About: The origin and underlying driving forces of the SARS-CoV-2 outbreak

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	The origin and underlying driving forces of the SARS-CoV-2 outbreak
Creator	Chang, Sui-Yuan Chen, Pei-Jer Yeh, Shiou-Hwei Wang, Hurng-Yi Hsieh, Chia-Hung Chaw, Shu-Miaw Chen, Shi-Lun Tai, Jui-Hung Yang, Wei-Shiung
Source	Medline; PMC
abstract	BACKGROUND: SARS-CoV-2 began spreading in December 2019 and has since become a pandemic that has impacted many aspects of human society. Several issues concerning the origin, time of introduction to humans, evolutionary patterns, and underlying force driving the SARS-CoV-2 outbreak remain unclear. METHOD: Genetic variation in 137 SARS-CoV-2 genomes and related coronaviruses as of 2/23/2020 was analyzed. RESULT: After correcting for mutational bias, the excess of low frequency mutations on both synonymous and nonsynonymous sites was revealed which is consistent with the recent outbreak of the virus. In contrast to adaptive evolution previously reported for SARS-CoV during its brief epidemic in 2003, our analysis of SARS-CoV-2 genomes shows signs of relaxation. The sequence similarity in the spike receptor binding domain between SARS-CoV-2 and a sequence from pangolin is probably due to an ancient intergenomic introgression that occurred approximately 40 years ago. The current outbreak of SARS-CoV-2 was estimated to have originated on 12/11/2019 (95% HPD 11/13/2019–12/23/2019). The effective population size of the virus showed an approximately 20-fold increase from the onset of the outbreak to the lockdown of Wuhan (1/23/2020) and ceased to increase afterwards, demonstrating the effectiveness of social distancing in preventing its spread. Two mutations, 84S in orf8 protein and 251 V in orf3 protein, occurred coincidentally with human intervention. The former first appeared on 1/5/2020 and plateaued around 1/23/2020. The latter rapidly increased in frequency after 1/23/2020. Thus, the roles of these mutations on infectivity need to be elucidated. Genetic diversity of SARS-CoV-2 collected from China is two times higher than those derived from the rest of the world. A network analysis found that haplotypes collected from Wuhan were interior and had more mutational connections, both of which are consistent with the observation that the SARS-CoV-2 outbreak originated in China. CONCLUSION: SARS-CoV-2 might have cryptically circulated within humans for years before being discovered. Data from the early outbreak and hospital archives are needed to trace its evolutionary path and determine the critical steps required for effective spreading.
has issue date	2020-06-07(xsd:dateTime)
bibo:doi	10.1186/s12929-020-00665-8
bibo:pmid	32507105
has license	cc-by
sha1sum (hex)	878188a25baf84e40354d04b50d629ba8eec3958
schema:url	https://doi.org/10.1186/s12929-020-00665-8
resource representing a document's title	The origin and underlying driving forces of the SARS-CoV-2 outbreak
has PubMed Central identifier	PMC7276232
has PubMed identifier	32507105
schema:publication	J Biomed Sci
resource representing a document's body	covid:878188a25baf84e40354d04b50d629ba8eec3958#body_text
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