate a short downstream readthrough (RT) domain to produce the capsid-readthrough fusion protein, CP-RT. We show that CP-RT is a second ilarvirus suppressor of silencing protein and is required for the model ilarvirus asparagus virus 2 to maintain persistent infection in the model plant Nicotiana benthamiana. These findings advance our understanding of ilarvirus molecular virology and virus-host interaction. Interestingly, there are substantial differences in the RT peptide between divergent groups of ilarviruses and, in at least two cases, a separate RT peptide appears to have evolved independently. Thus it will be of future interest to investigate the function of CP-RT in different ilarvirus lineages. [ABSTRACT FROM AUTHOR]

Introduction: Global monitoring of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2) genetic sequences and associated metadata is essential for coronavirus disease 2019 (COVID-19) response. Therefore, Sanger's partial genome sequencing technique was used to monitor the circulating variants of SARS-CoV-2 in Cameroon. Methodology: Nasopharyngeal specimen was collected from persons suspected of SARS-CoV-2 following the national guidelines between January and December 2021. All specimens with cycle threshold (Ct) below 30 after amplification were eligible for sequencing of the partial spike (S) gene of SARS-CoV-2 using the Sanger sequencing method. Results: During the year 2021, 1481 real time reverse transcriptase polymerase chain reaction (RT-PCR) SARS-CoV-2 positive samples were selected for partial sequencing of the S gene of SARS-CoV-2. Amongst these, 878 yielded good sequencing products. A total of 231 probable variants (26.3%) were identified. The variants were mainly represented by Delta (70.6%), Alpha (15.6%), Omicron (7.4%), Beta (3.5%), Mu (1.7%) and Gamma (0.4%). Phylogenetic analysis of the probable variants from Cameroon with reference strains confirmed that all prior and current variants of concern (VOC) clustered with their respective reference sequences. Conclusions: The surveillance strategy implemented in Cameroon, based on partial sequencing of the S gene enabled identification of the major circulating variants and provided information on the distribution of these variants, which contributed to implementing public health measures to control disease spread in the country. [ABSTRACT FROM AUTHOR]

Echovirus 11 (E11) has gained attention owing to its association with severe neonatal infections. Due to the limited data available, the World Health Organization (WHO) considers public health risk to the general population to be low. The present study investigated the genetic variation and molecular evolution of E11 genomes collected from May to December 2023. Whole genome sequencing (WGS) was performed for 16 E11 strains. Phylogenetic analysis on WG showed how all Italian strains belonged to genogroup D5, similarly to other E11 strains recently reported in France and Germany all together aggregated into separate clusters. A cluster‐specific recombination pattern was also identified using phylogenetic analysis of different genome regions. Echovirus 6 was identified as the major recombinant virus in 3Cpro and 3Dpol regions. The molecular clock analysis revealed that the recombination event probably occurred in June 2018 (95% HPD interval: Jan 2016–Jan 2020). Shannon entropy analyses, within P1 region, showed how 11 amino acids exhibited relatively high entropy. Five of them were exposed on the canyon region which is responsible for receptor binding with the neonatal Fc receptor. The present study showed the recombinant origin of a new lineage of E11 associated with severe neonatal infections. [ABSTRACT FROM AUTHOR]

In 2018, a local case of nephropathia epidemica was reported in Scania, southern Sweden, more than 500 km south of the previously known presence of human hantavirus infections in Sweden. Another case emerged in the same area in 2020. To investigate the zoonotic origin of those cases, we trapped rodents in Ballingslöv, Norra Sandby, and Sörby in southern Sweden during 2020-2021. We found Puumala virus (PUUV) in lung tissues from 9 of 74 Myodes glareolus bank voles by screening tissues using a hantavirus pan--large segment reverse transcription PCR. Genetic analysis revealed that the PUUV strains were distinct from those found in northern Sweden and Denmark and belonged to the Finnish PUUV lineage. Our findings suggest an introduction of PUUV from Finland or Karelia, causing the human PUUV infections in Scania. This discovery emphasizes the need to understand the evolution, cross-species transmission, and disease outcomes of this newly found PUUV variant. [ABSTRACT FROM AUTHOR]

Emerging pathogenic tick‐borne viruses (TBVs) have attracted a great deal of attention due to their significant impact on human and animal health. A novel orthonairovirus named Dadong virus (DDV) was isolated from Haemaphysalis concinna ticks in the Changbai Mountain region on the China–North Korea border. DDV can induce cytopathic effects in mammalian and human cell lines. Phylogenetic analysis showed that it belongs to the genus Orthonairovirus, family Nairoviridae, exhibiting 72.4%–81.3% nucleic acid identity to Tofla orthonairovirus, known to cause lethal infection in IFNAR KO mice. The first serological evidence of DDV circulating in cattle and mice was also obtained, with 4.0% (1/25) of cattle and 2.27% (1/44) of mice seropositive for DDV. Further investigations, including serological surveys using human samples, are required to assess the public health risk posed by DDV. [ABSTRACT FROM AUTHOR]

During October 2022-March 2023, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus caused outbreaks in South Korea, including 174 cases in wild birds. To understand the origin and role of wild birds in the evolution and spread of HPAI viruses, we sequenced 113 HPAI isolates from wild birds and performed phylogenetic analysis. We identified 16 different genotypes, indicating extensive genetic reassortment with viruses in wild birds. Phylodynamic analysis showed that the viruses were most likely introduced to the southern Gyeonggi-do/northern Chungcheongnamdo area through whooper swans (Cygnus cygnus) and spread southward. Cross-species transmission occurred between various wild bird species, including waterfowl and raptors, resulting in the persistence of HPAI in wild bird populations and further geographic spread as these birds migrated throughout South Korea. Enhanced genomic surveillance was an integral part of the HPAI outbreak response, aiding in timely understanding of the origin, evolution, and spread of the virus. [ABSTRACT FROM AUTHOR]

In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US. [ABSTRACT FROM AUTHOR]

During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain. [ABSTRACT FROM AUTHOR]

• Human metapneumovirus (HMPV) is an important respiratory pathogen that causes acute respiratory tract infection in children ≤5 years old. • The prevalence peak of HMPV in southern China appeared between March and May. • Respiratory syncytial virus is the most common respiratory virus coinfected with HMPV in children. • The predominant subtype of HMPV in this area is B1, followed by A2c subtype. • Long sunshine duration might decrease the HMPV prevalence. This study aimed to determine the epidemiological and genetic features of human metapneumovirus (HMPV) infection in children in southern China, and the effect of meteorological factors on infection. 14,817 children (≤14 years) with acute respiratory tract infections from 2010 to 2019 were examined for HMPV and other respiratory viruses by real-time quantitative polymerase chain reaction. Full-length F gene of 54 positive samples were sequenced and subjected to phylogenetic analysis. The correlation between the HMPV-positive rate and meteorological factors was analyzed by linear regression analysis. HMPV was detected in 524 (3.5%) children, who were mostly younger than 1 year. The seasonal peak of HMPV prevalence mainly occurred in spring. Respiratory syncytial virus was the most common virus coinfected with HMPV (5.3%). Phylogenetic analysis revealed that the sequenced HMPV strains belonged to four sublineages, including A2b (1.9%), A2c (31.5%), B1 (50.0%), and B2 (16.7%). After adjusting for all meteorological factors, sunshine duration was inversely correlated with the HMPV-positive rate. HMPV is an important respiratory pathogen that causes acute respiratory tract infections in children in southern China, particularly in children ≤5 years old. The prevalence peak of HMPV in this area appeared in spring, and the predominant subtype was B1. Meteorological factors, especially long sunshine duration, might decrease the HMPV prevalence. [ABSTRACT FROM AUTHOR]

Background: Whole‐genome sequencing (WGS) of Neisseria gonorrhoeae isolates combined with epidemiological and phenotypic data provides better understanding of population dynamics. Aim: The objective of this study was to investigate the molecular epidemiology of N. gonorrhoeae isolates from three centres in Spain and determine associations of antimicrobial resistance. Methods: Genetic characterization was performed in 170 N. gonorrhoeae isolates. WGS was carried out with the HiSeq platform (Illumina). Genome assemblies were submitted to the PubMLST Neisseria database website to determine NG‐MAST, MLST and NG‐STAR. Antimicrobial resistance genes and point mutations were identified with PubMLST. Phylogenomic comparison was based on whole‐genome single nucleotide polymorphism analysis. Results: Twenty‐six MLST, 49 NG‐MAST and 41 NG‐STAR sequence types were detected, the most prevalent being MLST‐ST9363 (27.1%), NG‐MAST ST569 (12.4%) and NG‐STAR ST193 (14.7%). Phylogenetic analysis identified 13 clusters comprising 69% of the isolates, with two of note: one involved cefixime‐resistant isolates from Barcelona presenting a mosaic penA X and belonging to MLST‐ST7363 and the other involved azithromycin‐resistant isolates from Mallorca that possessed the C2611T mutation in the four 23S rRNA alleles belonging to MLST‐ST1901. Conclusion: The population of N. gonorrhoeae is quite heterogeneous in Spain. Our results agree with previous data published in Europe, albeit with some differences in distribution between regions. This study describes the circulation of two gonococcal populations with a specific resistance profile and sequence type in a specific geographic area. WGS is an effective tool for epidemiological surveillance of gonococcal infection and detection of resistance genes. [ABSTRACT FROM AUTHOR]

Background: The Epstein-Barr virus (EBV) relates to the torch virus family and is believed to have a substantial impact on mortality and perinatal events, as shown by epidemiological and viral studies. Moreover, there have been documented cases of EBV transmission occurring via the placenta. Nevertheless, the specific location of the EBV infection inside the placenta remains uncertain. Methods: The genomic sequences connected to the latent EBV gene and the levels of lytic EBV gene expression in placental chorionic villous cells are examined in this work. A total of 86 placentas from patients who had miscarriage and 54 placentas from individuals who had successful births were obtained for analysis. Results: The research employed QPCR to detect the BRLF1 (Rta) EBV lytic gene and quantify DNA burden in miscarriage patients and controls. In miscarriage patients, endpoint PCR and Sanger sequencing validated a particular region of the EBER1 EBV latent gene. BRLF1 gene presence ranged from 2.5 × 10² to 9.3 × 104 copies/mL in 75 miscarriage patients. However, a sample of 5 people with healthy deliveries showed a range of 2.0 × 10² to 2.9 × 10² copies/mL. All miscarriage samples were observed EBER1. The sequencing results indicated full sequence identity to EBV strains. Conclusion: The detection of EBV gene expression in placental tissues in Iraq is a novel finding. The examination of EBV is of utmost importance in pregnant women who are experiencing severe illness, since it has the potential to lead to mortality in both the mother and the developing fetus. [ABSTRACT FROM AUTHOR]

The authentic SARS-CoV-2 requires to be handled in Biosafety Level 3 laboratories, which restrains investigation by the broader scientific community. Here, we report the development of a novel SARS-CoV-2 viral vector composed of all 4 SARS-CoV-2 structural proteins, the packaging signal sequence of SARS-CoV-2, a reporter gene, and an RNA amplification component of Venezuelan equine encephalitis virus (VEEV). This VEE-SARS-CoV-2 viral vector transduces target cells in an ACE2-dependent manner, and all 4 structural proteins of SARS-CoV-2 are indispensable for its transduction activity. Comparative studies show that the incorporation of the VEEV self-amplification mechanism increases the gene expression level by ~ 65-fold and extends the transgene expression up to 11 days in transduced cells. Additionally, we demonstrated the significant applications of this new VEE-SARS-CoV-2 vector for neutralizing antibody quantification and antiviral drug testing. The VEE-SARS-CoV-2 vectors developed will be an important and versatile tool for investigating SARS-CoV-2 molecular virology, developing antiviral agents targeting receptor binding, and studying RNA genome packaging and function of the essential but not well studied structural proteins of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Herpesviruses are large DNA viruses that have long been used as powerful gene therapy tools. In recent years, the ability of herpesviruses to stimulate both innate and adaptive immune responses has led to their transition to various applications as vaccine vectors. This vaccinology branch is growing at an unprecedented and accelerated rate. To date, human herpesvirus-based vectors have been used in vaccines to combat a variety of infectious agents, including the Ebola virus, foot and mouth disease virus, and human immunodeficiency viruses. Additionally, these vectors are being tested as potential vaccines for cancer-associated antigens. Thanks to advances in recombinant DNA technology, immunology, and genomics, numerous steps in vaccine development have been greatly improved. A better understanding of herpesvirus biology and the interactions between these viruses and the host cells will undoubtedly foster the use of herpesvirus-based vaccine vectors in clinical settings. To overcome the existing drawbacks of these vectors, ongoing research is needed to further advance our knowledge of herpesvirus biology and to develop safer and more effective vaccine vectors. Advanced molecular virology and cell biology techniques must be used to better understand the mechanisms by which herpesviruses manipulate host cells and how viral gene expression is regulated during infection. In this review, we cover the underlying molecular structure of herpesviruses and the strategies used to engineer their genomes to optimize capacity and efficacy as vaccine vectors. Also, we assess the available data on the successful application of herpesvirus-based vaccines for combating diseases such as viral infections and the potential drawbacks and alternative approaches to surmount them. [ABSTRACT FROM AUTHOR]

Raman spectroscopy was applied to study the structural differences between herpes simplex virus Type I (HSV-1) and Epstein–Barr virus (EBV). Raman spectra were first collected with statistical validity on clusters of the respective virions and analyzed according to principal component analysis (PCA). Then, average spectra were computed and a machine-learning approach applied to deconvolute them into sub-band components in order to perform comparative analyses. The Raman results revealed marked structural differences between the two viral strains, which could mainly be traced back to the massive presence of carbohydrates in the glycoproteins of EBV virions. Clear differences could also be recorded for selected tyrosine and tryptophan Raman bands sensitive to pH at the virion/environment interface. According to the observed spectral differences, Raman signatures of known biomolecules were interpreted to link structural differences with the viral functions of the two strains. The present study confirms the unique ability of Raman spectroscopy for answering structural questions at the molecular level in virology and, despite the structural complexity of viral structures, its capacity to readily and reliably differentiate between different virus types and strains. [ABSTRACT FROM AUTHOR]

The article explores the concept of "sociovirology" and its application in studying the evolution of virus life-history traits. It emphasizes the social nature of viruses and the importance of understanding their interactions with hosts. The article discusses the challenges of measuring virus fitness in a social context and the role of relatedness in shaping selective pressures on virus populations. It also suggests that evolutionary epidemiology and multiple infection theory can provide useful frameworks for studying virus evolution. The article raises questions about the appropriateness of the term "sociovirology" and highlights the need for a formal definition of fitness in this context. [Extracted from the article]

Background: Sarawak has one of the highest diversity of fruit bats species (family Pteropodidae) in Malaysia, with 19 species described. Most coronavirus (CoV) studies have mainly focused on insectivorous bats, resulting in a lack of information on CoVs present in frugivorous bats. In addition, bat CoV surveillance activities are lacking in Malaysia. Objectives: Our study focuses on determining the presence of bat CoVs in dusky fruit bat (Penthetor lucasi). Methods: Guano samples belonging to P. lucasi were collected from Wind Cave Nature Reserve. The samples were screened for the presence of CoVs using validated hemi‐nested consensus RNA‐dependent RNA polymerase consensus primers. Results: The bat CoV positivity rate was 38.5% (n = 15/39), with the viruses belonging to two subgenera: Alphacoronavirus (α‐CoV) and Betacoronavirus (β‐CoV). Phylogenetic analysis revealed that CoVs from 14 samples of P. lucasi belong to the genus α‐CoV and may represent previously described genetic lineages in insectivorous bats in Wind Cave. However, only one sample of P. lucasi was detected with β‐CoV which is closely related to subgenus Nobecovirus, which is commonly seen in frugivorous bats. Conclusions: This study provides the first available data on CoVs circulating in P. lucasi. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has posed a significant global threat, leading to several initiatives for its control and management. One such initiative involves wastewater-based epidemiology, which has gained attention for its potential to provide early warning of virus outbreaks and real-time information on its spread. In this study, wastewater samples from two wastewater treatment plants (WWTPs) located in the southeast of Spain (region of Murcia), namely Murcia, and Cartagena, were analyzed using RT-qPCR and high-throughput sequencing techniques to describe the evolution of SARS-CoV-2 in the South-East of Spain. Additionally, phylogenetic analysis and machine learning approaches were applied to develop a pre-screening tool for the identification of differences among the variant composition of different wastewater samples. The results confirmed that the levels of SARS-CoV-2 in these wastewater samples changed concerning the number of SARS-CoV-2 cases detected in the population, and variant occurrences were in line with clinical reported data. The sequence analyses helped to describe how the different SARS-CoV-2 variants have been replaced over time. Additionally, the phylogenetic analysis showed that samples obtained at close sampling times exhibited a higher similarity than those obtained more distantly in time. A second analysis using a machine learning approach based on the mutations found in the SARS-CoV-2 spike protein was also conducted. Hierarchical clustering (HC) was used as an efficient unsupervised approach for data analysis. Results indicated that samples obtained in October 2022 in Murcia and Cartagena were significantly different, which corresponded well with the different virus variants circulating in the two locations. The proposed methods in this study are adequate for comparing consensus sequence types of the SARS-CoV-2 sequences as a preliminary evaluation of potential changes in the variants that are circulating in a given population at a specific time point. [ABSTRACT FROM AUTHOR]

According to the World Health Organization, approximately 20 million people worldwide are infected annually with the hepatitis E virus (HEV). There are four main genotypes of HEV. Genotype 1 and genotype 2 are common in developing countries and are transmitted by contaminated water from a fecal–oral route. Genotype 3 and genotype 4 are common in developed countries and can lead to occasional transmission to humans via undercooked meat. Hepatitis E virus 1 and HEV3 can lead to fulminant hepatitis, and HEV3 can lead to chronic hepatitis and cirrhosis in immunocompromised patients. The majority of patients with HEV infection are asymptomatic and usually have spontaneous viral clearance without treatment. However, infection in immunocompromised individuals can lead to chronic HEV infection. Both acute and chronic HEV infections can have extrahepatic manifestations. No specific treatment is required for acute HEV infection, no treatment has been approved in chronic infection, and no HEV vaccine has been approved by the (United States) Food and Drug Administration. This review focuses on the molecular virology (HEV life cycle, genotypes, model systems, zoonosis), pathogenesis, clinical manifestation, and treatment of chronic HEV infection, especially in immunocompromised patients, to provide clinicians a better understanding of the global distribution of these infections and the significant effect they can have on immunocompromised patients. [ABSTRACT FROM AUTHOR]

Bovine ephemeral fever (BEF) is a vector-borne disease of ruminants in tropical and subtropical areas, leading to significant economic losses to the cattle and milk industry in many countries, including Turkey. Cattle showing high fever, stagnation, and recumbency have been extensively reported in Turkey's south and south eastern regions in 2020. Here, the genetic analysis and molecular epidemiology of the virus obtained from the last BEF outbreak were investigated. Of 32 symptomatic cattle selected from three provinces in Turkey, 23 were positive for bovine ephemeral fever virus (BEFV), and three entire G genes were identified by sequencing. The new BEFV isolates were genetically similar to some Turkish and Israeli isolates from 2008 and 2012 (>98 nucleotide (nt), 97% amino acid (aa)), and phylogenetic analysis based on the surface glycoprotein (G) gene revealed that BEFV isolates are of Middle Eastern origin. The G protein amino acid alignment showed that BEFV circulated in the same region with minor differences over the years. In this context, we recommend closely monitoring BEF outbreaks in neighbouring countries and prompt vaccination of susceptible cattle in areas at risk for BEFV in Turkey in the event of an outbreak. [ABSTRACT FROM AUTHOR]

Hepatitis E virus (HEV) is an emerging causative agent of acute hepatitis. To clarify the epidemiology of HEV and characterize the genetic diversity of the virus in Japan, nationwide enhanced surveillance and molecular characterization studies of HEV in Japan were undertaken from 2014 to 2021. In total, 2770 hepatitis E cases were reported, of which 88% were domestic cases, while only 4.1% represented cases following infection abroad. In addition, 57% of domestic infections occurred in males aged in their 40s–70s. For domestic cases, infection via pork meat consumption continued to be the most reported route. Analysis of the 324 sequences detected between 2016 and 2021 showed that the majority of domestic HEV strains belong to Genotype 3a (G3a) and G3b. In contrast, six of eight cases of G1 HEV reflected infection abroad. Our results suggest that HEV is circulating widely in Japan, with genotypes G3a and G3b being most prevalent. Continued surveillance is necessary to monitor future trends and changes in the epidemiology of HEV in Japan. [ABSTRACT FROM AUTHOR]

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. The study aimed to identify the antimicrobial resistance and accessory genes, the clonal relatedness, and the evolutionary dynamics of selected CRKP isolates recovered in an adult and pediatric intensive care unit of a tertiary hospital in Greece. Methods: Twenty-four CRKP isolates recovered during 2018–2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST, and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed using various bioinformatics software. Results: The isolates belonged to eight sequence types: 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM, and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16, and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323, and ST39 were classified into distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs. Conclusions: The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates. [ABSTRACT FROM AUTHOR]

Background: An unprecedent increase in the number of cases and deaths reported from dengue virus (DENV) infection has occurred in the southwestern Indian ocean in recent years. From 2017 to mid-2021 more than 70,000 confirmed dengue cases were reported in Reunion Island, and 1967 cases were recorded in the Seychelles from 2015 to 2016. Both these outbreaks displayed similar trends, with the initial circulation of DENV-2 which was replaced by DENV-1. Here, we aim to determine the origin of the DENV-1 epidemic strains and to explore their genetic characteristics along the uninterrupted circulation, particularly in Reunion. Methods: Nucleic acids were extracted from blood samples collected from dengue positive patients; DENV-1 was identified by RT-qPCR. Positive samples were used to infect VERO cells. Genome sequences were obtained from either blood samples or infected-cell supernatants through a combination of both Illumina or MinION technologies. Results: Phylogenetic analyses of partial or whole genome sequences revealed that all DENV-1 sequences from Reunion formed a monophyletic cluster that belonged to genotype I and were closely related to one isolate from Sri Lanka (OL752439.1, 2020). Sequences from the Seychelles belonged to the same major phylogenetic branch of genotype V, but fell into two paraphyletic clusters, with greatest similarity for one cluster to 2016–2017 isolate from Bangladesh, Singapore and China, and for the other cluster to ancestral isolates from Singapore, dating back to 2012. Compared to publicly available DENV-1 genotype I sequences, fifteen non-synonymous mutations were identified in the Reunion strains, including one in the capsid and the others in nonstructural proteins (NS) (three in NS1, two in NS2B, one in NS3, one in NS4B, and seven in NS5). Conclusion: In contrast to what was seen in previous outbreaks, recent DENV-1 outbreaks in Reunion and the Seychelles were caused by distinct genotypes, all likely originating from Asia where dengue is (hyper)endemic in many countries. Epidemic DENV-1 strains from Reunion harbored specific non-synonymous mutations whose biological significance needs to be further investigated. [ABSTRACT FROM AUTHOR]

Mpox is a viral zoonotic disease endemic in Central and West Africa that is caused by the Mpox virus, which belongs to the Orthopoxvirus genus and Poxviridae family. The clinical manifestations of mpox infection are milder than those of smallpox, and the incubation time of mpox varies from 5 to 21 days. Since May 2022, the mpox outbreak (formerly known as monkeypox) has suddenly and unexpectedly spread in non‐endemic countries, suggesting that there may have been some undetected transmissions. Based on molecular analysis, there are two major genetic clades that represent the mpox virus: Clade I (formerly the Congo Basin clade OR the Central African clade) and Clade II (formerly the West African clade). It is believed that people who are asymptomatic or paucisymptomatic may spread the mpox virus. Infectious viruses cannot be distinguished by PCR testing; therefore, virus culture should be carried out. Recent evidence regarding the detection of the mpox virus (Clade IIb) in air samples collected from the patient's environment during the 2022 mpox outbreak was reviewed. Further studies are needed to evaluate the extent to which the presence of mpox virus DNA in the air could affect immunocompromised patients in healthcare facilities, and further epidemiological studies are crucial, especially in Africa. [ABSTRACT FROM AUTHOR]

This study was performed to investigate the presence and characteristics of the oxazolidinone resistance genes optrA and cfr(D) in Streptococcus parasuis. In total, 36 Streptococcus isolates (30 Streptococcus suis isolates, 6 Streptococcus parasuis isolates) were collected from pig farms in China in 2020–2021, using PCR to determine the presence of optrA and cfr. Then, 2 of the 36 Streptococcus isolates were further processed as follows. Whole-genome sequencing and de novo assembly were employed to analyze the genetic environment of the optrA and cfr(D) genes. Conjugation and inverse PCR were employed to verify the transferability of optrA and cfr(D). The optrA and cfr(D) genes were identified in two S. parasuis strains named SS17 and SS20, respectively. The optrA of the two isolates was located on chromosomes invariably associated with the araC gene and Tn554, which carry the resistance genes erm(A) and ant(9). The two plasmids that carry cfr(D), pSS17 (7550 bp) and pSS20-1 (7550 bp) have 100% nucleotide sequence identity. The cfr(D) was flanked by GMP synthase and IS1202. The findings of this study extend the current knowledge of the genetic background of optrA and cfr(D) and indicate that Tn554 and IS1202 may play an important role in the transmission of optrA and cfr(D), respectively. [ABSTRACT FROM AUTHOR]

Appropriate treatment options are lacking for hepatitis E virus (HEV)-infected pregnant women and immunocompromised individuals. Thus, we aimed to identify efficient anti-HEV drugs through high-throughput screening, validate them in vitro and in vivo (in a preclinical animal study), and elucidate their underlying antiviral mechanism of action. Using appropriate cellular and rodent HEV infection models, we studied a critical pathway for host-HEV interactions and performed a preclinical study of the corresponding antivirals, which target proteostasis of the HEV replicase. We found 17 inhibitors that target HEV-HSP90 interactions by unbiased compound library screening on human hepatocytes harboring an HEV replicon. Inhibitors of HSP90 (iHSP90) markedly suppressed HEV replication with efficacy exceeding that of conventional antivirals (IFNα and ribavirin) in vitro. Mechanistically, iHSP90 treatment released the viral replicase ORF1 protein from the ORF1-HSP90 complex and triggered rapid ubiquitin/proteasome-mediated degradation of ORF1, resulting in abrogated HEV replication. Furthermore, a preclinical trial in a Mongolian gerbil HEV infection model showed this novel anti-HEV strategy to be safe, efficient, and able to prevent HEV-induced liver damage. In this study, we uncover a proteostatic pathway that is critical for host-HEV interactions and we provide a foundation from which to translate this new understanding of the HEV life cycle into clinically promising antivirals. Appropriate treatment options for hepatitis E virus (HEV)-infected pregnant women and immunocompromised patients are lacking; hence, there is an urgent need for safe and effective HEV-specific therapies. This study identified new antivirals (inhibitors of HSP90) that significantly limit HEV infection by targeting the viral replicase for degradation. Moreover, these anti-HEV drugs were validated in an HEV rodent model and were found to be safe and efficient for prevention of HEV-induced liver injury in preclinical experiments. Our findings substantially promote the understanding of HEV pathobiology and pave the way for antiviral development. [Display omitted] • We identified 17 HSP90 inhibitors via high-throughput screening of anti-HEV compounds using replicon models. • Inhibiting the HEV replicase-HSP90 interaction releases ORF1 for K48-linked ubiquitination and proteasomal degradation. • Cytosolic ORF1-HSP90 aggregates are critical for HEV replication. • Preclinical studies demonstrate that targeting HSP90 prevents sustained HEV infection and liver injury in rodents. [ABSTRACT FROM AUTHOR]

HIV-1 replication can be suppressed with antiretroviral therapy (ART), but individuals who stop taking ART soon become viremic again. Some people experience extended times of detectable viremia despite optimal adherence to ART. In this issue of the JCI, White, Wu, and coauthors elucidate a source of nonsuppressible viremia (NSV) in treatment-adherent patients — clonally expanded T cells harboring HIV-1 proviruses with small deletions or mutations in the 5′-leader, the UTR that includes the major splice donor site of viral RNA. These mutations altered viral RNA-splicing efficiency and RNA dimerization and packaging, yet still allowed production of detectable levels of noninfectious virus particles. These particles lacked the HIV-1 Env surface protein required for cell entry and failed to form the mature capsid cone required for infectivity. These studies improve our understanding of NSV and the regulation of viral functions in the 5′-leader with implications for rationalized care in individuals with NSV. [ABSTRACT FROM AUTHOR]

Background: Hainan Province, China, has been an endemic region with high transmission of Plasmodium falciparum and Plasmodium vivax. Indigenous malaria caused by P. vivax was eliminated in Hainan in 2011, while imported vivax malaria remains. However, the geographical origin of P. vivax cases in Hainan remains unclear. Methods: Indigenous and imported P. vivax isolates (n = 45) were collected from Hainan Province, and the 6 kb mitochondrial genome was obtained. Nucleotide (π) and haplotype (h) diversity were estimated using DnaSP. The numbers of synonymous nucleotide substitutions per synonymous site (dS) and nonsynonymous nucleotide substitutions per nonsynonymous site (dN) were calculated using the SNAP program. Arlequin software was used to estimate the genetic diversity index and assess population differentiation. Bayesian phylogenetic analysis of P. vivax was performed using MrBayes. A haplotype network was generated using the NETWORK program. Results: In total, 983 complete mitochondrial genome sequences were collected, including 45 from this study and 938 publicly available from the NCBI. Thirty-three SNPs were identified, and 18 haplotypes were defined. The haplotype (0.834) and nucleotide (0.00061) diversity in the Hainan populations were higher than China's Anhui and Guizhou population, and the majority of pairwise FST values in Hainan exceeded 0.25, suggesting strong differentiation among most populations except in Southeast Asia. Most Hainan haplotypes were connected to South/East Asian and China's others haplotypes, but less connected with populations from China's Anhui and Guizhou provinces. Mitochondrial lineages of Hainan P. vivax belonged to clade 1 of four well-supported clades in a phylogenetic tree, most haplotypes of indigenous cases formed a subclade of clade 1, and the origin of seven imported cases (50%) could be inferred from the phylogenetic tree, but five imported cases (42.8%) could not be traced using the phylogenetic tree alone, necessitating epidemiological investigation. Conclusions: Indigenous cases in Hainan display high genetic (haplotype and nucleotide) diversity. Haplotype network analysis also revealed most haplotypes in Hainan were connected to the Southeast Asian populations and divergence to a cluster of China's other populations. According to the mtDNA phylogenetic tree, some haplotypes were shared between geographic populations, and some haplotypes have formed lineages. Multiple tests are needed to further explore the origin and expansion of P. vivax populations. [ABSTRACT FROM AUTHOR]

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The study was planned to carry out the molecular characterization of the respiratory syncytial virus (RSV) circulating strains and to elucidate the gene expression of autophagy and mammalian target of rapamycin (mTOR) signaling pathways in children with acute lower respiratory tract infection (ALRTI). Nasopharyngeal aspirate (NPA) samples (n = 145) from children suffering from ALRTI were subjected to the detection of RSV. Of them, 31 RSV positive strains were subjected for sequencing. Semi‐quantitative gene expression analysis for mTOR signaling and autophagy pathway genes was performed in respiratory tract epithelial cells using 25 RSV positive cases, and 10 age and sex matched healthy control subjects. Five representative genes were selected for each pathway and subjected to SYBR green real‐time polymerase chain reaction. RSV was positive in 69 (47.6%) samples and the representative (n = 31) RSV strains belonged to RSV‐A. Thirty‐one strains of RSV‐A on phylogenetic analysis clustered with the novel ON1 genotype having 72 bp nucleotide duplicationby targeting the ecto‐domain portion of the G gene. Further, the stains belonged to lineage 1 (51.6%), followed by lineage 3 (29%) and lineage 2 (19.4%). Autophagy gene expression analysis revealed significant upregulation in NPC1 and ATG3 autophagy genes. mTOR, AKT1, and TSC1 genes of the mTOR pathway were significantly downregulated in RSV positive patients. Thus, RSV infection inducing autophagy pathway genes (NPC1 and ATG3) and suppressing mTOR signaling pathway genes (AKT1, mTOR, and TSC1) to possibly evade the host immune system through dysregulating these pathways for its way of survival within the host. [ABSTRACT FROM AUTHOR]

Hepatitis B virus (HBV) and hepatitis D virus (HDV) coinfection confers a greater risk for accelerated liver disease progression. Full‐length characterization of HDV genome is necessary to understand pathogenesis and treatment response. However, owing to its high variability and tight structure, sequencing approaches remain challenging. Herein, we present a workflow to amplify, sequence, and analyze the whole HDV genome in a single fragment. Sequencing was based on the Oxford Nanopore Technologies long‐read sequencing followed by a turnkey analysis pipeline (VIRiONT, VIRal in‐house ONT sequencing analysis pipeline) that we developed and make available online for free. For the first time, HDV genome was successfully amplified and full‐length sequenced in a single fragment, allowing accurate subtyping from 30 clinical samples. High variability of edition, a crucial step in viral life cycle, was found among samples (from 0% to 59%). Additionally, a new subtype of HDV genotype 1 was identified. We provide a complete workflow for assessment of HDV genome at full‐length quasispecies resolution overcoming genome assembly issues and helping to identify modifications throughout the whole genome. This will help a better understanding of the impact of genotype/subtype, viral dynamics, and structural variants on HDV pathogenesis and treatment response. [ABSTRACT FROM AUTHOR]

Live attenuated varicella‐zoster virus (VZV) vaccines are used to prevent chickenpox and shingles. Single nucleotide polymorphisms (SNPs) that occur during the attenuation of parental strains are critical indicators of vaccine safety. To assess the attenuation of commercial VZV vaccines, genetic variants were comprehensively examined through high‐throughput sequencing of viral DNA isolated from four VZV vaccines (Barycela, VarilRix, VariVax, and SKY Varicella). Whole‐genome comparison of the four vaccines with the wild‐type strain (Dumas) revealed that the sequences are highly conserved on a genome‐wide scale. Among the 196 common variants across the four vaccines, 195 were already present in the genome of the parental strain (pOka), indicating that the variants occurred during the generation of the parental strain from the Dumas strain. Compared to the pOka genome, the vaccines exhibited distinct variant frequencies on a genome‐wide and within an attenuation‐related open reading frame. In particular, attenuation‐associated 42 SNPs showed that Barycela, VarilRix, VariVax, and SKY Varicella are in ascending order regarding similarity with pOka‐like genotypes, which in turn, might provide genomic evidence for the levels of attenuation. Finally, the phylogenetic network analysis demonstrated that genetic distances from the parental strain correlated with the attenuation levels of the vaccines. [ABSTRACT FROM AUTHOR]

Mpox is caused by the mpox virus, which belongs to the Orthopoxvirus genus and Poxviridae family. Animal hosts, such as African rodents, mice, prairie dogs, and non‐human primates, play important roles in the development and transmission of outbreaks. Laboratory animal infection experiments have demonstrated that some animals are susceptible to mpox virus. This review summarizes the current progress on the animal hosts for mpox virus. The surveillance of mpox virus in animal hosts will provide important insights into virus tracing, analysis of mutation evolutionary patterns, transmission mechanisms, and development of control measures. [ABSTRACT FROM AUTHOR]

The ongoing outbreak of monkeypox virus (hMPXV1) is the largest recorded in historically nonendemic countries. Genomic surveillance has emerged as a pivotal tool to track the spread and monitor the evolution of viral pathogens. Therefore, to assess the genetic diversity of circulating hMPXV1 in northern Italy in June to July 2022, we sequenced and analyzed five complete genomes of viruses sampled from patients presenting with a typical course of hMPXV1 infection. Phylogenetic analysis confirmed that all five genomes belong to the predominant epidemic lineage (B.1). Inspection of genetic changes and comparison with the reference sequence showed the presence of 12 nucleotide substitutions. Seven are nonsynonymous mutations leading to amino acid changes in six proteins belonging to different functional classes. Moreover, 11 of these 12 nucleotide mutations involve GA>AA or TC>TT replacements, suggesting that host APOBEC3 enzymes are responsible for the generation of substitutions in circulating viruses. Finally, metagenomic analysis evidenced bacterial superinfection (Streptococcus pyogenes) in one patient. Through this study, we contributed to expand the number of complete genomes of viruses circulating in Italy and characterize them as belonging to the predominant outbreak lineage. [ABSTRACT FROM AUTHOR]

The H10 subtypes of avian influenza viruses pose a continual threat to the poultry industry and human health. The sporadic spillover of H10 subtypes viruses from poultry to humans is represented by the H10N8 human cases in 2013 and the recent H10N3 human infection in 2021. However, the genesis and characteristics of the recent reassortment H10N3 viruses have not been systemically investigated. In this study, we characterized 20 H10N3 viruses isolated in live poultry markets during routine nationwide surveillance in China from 2014 to 2021. The viruses in the recent reassortant genotype acquired their hemagglutinin (HA) and neuraminidase (NA) genes from the duck H10 viruses and H7N3 viruses, respectively, whereas the internal genes were derived from chicken H9N2 viruses as early as 2019. Receptor‐binding analysis indicated that two of the tested H10N3 viruses had a higher affinity for human‐type receptors than for avian‐type receptors, highlighting the potential risk of avian‐to‐human transmission. Animal studies showed that only viruses belonging to the recent reassortant genotype were pathogenic in mice; two tested viruses transmitted via direct contact and one virus transmitted by respiratory droplets in guinea pigs, though with limited efficiency. These findings emphasize the need for enhanced surveillance of H10N3 viruses. Importance: Avian influenza virus, which frequently jumps to humans and causes severe illness and death, poses a continuing threat to public health. Understanding the genesis and characteristics of avian influenza viruses will help prevent future human influenza pandemics. In this study, we provide evidence that the human‐infecing H10N3 viruses are reassortants with internal genes from chicken H9N2 viruses and surface genes from duck viruses, suggesting a critical role for ducks in the generation of viruses with human‐infecting potential. Our findings demonstrate that some H10N3 viruses exhibit higher affinity for human‐type receptors than for avian‐type receptors, and some can transmit via direct contact and/or respiratory droplets in the guinea pig model, suggesting the potential risk posed by H10N3 viruses. [ABSTRACT FROM AUTHOR]

The present study aimed to evaluate the prevalence of antimicrobial resistance and clonal relationships in Proteus mirabilis isolated from chicken meat, beef, pork, and community-acquired urinary tract infections (UTI-CA). Chicken meat isolates showed the highest multidrug resistance (MDR), followed by those from pork and UTI-CA, whereas beef had relatively few MDR strains. All sources had strains that carried blaCTX-M-65, whereas blaCTX-M-2 and blaCMY-2 were only detected in chicken meat and UTI-CA isolates. This indicates that chicken meat should be considered an important risk factor for the spread of P. mirabilis carrying ESBL and AmpC. Furthermore, ESBL/AmpC producing strains were resistant to a greater number of antimicrobials and possessed more resistance genes than non-producing strains. In addition, the antimicrobial resistance genes qnrD, aac(6′)-Ib-cr, sul1, sul2, fosA3, cmlA, and floR were also found. Molecular typing showed a genetic similarity between chicken meat and UTI-CA isolates, including some strains with 100% similarity, indicating that chicken can be a source of P. mirabilis causing UTI-CA. It was concluded that meat, especially chicken meat, can be an important source of dissemination of multidrug-resistant P. mirabilis in the community. [ABSTRACT FROM AUTHOR]

Lumpy skin disease (LSD) is a contagious trans-boundary viral disease of cattle, caused by lumpy skin disease virus (LSDV) under the genus Capripoxvirus of Poxviridae family. The genus Capripoxvirus also comprises goatpox virus (GTPV) and sheeppox virus (SPPV), which affect sheep and goat respectively and are antigenically similar to LSDV. LSD has recently been spread in Asia following outbreaks in the Middle East and Europe. The present study is aimed with the objective of molecular characterization and genetic analysis of LSD virus obtained from the infected cattle in Puducherry, India. PCR confirms the presence of the LSDV genome in the clinical sample. Phylogenetic analysis and complete assessment of multiple sequence alignments between LSDV, GTPV and SPPV P32 gene sequences revealed least variation between sheeppox virus and LSD virus (1.5% variation) and highest variation between sheeppox and goatpox virus (2.8% variation). Based on the present study, it is also confirmed and concluded that P32 gene can be used for differentiating LSD, sheeppox and goatpox viruses. The phylogenetic analysis revealed that the LSDV under this study was clustered in a separate clade with the other LSDV sequences of Turkey, Kazakhstan, Kenya, Russia, Serbia, Nigeria and other Indian LSDV sequences available in the GenBank. The query LSDV sequence was closely related with other LSD viruses circulating in India suggesting a single LSDV strain is circulating in the country. This result underlines the importance of continuous monitoring and characterization of circulating strains. [ABSTRACT FROM AUTHOR]

Japanese encephalitis viruses (JEVs) are globally prevalent as deadly pathogens in humans and animals, including pig, horse and cattle. Japanese encephalitis (JE) still remains an important cause of epidemic encephalitis worldwide and exists in a zoonotic transmission cycle. Assam is one of the highly endemic states for JE in India. In the present study, to understand the epidemiological status of JE circulating in pigs and mosquito, particularly in Assam, India, molecular detection of JEV and the genome sequencing of JEV isolates from pigs and mosquitoes was conducted. The genome analysis of two JEV isolates from pigs and mosquitoes revealed 7 and 20 numbers of unique points of polymorphism of nucleotide during alignment of the sequences with other available sequences, respectively. Phylogenetic analysis revealed that the isolates of the present investigation belong to genotype III and are closely related with the strains of neighboring country China. This study highlights the transboundary nature of the JEV genotype III circulation, which maintained the same genotype through mosquito-swine transmission cycles. [ABSTRACT FROM AUTHOR]