Novel picornavirus in domestic rabbits (Oryctolagus cuniculus var. domestica)

Pankovics, Péter; Boros, Ákos; Bíró, Hunor; Horváth, Katalin Barbara; Phan, Tung Gia; Delwart, Eric; Reuter, Gábor

doi:10.1016/j.meegid.2015.11.012

Cited by 22 publications

(19 citation statements)

References 47 publications

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“…The Miniopterus fuliginosus bat picornavirus (BtMf-PicoV-2/GD2012) identified in China was the closest available relative [ 11 ]. The rabbit picornavirus had been tentatively placed into the Kobuvirus genus as it possessed certain qualifying characteristics [ 65 ]. However, this novel clade shares much lower similarities (46.3–54.9% nucleotide identities and 38.9–47.4% amino acid similarities) to other classified kobuviruses and decreased to below 39.7% nucleotide identity when compared to the genera Mischivirus , Enterovirus , Sapelovirus , Apthovirus and Cardiovirus .…”

Section: Resultsmentioning

confidence: 99%

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa

et al. 2018

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Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.

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Section: Resultsmentioning

confidence: 99%

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa

et al. 2018

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“…The genome structure is composed of a leader protein (L), followed by structural capsid proteins (VP0, VP3, and VP1) and non-structural proteins (2 A–2 C and 3 A–3 D) ( Yamashita et al 1998 , 2003; Ng et al 2012 ). To date, kobuviruses have been found in multiple host taxa including humans, lagomorpha (rabbits), chiroptera (bats), rodentia, artiodactyla, carnivora, and aves, as well as in environmental samples (Yamashita et al 2003; Reuter et al 2008 , 2010 ; Kapoor et al 2011a ; Wu et al 2012 ; Lodder et al 2013 ; Smits et al 2013 ; Oem et al 2014 ; Pankovics et al 2015 , 2016 ). Kobuviruses are currently grouped into six different species (AiV A to F) and unassigned kobuviruses according to the latest report of International Committee on Taxonomy of Viruses ( https://talk.ictvonline.org/taxonomy/ ).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and cross-species transmission of kobuviruses in Vietnam

Dũng

Ivens

et al. 2018

Virus Evolution

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Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods. We estimated and compared time of origin of kobuviruses in different host orders; we also examined the cross-species transmission of kobuviruses within the same host order and between different host orders. Our data provide new knowledge of rodent and bat kobuviruses, which are most closely related to human kobuviruses. The novel bat kobuviruses isolated from bat roosts in Southern Vietnam were genetically distinct from previously described bat kobuviruses, but closely related to kobuviruses found in rodents. We additionally found evidence of frequent cross-species transmissions of kobuviruses within rodents. Overall, our phylogenetic analyses reveal multiple cross-species transmissions both within and among mammalian species, which increases our understanding of kobuviruses genetic diversity and the complexity of their evolutionary history.

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“…It instead contains three hairpin structures at the beginning of the 5'UTR region, as has been found in murine kobuvirus 1 strain M-5/USA/2010 (JF755427) and rabbit kobuvirus 1 strain rabbit01/2013/HUN (KT325852) [35,36]. A converse example is the porcine kobuvirus 1 strain sw/S-1-HUN/2007 (EU787450), in which the ORI secondary structure with the pseudoknot is followed by type-IV IRES structures [37].…”

Section: Mf977323mentioning

confidence: 91%