Commentary: Origin and evolution of pathogenic coronaviruses

Adachi, Shun; Koma, Takaaki; Doi, Naoya; Nomaguchi, Masako; Adachi, Akio

doi:10.3389/fimmu.2020.00811

“…Phylogenetic comparison of coronavirus sequences from the patients of different geographical regions, and climatic conditions supports the natural origin of SARS-CoV-2 (Adachi et al, 2020;Andersen et al, 2020;Lu et al, 2020;Shereen et al, 2020;Zhou et al, 2020a). The complete genomes of the novel SARS-CoV-2 sequenced from different patients share more than 99.9% sequence identity (Tang et al, 2020) suggesting a very recent host shift of this virus to humans (Lu et al, 2020;Tang et al, 2020;Zhou et al, 2020b).…”

Section: Genome Evolution Of the Sars-cov-2mentioning

confidence: 65%

Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease

Hoque

¹

,

Chaudhury

²

,

Akanda

³

et al. 2020

PeerJ

View full text Add to dashboard Cite

The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by a novel evolutionarily divergent RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus first emerged in Wuhan, China in December 2019, and subsequently spreaded around the world. Genomic analyses revealed that this zoonotic virus may be evolved naturally but not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Comprehensive annotations of the whole-genomes revealed hundreds of nucleotides, and amino acids mutations, substitutions and/or deletions at different positions of the ever changing SARS-CoV-2 genome. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, cheap, rapid, and specific diagnostic tools targeting antigens or CRISPR-Cas-mediated method or a newly developed plug and play method should be available for the resource-poor developing countries. A large number of candidate drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools, and the preventive or therapeutic remedies of the COVID-19. We also discussed the future scopes for research, effective management, and surveillance of the newly emerged COVID-19 disease.

show abstract

“…Phylogenetic comparison of coronavirus sequences from the patients of different geographical regions, and climatic conditions supports the natural origin of SARS-CoV-2 (Adachi et al, 2020;Andersen et al, 2020;Lu et al, 2020;Shereen et al, 2020;Zhou et al, 2020a). The complete genomes of the novel SARS-CoV-2 sequenced from different patients share more than 99.9% sequence identity (Tang et al, 2020) suggesting a very recent host shift of this virus to PeerJ reviewing PDF | (2020:05:48746:1:1:NEW 26 Jun 2020)…”

Section: Genome Evolution Of the Sars-cov-2mentioning

confidence: 71%

Peer Review #2 of "Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease (v0.1)"

Shehata¹

2020

0

View full text Add to dashboard Cite

The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by a novel evolutionarily divergent RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus first emerged in Wuhan, China in December 2019, and subsequently spreaded around the world. Genomic analyses revealed that this zoonotic virus may be evolved naturally but not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Comprehensive annotations of the whole-genomes revealed hundreds of nucleotides, and amino acids mutations, substitutions and/or deletions at different positions of the ever changing SARS-CoV-2 genome. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, cheap, rapid, and specific diagnostic tools targeting antigens or CRISPR-Cas-mediated method or a newly developed plug and play method should be available for the resource-poor developing countries. A large number of candidate drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools, and the preventive or therapeutic remedies of the COVID-19. We also

show abstract

“…In spite of having interest on several genes of the SARS-CoV-2 genome, the evolutionary biologists tend to focus on a functionally conserved but sequentially diverged genes. This is because the role for the critical gene is conserved in various species, while it is rapidly evolving, indicating that a diverging force acts on the gene, e.g., by co-evolution such as symbiosis, evolutionary arms race or others (Adachi et al, 2020). Conversely, phylogenomic analysis of three super-clades (S, V, and G) isolated from the outbreaks of distinct geographic locations (China, USA and Europe) could not clearly reflect the hypothetical ongoing adaptation of SARS-CoV-2, which alternately refer to mere genetic drift and founder effects due to rapid spreading of the virus (Chiara et al, 2020).…”

Section: Genome-wide Mutations In the Sars-cov-2 Strainsmentioning

confidence: 99%

Genomic Diversity and Evolution, Diagnosis, Prevention, and Therapeutics of the Pandemic COVID-19 Disease

Hoque¹,

Chaudhury²,

Akanda³

et al. 2020

Preprint

View full text Add to dashboard Cite

A novel coronavirus COVID-19 was first emerged in Wuhan city of Hubei Province in China in December 2019. The COVID-19, since then spreads to 213 countries and territories, and has become a pandemic. Genomic analyses have indicated that the virus, popularly named as corona, originated through a natural process and is probably not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Genome-wide annotation of thousands of genomes revealed that more than 1,407 nucleotide mutations and 722 amino acids replacements occurred at different positions of the SARS-CoV-2. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, rapid, and specific diagnostic tools targeting IgM/IgG or newly developed plug and play methods should be available for resource-poor developing countries. Some drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools and the preventive or therapeutic remedies of the COVID-19, and discusses on scopes for further research and effective management and surveillance of COVID-19.

show abstract

Commentary: Origin and evolution of pathogenic coronaviruses

Cited by 48 publications

References 12 publications

Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease

Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease

Peer Review #2 of "Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease (v0.1)"

Genomic Diversity and Evolution, Diagnosis, Prevention, and Therapeutics of the Pandemic COVID-19 Disease

Contact Info

Product

Resources

About