Beatrix Kapusinszky

The Fecal Viral Flora of Wild Rodents

The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.

High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

ABSTRACT Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for high-throughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the United States (San Francisco, CA), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, and plants (BLASTx E score, <10−4), including known pathogens (>90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae), and insects (Dicistroviridae, Nodaviridae, and Parvoviridae). The full and partial genomes of a novel kobuvirus, salivirus, and sapovirus are described. A novel astrovirus (casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the single-stranded RNA picorna-like virus superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses.

Acute diarrhea in West-African children: diverse enteric viruses and a novel parvovirus genus

ABSTRACT Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed <39% and <31% identities to those of previously known parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.

Nearly Constant Shedding of Diverse Enteric Viruses by Two Healthy Infants

ABSTRACT Stool samples from two healthy infant siblings collected at about weekly intervals during their first year of life were analyzed by PCR for 15 different enteric viral genera. Adenovirus, Aichi virus, Anellovirus, Astrovirus, Bocavirus, Enterovirus, Parechovirus, Picobirnavirus, and Rotavirus were detected. Not detected were Coronavirus, Cardiovirus, Cosavirus, Salivirus, Sapovirus, and Norovirus. Long-term virus shedding, lasting from one to 12 months, was observed for adenoviruses, anelloviruses, bocaviruses, enteroviruses, parechoviruses, and picobirnaviruses. Repeated administration of oral poliovirus vaccine resulted in progressively shorter periods of poliovirus detection. Four nonpolio enterovirus genotypes were also detected. An average of 1.8 distinct human viruses were found per time point. Ninety-two percent (66/72) of the fecal samples tested contained one to five different human viruses. Two British siblings in the mid-1980s showed nearly constant fecal viral shedding. Our results demonstrate that frequent enteric infections with diverse viruses occur during early childhood in the absence of severe clinical symptoms.

What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken

Abstract We describe here the metagenomics-derived viral sequences detected in beef, pork, and chicken purchased from stores in San Francisco. In beef we detected four previously reported viruses (two parvoviruses belonging to different genera, an anellovirus, and one circovirus-like virus) and one novel bovine polyomavirus species (BPyV2-SF) whose closest relatives infect primates. Detection of porcine hokovirus in beef indicated that this parvovirus can infect both ungulate species. In pork we detected four known parvoviruses from three genera, an anellovirus, and pig circovirus 2. Chicken meat contained numerous gyrovirus sequences including those of chicken anemia virus and of a novel gyrovirus species (GyV7-SF). Our results provide an initial characterization of some of the viruses commonly found in US store-bought meats which included a diverse group of parvoviruses and viral families with small circular DNA genomes. Whether any of these viruses can infect humans will require testing human sera for specific antibodies.

Faecal virome of cats in an animal shelter

We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.

Genetic diversity of the genus Cosavirus in the family Picornaviridae: a new species, recombination, and 26 new genotypes.

The proposed viral genus human Cosavirus (HCoSV) consists of diverse picornaviruses found at high prevalence in the feces of children from developing countries. We sequenced four near-full length genomes and 45 partial VP1 region from HCoSV in human feces from healthy children and children with acute flaccid paralysis in Pakistan, Nigeria and Tunisia and from healthy and diarrhetic adults in Nepal. Genetic analyses of the near-full length genomes revealed presence of a new candidate cosavirus species provisionally labelled as species F (HCoSV-F). A HCoSV genome showed evidence of recombination between species D and E viruses at the P1/P2 junction indicating that these viruses may be reclassified as a single highly diverse species. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we identified 26 new HCoSV genotypes belonging to species A, D, and E. The detection of a large number of HCoSV genotypes based on still limited geographic sampling indicates that the phenotypic effects of cosaviruses on infected subjects are likely to be as highly diverse as those of human enteroviruses.

Astrovirus in wild boars (Sus scrofa) in Hungary

The family Astroviridae consists of two genera, Avastrovirus and Mamastrovirus whose members are associated with gastroenteritis in avian and mammalian hosts, respectively. In this study, we report the first detection of astrovirus from fecal specimens of wild boars (Sus scrofa) using viral metagenomics and complete genome sequencing. The wild boar astrovirus (WBAstV-1/2011/HUN, JQ340310) genome is 6707 nucleotide long and had 76%, 95% and 56% amino acid (aa) identity in the ORF1a (852aa), ORF1b (522aa) and ORF2 (845aa) regions, respectively, to porcine astrovirus 4 (PAstV-4, JF713713), the closest match. This study indicates that wild boar could be a reservoir for astroviruses.

Characterization of a novel porcine enterovirus in wild boars in Hungary

Porcine enteroviruses (PEVs) are members of the family Picornaviridae, genus Enterovirus. Until now, only three different PEV genotypes (PEV-9 and -10, and PEV-3H/PEV-14) have been detected in domestic pigs, and there is no information about the presence of PEVs in wild animals. Here, we identify and characterize the complete genomes of PEV originated from 5 of 10 (50%) of wild boar (Sus scrofa) piglets by RT-PCR and pyrosequencing. Wild boar/WBD/2011/HUN (JN807387) PEV showed only 67% amino acid identity in VP1 compared to the most closely related prototype PEV-3H/PEV-14. Wild boar enterovirus represents a novel PEV genotype, provisionally called PEV-15.

Local Virus Extinctions following a Host Population Bottleneck

ABSTRACT A small number of African green monkeys (AGMs) were introduced into the Caribbean from West Africa in the 1600s. To determine the impact of this population bottleneck on the AGM virome, we used metagenomics to compare the viral nucleic acids in the plasma of 43 wild AGMs from West Africa (Gambia) to those in 44 AGMs from the Caribbean (St. Kitts and Nevis). Three viruses were detected in the blood of Gambian primates: simian immunodeficiency virus (SIVagm; in 42% of animals), a novel simian pegivirus (SPgVagm; in 7% of animals), and numerous novel simian anelloviruses (in 100% of animals). Only anelloviruses were detected in the Caribbean AGMs with a prevalence and levels of viral genetic diversity similar to those in the Gambian animals. A host population bottleneck therefore resulted in the exclusion of adult-acquired SIV and pegivirus from the Caribbean AGMs. The successful importation of AGM anelloviruses into the Caribbean may be the result of their early transmission to infants, very high prevalence in African AGMs, and frequent coinfections with as many as 11 distinct variants. IMPORTANCE The extent to which viruses can persist in small isolated populations depends on multiple host, viral, and environmental factors. The absence of prior infections may put an immunologically naive population at risk for disease outbreaks. Isolated populations originating from a small number of founder individuals are therefore considered at increased risk following contact with populations with a greater variety of viruses. Here, we compared the plasma virome of West African green monkeys to that in their descendants after importation of a small number of animals to the Caribbean. A lentivirus and a pegivirus were found in the West African population but not in the Caribbean population. Highly diverse anelloviruses were found in both populations. A small founder population, limited to infants and young juvenile monkeys, may have eliminated the sexually transmitted viruses from the Caribbean AGMs, while anelloviruses, acquired at an earlier age, persisted through the host population bottleneck.