In a recent article published in the bioRxiv * prepress server, the researchers illustrated the transmission of coronavirus 2 (SARS-CoV-2) from zooanthroponotic severe acute respiratory syndrome and host-specific viral mutations.
Study: Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by phylogenetic analysis of the entire genome. Image credit: Gallinago_media / Shutterstock
Fund
Coronaviruses, including SARS-CoV-2, can potentially infect a wide variety of animal hosts. Although the ancestral animal reservoir of SARS-CoV-2 is unknown, it has close relatives in bats. In addition, a variant of the ancestor SARS-CoV-2 probably spread to humans through an intermediate animal host in Wuhan, China, at a seafood market.
SARS-CoV-2 is a widespread virus that infects and evolves in multiple mammals, including pets and captives, humans and wildlife. Transmission through non-human species increases the possibility of SARS-CoV-2 deposits, making eradication more difficult and offering the virus possibilities for new evolutionary pathways, such as the emergence of new mutant lineages and the selection of adaptive mutations.
Numerous studies have shown that SARS-CoV-2 is transmitted from humans to specific animal species and, in some cases, backwards to humans. However, although these case reports have been helpful in identifying patterns of coronavirus 2019 disease transmission and adaptability (COVID-19) between particular animal species, there is no systematic worldwide analysis of current data.
About the study
In their current work, researchers thoroughly investigated the transmission of SARS-CoV-2 between mammalian species, both human and non-human, to discover mutations associated with each species through phylogenetic analysis and publicly available viral genome sequences.
Using a large data set, the team systematically examined SARS-CoV-2 sequences generated from animal hosts. They used the Global Influenza Data Sharing Initiative (GISAID) to retrieve all existing SARS-CoV-2 genomic sequences obtained from non-human animals.
Inferred transmission events between humans and animals. The billboards show a representative tree for each species with animal-to-human transmissions marked on the tree. The trees are rooted in the Wuhan reference genome. The eif panels show the distribution (violin plot next to dots represented with jitter to avoid overlap) of the inferred transmission counts (through 10 replicated trees) in each animal species, both in trees filtered with bootstrap and in trees not filtered.
Scientists estimated the relative frequencies of transmission between humans and four other commonly affected animals (Felis catus domesticus (cats), Canis lupus familaris (dogs), Odocoileus virginianus (deer), and minks) using phylogenetic approaches. They employed the restoration of the ancestral state in viral phylogenetic trees to thoroughly explore the likely incidents of animal-to-human transmission, including the direction of transmission. The goal of the team was to develop a uniform comparative methodology for interspecies transmission rather than extrapolating absolute interspecies transmission frequencies of COVID-19.
The researchers used genome-wide association studies (GWAS) to investigate mutations linked to specific animal species in relation to humans. They used POUTINE, a technique that implicitly regulates population structure and the interconnection between mutations by addressing only homoplastic mutations that are similar by state and not by offspring, which occurs independently numerous times within phylogeny to carry out GWAS. In addition, the researchers conducted a separate GWAS to discover variants correlated with each species.
Manhattan plots that summarize the achievements of GWAS in each animal species. In each panel, the x-axis represents the position of the nucleotides in the SARS-CoV-2 reference genome, and the y-axis represents the -log10 of the p-spot values averaged in replicas. Statistically significant hits with family-corrected p-values below 0.05 are shown in red (not synonymous) or blue (synonym), while non-statistically significant p-values are shown in black.
Results
The authors found that mink had the highest rate of SARS-CoV-2 transmission from animal to human, according to the previous literature. In contrast, other species examined such as dogs, cats, and deer had negligible levels of SARS-CoV-2 transmission to humans. However, despite these findings, the possibility of transmitting SARS-CoV-2 from cats or dogs to humans cannot be ruled out, which could be more easily discovered with prospective domestic transmission research or deeper sampling.
Transmission of SARS-CoV-2 from humans to animals was consistent across species, and slight discrepancies may be due to different sampling approaches. While possible sampling biases may restrict predicted transmission events, the current results serve as a valuable baseline for future research.
The team recovered the N501T mutation previously linked to mink and two additional amino acid variations in other SARS-CoV-2 genes. They also discovered several unique deer mutations, including non-synonymous and synonymous substitutions. None of the single nucleotide variants (SNVs) were substantially related to dogs or cats in GWAS, while 26 SNVs were closely correlated with deer and three with mink.
In fact, one in three mink hits appears in all 10 replicas, and at least 50% of the replicas housed the remaining two. The three mutations, including the N501T, were not synonymous. In addition, seven of the 26 deer blows appeared in all 10 aftershocks, and five of them 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 successes were cysteine (C)> uracil (U) transition mutations.
Conclusions
Overall, the results of the study found a significant incidence of COVID-19 transfer from mink to human, while animal-to-human transmission of COVID-19 from dogs, cats, and deer was uncommon. . The team noted that future research should study SNVs strongly correlated with deer and mink to see if they have a role in variable pathogenesis, immune evasion, or altered host response.
Current findings support prolonged deer-to-deer COVID-19 transmission and emphasize the need to investigate animal-related SARS-CoV-2 mutations to determine their potential influence on human and animal health. . Based on accessible genomic sequences, the present work offers a quantitative methodology to control the transmission of COVID-19 between animals and identifies numerous possible adaptive mutations in animals for further research.
* Important news
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, guided by clinical practice / health-related behavior, or treated as established information.