SARS-CoV-2 is a generalist virus that infects and evolves in many mammals and humans.

In a recent article published in bioRxiv* Preprint server, researchers have described severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in animals and humans and host-specific viral mutations.

study: Animal human transmission and host-specific viral mutations in SARS-CoV-2 revealed by genome-wide phylogeny analysis.. Image Credit: Gallinago_media / Shutterstock

Background

coronavirus, SARS-CoV-2, can infect a range of animal hosts. The reservoir of the ancestral SARS-CoV-2 animal is unknown, but there are close relatives of the bat. In addition, the ancestral SARS-CoV-2 variant infects humans, probably via an intermediate animal host in the fish market in Wuhan, China.

SARS-CoV-2 is a generalist virus that infects and evolves in multiple mammals, including companion animals, captive animals, humans, and wildlife. Infections mediated by non-human species increase the likelihood of SARS-CoV-2 reservoir formation, make eradication more difficult, and enable new evolutionary pathways such as the emergence of new mutant strains and adaptive mutation selection. Provides sex to the virus.

Numerous studies have shown that SARS-CoV-2 can infect certain animal species from humans and, in some cases, back-infect humans. However, despite the fact that these case reports help identify the infection pattern of coronavirus disease 2019 (COVID-19) and its adaptability between specific animal species, the current data worldwide Systematic analysis is lacking.

About research

In current studies, researchers use phylogenetic analysis and publicly accessible viral genomic sequences to reveal mutations associated with various species, both human and non-human mammalian species. We thoroughly investigated SARS-CoV-2 infection during the period.

The team used a large dataset to systematically examine SARS-CoV-2 sequences generated from animal hosts. They used the Global Initiative for Sharing All Influenza Data (GISAID) to obtain all existing SARS-CoV-2 genomic sequences from non-human animals.

A transmission event inferred between humans and animals. The panel ad shows a representative tree of all species, and the tree is marked with animal-to-human transmission. The tree is rooted in the Wuhan reference genome. Panels e and f show the distribution of estimated transmission numbers for each animal species (over 10 replicating trees) in both bootstrap-filtered and unfiltered trees (in jitter to avoid overlap). Violin plot along the plotted points) is displayed.

Scientists have estimated the relative frequency of infection between humans and four other often afflicted animals (Domestic cat (Cat), Canis lupus (dog), Odocoileus virginianus (Deer), and mink) Use a phylogenetic approach. They adopted restoration of ancestral status in the phylogenetic tree of the virus to thoroughly investigate possible cases of animal-to-human transmission, including the direction of transmission. The team’s goal was not to estimate the absolute frequency of cross-species transmission, but to develop a unified comparison method for cross-species transmission. COVID-19 infection..

Researchers used Genome-Wide Association Study (GWAS) to investigate mutations associated with specific animal species compared to humans. They used POUTINE. This interconnects population structures and mutations by addressing only homoplasmic mutations that occur multiple times independently within the phylogeny for performing GWAS and are state-similar rather than progeny. Is a technique to implicitly control. In addition, researchers ran GWAS individually to discover various related variants.

Manhattan creates a plot summarizing GWAS hits for each animal species. In all panels, the x-axis represents the nucleotide position of the SARS-CoV-2 reference genome and the y-axis represents the point-by-point p-value -log10 averaged throughout replication. Statistically significant hits with a family-specific modified p-value less than 0.05 are shown in red (non-synonymous) or blue (synonymous), and non-statistically significant p-values ​​are shown in black.

result

The authors found that mink had the highest rate of SARS-CoV-2 transmission from animals to humans, consistent with previous literature. On the contrary, other investigated species such as dogs, cats and deer had low levels of SARS-CoV-2 infection in humans. However, despite these findings, the possibility of SARS-CoV-2 transmission from cats or dogs to humans cannot be ruled out. This can be found more easily in future home infection studies or deeper sampling.

Transmission of SARS-CoV-2 from humans to animals is consistent across species, and slight discrepancies may be due to different sampling approaches. Potential sampling biases can limit the expected transmission events, but current findings serve as a valuable baseline for future research.

The team recovered the N501T mutation previously linked to mink and two additional amino acid mutations in the other SARS-CoV-2 genes. They also found several unique deer mutations, including non-synonymous and synonymous substitutions. None of the single nucleotide polymorphisms (SNVs) were substantially associated with dogs and cats in GWAS, while 26 SNVs were closely associated with deer and three were closely associated with mink. rice field.

In fact, one of Mink’s three hits appeared in all ten duplicates, with at least 50% of the duplicates containing the remaining two. The three mutations, including N501T, were not synonymous. In addition, 7 of the 26 deer hits appeared in all 10 replicas, 5 of which were present in at least 50% of the runs. Five of the 26 hits were intergenic mutations, while 12 were synonymous mutations. In addition, 21 of the hits were cysteine ​​(C)> uracil (U) transition mutations.

Conclusion

Together, the findings revealed a significant frequency of mink-to-human COVID-19 transmission, but animal-to-human COVID-19 transmission from dogs, cats, and deer was rare. The team noted that future studies would need to look at SNVs that strongly correlate with deer and mink to see if they function in a variety of causes, antigenic escape, or altered host responses.

Current findings support animal-related SARS-CoV-2 mutations to support prolonged deer-to-deer transmission of COVID-19 and to determine potential effects on animal and human health. Emphasizes the need to do. From accessible genomic sequences, this study provides a quantitative methodology for monitoring COVID-19 infection between animals and identifies a number of possible adaptive mutations in animals for further investigation.

*Important Notices

bioRxiv Publish preliminary scientific reports that should not be considered definitive as they have not been peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.