Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

Handley, Scott A.; Thackray, Larissa B.; Zhao, Guoyan; Presti, Rachel; Miller, Andrew D.; Droit, Lindsay; Abbink, Peter; Maxfield, Lori F.; Kambal, Amal; Duan, Erning; Stanley, Kelly; Kramer, Joshua; Macri, Sheila Cummings Sm; Permar, Sallie R.; Schmitz, Jörn E.; Mansfield, Keith G.; Brenchley, Jason M.; Veazey, Ronald S.; Stappenbeck, Thaddeus S.; Wang, David; Barouch, Dan H.; Virgin, Herbert W.

doi:10.1016/j.cell.2012.09.024

Cited by 255 publications

(326 citation statements)

References 45 publications

(63 reference statements)

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“…2a). The newly identified porcine bufavirus formed a group with the Hungarian strain Swine/Zsana/2013/HUN (Hargitai et al, 2016), which occupied the basal position to the human bufaviruses and a WUHARV parvovirus (Handley et al, 2012). All three genotypes of human bufaviruses formed a well-supported group whereas the WUHARV parvovirus was in a sister branch.…”

mentioning

confidence: 93%

Identification of a novel bufavirus in domestic pigs by a viral metagenomic approach

Schwarz

Ullman

Ahola

et al. 2016

Journal of General Virology

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Bufavirus is a single-stranded DNA virus belonging to the genus Protoparvovirus. This study reports the identification and characterization of a porcine bufavirus by a metagenomic approach, and a limited epidemiology investigation of bufavirus in six swine farms. A comparative genome analysis showed a similarity of 93 % to a Hungarian porcine bufavirus. Bayesian and maximumlikelihood analyses of genome sequences showed a close relationship of porcine bufaviruses to human and monkey bufaviruses. Molecular dating of the most recent common ancestors supported a recent introduction of bufaviruses into human and pig populations, respectively. A real-time PCR method was developed to screen 60 faecal samples for the porcine bufavirus DNA, and eight positive samples were found in two neighbouring farms, suggesting a relatively low prevalence (13.3 %). No direct transmission of porcine bufaviruses between two neighbouring farms was found, suggesting that bufaviruses may have spread widely in different geographical regions.Bufavirus belongs to the genus Protoparvovirus in the subfamily Parvovirinae (Cotmore et al., 2014). The virus has a single-stranded DNA genome, encoding non-structural protein 1 (NS1), a putative structural protein 1 (VP1), a small hypothetical protein of 130 aa residues and a structural protein 2 (VP2), as demonstrated in a reference genome (GenBank accession number: NC_024888). Genome comparison and phylogenetic analysis have grouped human bufaviruses into three genotypes (Yahiro et al., 2014). Bufavirus has first been identified in faeces of children with acute diarrhoea in Burkina Faso, a landlocked country in West Africa, and found in one Tunisian child (Phan et al., 2012). Subsequently, the virus has been discovered sporadically in cases of diarrhoea in Bhutan (Yahiro et al., 2014), Finland (V€ ais€ anen et al., 2014, the Netherlands (Smits et al., 2014), Turkey (Altay et al., 2015), Thailand (Chieochansin et al., 2015) and China (Huang et al., 2015). The role of bufaviruses as an etiologic agent of human gastroenteritis has not been firmly established yet. Further metagenomic investigations show distinct lineages of bufavirus in wild shrews and non-human primates from Zambia (Sasaki et al., 2015), in Hungarian bats (Kemenesi et al., 2015) and pigs (Hargitai et al., 2016) and in Chinese rats (Yang et al., 2016). This report describes the identification and characterization of bufavirus in faeces of domestic pigs by a metagenomic approach.A total of 60 samples were collected from 6-10-week-old pigs, on five Austrian farms and one Hungarian farm (Fig. 1). The samples consisted of five diarrhoeic (semiliquid or liquid form) and five normal faeces per farm. One diarrhoeic and one normal sample from each farm were used for the metagenomic studies and all samples were used for subsequent epidemiological investigation. About 200 mg of faeces were diluted to 1 ml of water, vortexed vigorously for 1 min and centrifuged at 14 000 g for 10 min. Supernatant (400 µl) was treated with 400 U ml À1 DNase I (Ro...

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mentioning

confidence: 93%

Identification of a novel bufavirus in domestic pigs by a viral metagenomic approach

Schwarz

Ullman

Ahola

et al. 2016

Journal of General Virology

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“…Considering that the samples were collected during a short period of time and from only one macaque colony, a much greater, human NoV-like diversity of ReCVs can be expected. Recently, capsid sequences for several G1.1 ReCVs and sequence information for two additional ReCV strains were published (Handley et al, 2012;Smits et al, 2012;. The WUHARV strain (Handley et al, 2012) detected in macaque stool samples grouped with the G1.2 ReCVs, while the ReCV Bangladesh/289 strain (Smits et al, 2012) detected in human stool samples separated from all the macaque strains with distances equivalent to those between human NoV genogroups and was assigned to a third genogroup (G3) (Fig.…”

Section: Genetic Diversitymentioning

confidence: 99%

Rhesus enteric calicivirus surrogate model for human norovirus gastroenteritis

Farkas

2015

Journal of General Virology

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Human noroviruses are one of the major causes of acute gastroenteritis worldwide. Due to the lack of an efficient human norovirus cell culture system coupled with an animal model, human norovirus research mainly relies on human volunteer studies and surrogate models. Current models either utilize human norovirus-infected animals including the gnotobiotic pig or calf and the chimpanzee models, or employ other members of the family Caliciviridae including cell culture propagable surrogate caliciviruses such as the feline calicivirus, murine norovirus and most recently the Tulane virus. One of the major features of human noroviruses is their extreme biological diversity, including genetic, antigenic and histo-blood group antigen binding diversity, and possible differences of virulence and environmental stability. This extreme biological diversity and its effect on intervention/prevention strategies cannot be modelled by uniform groups of surrogates, much less by single isolates. Tulane virus, the prototype recovirus strain, was discovered in 2008. Since then, several other novel recoviruses have been described and cell culture adapted. Recent studies indicate that the epidemiology, the biological features and diversity of recoviruses and the course of infection and clinical disease in recovirus-infected macaques more closely reflect those properties of human noroviruses than any of the current surrogates. This review aims to summarize what is currently known about recoviruses, highlight their biological similarities to human noroviruses and discuss applications of the model in addressing questions relevant for human norovirus research.

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“…Nucleic acids were randomly amplified by sequence-independent PCR using barcoded primers, pooled, and sequenced in one run on the Roche Titanium/FLX platform as described previously. 8 Sequences were compared with publicly available sequence databases using a customized bioinformatics platform as previously described to identify microbial sequences present in the sample. 9 Contig assembly was performed with the Newbler assembler.…”

Section: Methodsmentioning

confidence: 99%

An Outbreak of Acute Febrile Illness Caused by Sandfly Fever Sicilian Virus in the Afar Region of Ethiopia, 2011

Woyessa¹,

Omballa²,

Wang³

et al. 2014

The American Society of Tropical Medicine and Hygiene

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Abstract. In malaria-endemic regions, many medical facilities have limited capacity to diagnose non-malarial etiologies of acute febrile illness (AFI). As a result, the etiology of AFI is seldom determined, although AFI remains a major cause of morbidity in developing countries. An outbreak of AFI was reported in the Afar region of Ethiopia in August of 2011. Retrospectively, 12,816 suspected AFI cases were identified by review of medical records. Symptoms were mild and selflimiting within 3 days after the date of onset; no fatalities were identified. All initial test results of AFI patient specimens were negative for selected pathogens using standard microbiological and molecular techniques. High-throughput sequencing of nucleic acid extracts of serum specimens from 29 AFI cases identified 17 (59%) of 29 samples as positive for Sandfly Fever Sicilian Virus (SFSV). These results were further confirmed by specific reverse transcription polymerase chain reaction. This is the first study implicating SFSV as an etiological agent for AFI in Ethiopia.

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Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

Cited by 255 publications

References 45 publications

Identification of a novel bufavirus in domestic pigs by a viral metagenomic approach

Identification of a novel bufavirus in domestic pigs by a viral metagenomic approach

Rhesus enteric calicivirus surrogate model for human norovirus gastroenteritis

An Outbreak of Acute Febrile Illness Caused by Sandfly Fever Sicilian Virus in the Afar Region of Ethiopia, 2011

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