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. 2021 Aug 27;13(9):1709.
doi: 10.3390/v13091709.

No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity

Lu Lu  1 , Jordan Ashworth  1 , Dung Nguyen  2 , Kejin Li  3 , Donald B Smith  2   3 , Mark Woolhouse  1 , On Behalf Of The Vizions Consortium
Affiliations

No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity

Lu Lu et al. Viruses. .

Abstract

Hospital-based and community-based 'high-risk cohort' studies investigating humans at risk of zoonotic infection due to occupational or residential exposure to animals were conducted in Vietnam, with diverse viruses identified from faecal samples collected from humans, domestic and wild animals. In this study, we focus on the positive-sense RNA virus family Picornaviridae, investigating the prevalence, diversity, and potential for cross-species transmission. Through metagenomic sequencing, we found picornavirus contigs in 23% of samples, belonging to 15 picornavirus genera. Prevalence was highest in bats (67%) while diversity was highest in rats (nine genera). In addition, 22% of the contigs were derived from novel viruses: Twelve phylogenetically distinct clusters were observed in rats of which seven belong to novel species or types in the genera Hunnivirus, Parechovirus, Cardiovirus, Mosavirus and Mupivirus; four distinct clusters were found in bats, belonging to one novel parechovirus species and one related to an unclassified picornavirus. There was no evidence for zoonotic transmission in our data. Our study provides an improved knowledge of the diversity and prevalence of picornaviruses, including a variety of novel picornaviruses in rats and bats. We highlight the importance of monitoring the human-animal interface for possible spill-over events.

Keywords: animal–human interface; bats; metagenomic sequencing; picornavirus; rats.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Prevalence of picornavirus contigs by host. (A) Proportion of samples with picornavirus sequences detected in each host type. (B) Samples with picornavirus sequences identified in Dong Thap province (highlighted in red in dashed square). Symbol colours indicate host (used consistently in all figures), and for human samples symbol shape indicates those from the risk cohort study (circles) and hospital patients (triangles).
Figure 2
Figure 2
Prevalence of picornavirus species in different hosts by DIAMOND BLASTX top hit.
Figure 3
Figure 3
Identity of contigs to the closest related sequence in NCBI. Circle size indicates the number of contigs, and fill colour indicates the host. Contigs with <70% aa identity to reference sequences (dotted line) may represent members of novel species.
Figure 4
Figure 4
Phylogenetic analyses of putatively novel species or types found in rats and bats and representative members of the family Picornaviridae based on the coding region of P1. The branches of 5 genera and an unclassified picornavirus with novel clusters (labelled with C)/sequences from rats (green in tips) and bats (orange in tips) found in Vietnam are highlighted in red. The trees are constructed using maximum likelihood methods with HKY + G4 + I model and 1000 bootstraps. Scale bar indicates number of nucleotide substitutions per site.
Figure 5
Figure 5
Hunnivirus sequences in rats and other hosts. (A) Simplified MCC tree representing the time-scale phylogeny of hunniviruses. Bayesian time-scaled tree of VP1 sequences detected in Vietnamese rats and reference sequences in NCBI (highlighted in asterisk). Different host species are labelled on the tips and distinct by colours and symbols (rat in different shades of green, cat in orange, bovine and ovine in dark blue); the six clusters found in Vietnamese rats (Rat-C1-C6) are labelled on the right; the internal node of Rat-C6, a putative member of a novel species, is highlighted with red star. (B) Locations of rat samples with hunniviruses, coloured by different clusters identified in the phylogenetic tree. (C) Amino acid identities of polyprotein among rat clusters and other hosts. (D) Nucleotide distance scan across the polyprotein coding region of rat clusters (Rat-C1 to C6) against HuA-A1 and comparing to other known hunnivirus types.
Figure 6
Figure 6
Parechovirus sequences in bats, rats, and other hosts. (A) Simplified MCC tree representing the time-scale phylogeny of parechoviruses. Bayesian time-scaled tree of VP1 sequences detected in Vietnamese rats and reference sequences in NCBI (highlighted in asterisk). Currently identified species in the genus Parechovirus are labelled on the nodes. Different host species are indicated on the tips and distinct by colours and symbols; sequences from a Vietnamese rat (Parechovirus|VZ-Rat) and the clusters (Parechovirus|Bat-C1 to C3) found in Vietnamese bats are labelled on the right; the internal node of the putatively novel species found in bats is highlighted with red star. (B) Locations of bat and rat samples with parechovirus sequences, coloured by different clusters identified in the phylogenetic tree. (C) Genetic identities in polyprotein among bat and rat sequences found in Vietnam comparing to reference sequences of species in the genus Parechovirus. (D) Genetic distance scan across the entire polyprotein coding region of bat clusters and rat sequence found in Vietnam, comparing to reference sequences of Parechovirus A.
Figure 7
Figure 7
Phylogenetic relationships between picornaviruses found in rats, bats, and other hosts. (A) Cardiovirus, (B) Mupivirus, (C) Mosavirus and (D) unclassified picornavirus. Maximum likelihood tree of VP1 sequences detected in Vietnam and reference sequences in NCBI (highlighted with an asterisk). Virus species are labelled on the nodes. Different host species are indicated on the tips and distinguished by colours and symbols; sequences from the clusters found in Vietnamese are labelled on the right. The internal node of members of a putative novel mosavirus species is highlighted with red star.
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