A theoretical exploration of the origin and early evolution of a pandemic

Ruan, Yi; Wen, Haijun; He, Xionglei; Wu, Chung‐I

doi:10.1016/j.scib.2020.12.020

Cited by 27 publications

(42 citation statements)

References 46 publications

(66 reference statements)

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“…Genetic diversity is transmitted during infection via N0 virions, which would proliferate to Nt virions at time t in the new host. We use the branching process to track the genetic drift during the rapid growth phase of the viral population (CHEN et al 2017;RUAN et al 2021a;RUAN et al 2021b).…”

Section: Resultsmentioning

confidence: 99%

“…We let E(k) = 2 for neutral mutations and E(k) = 3 for s = 0.5 in the W-model. V(k) is usually set at 10E(k) as done before (RUAN et al 2021a;RUAN et al 2021b). The adaptive mutation rate is set at either μ = 0.01 or μ = 0.0001 per generation.…”

Section: The Fate Of Mutations Within Hostsmentioning

confidence: 99%

“…Simulating the fate of new mutations within host under different selection strength. As done before (RUAN et al 2021a;RUAN et al 2021b), we simulate mutation accumulation of virus within host by branching process. In the branching process, each virion would produce k descendants in a period of time, say 24 hours, with the mean and variance of E(k) and V(k), respectively.…”

Section: Genetic Drift When Population Grows (E(k) > 1)mentioning

confidence: 99%

“…Genetic drift during the proliferation in the host is simulated by the branching process model of Ref. (CHEN et al 2017;RUAN et al 2021a;RUAN et al 2021b).…”

Section: Relationships Between Within-host Diversity and Between-host Polymorphismmentioning

confidence: 99%

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One viral sequence for each host? – The neglected within-host diversity as the main stage of SARS-CoV-2 evolution

Ruan

Hou

et al. 2021

Preprint

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The standard practice of presenting one viral sequence for each infected individual implicitly assumes low within-host genetic diversity. It places the emphasis on the viral evolution between, rather than within, hosts. To determine this diversity, we collect SARS-CoV-2 samples from the same patient multiple times. Our own data in conjunction with previous reports show that two viral samples collected from the same individual are often very different due to the substantial within-host diversity. Each sample captures only a small part of the total diversity that is transiently and locally released from infected cells. Hence, the global SARS-CoV-2 population is a meta-population consisting of the viruses in all the infected hosts, each of which harboring a genetically diverse sub-population. Advantageous mutations must be present first as the within-host diversity before they are revealed as between-host polymorphism. The early detection of such diversity in multiple hosts could be an alarm for potentially dangerous mutations. In conclusion, the main forces of viral evolution, i.e., mutation, drift, recombination and selection, all operate within hosts and should be studied accordingly. Several significant implications are discussed.

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Section: Resultsmentioning

confidence: 99%

Section: The Fate Of Mutations Within Hostsmentioning

confidence: 99%

Section: Genetic Drift When Population Grows (E(k) > 1)mentioning

confidence: 99%

“…Genetic drift during the proliferation in the host is simulated by the branching process model of Ref. (CHEN et al 2017;RUAN et al 2021a;RUAN et al 2021b).…”

Section: Relationships Between Within-host Diversity and Between-host Polymorphismmentioning

confidence: 99%

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One viral sequence for each host? – The neglected within-host diversity as the main stage of SARS-CoV-2 evolution

Ruan

Hou

et al. 2021

Preprint

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“…Moreover, China's recent development in globalization, urbanization, and transportation networks can further magnify the effect of spillovers 52 . Due to significantly increased animal-human contact probability for alternative meat, any animal host or contaminated meat from its place of origin can conveniently reach any mega city with an immunologically naive population to initiate a successful zoonotic transmission and subsequent pandemic 8,53 .…”

Section: Discussionmentioning

confidence: 99%

How One Pandemic Led To Another: Asfv, the Disruption Contributing To Sars-Cov-2 Emergence in Wuhan

Xia¹,

Hughes²,

Robertson³

et al. 2021

Preprint

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The spillover of a virus from one host species to another requires both molecular and ecological risk factors to align. While extensive research both before and after the emergence of SARS-CoV-2 in 2019 implicates horseshoe bat as the significant reservoir genus for the new coronavirus, it remains unclear why it emerged at this time. One massive disruption to human-animal contact in 2019 is linked to the on-going African swine fever virus (ASFV) pandemic. This began in Georgia in 2007 and was introduced to China in 2018. Pork is the major meat source in the Chinese diet. Severe fluctuations in the pork market prior to December 2019, may have increased the transmission of zoonotic pathogens, including severe acute respiratory syndrome–related coronaviruses, from wildlife to humans, wildlife to livestock and non-local animals to local animals. The major production and consumption regions for pork are geographically separated in China. The dramatic shortage of pork following restrictions of pig movement and culling resulted in price increases, leading to alternative meat consumption and unusual animal and meat movements nationwide such as wildlife and thus greatly increased opportunities for human-sarbecovirus contacts. Pork prices were particularly high in southern provinces (Guangdong, Guangxi, Fujian, Jiangxi, Hunan, and Hubei), where wildlife is farmed on different scales and more frequently consumed. Shandong experienced the biggest losses in pork production (~2 million metric tons), which is also the largest mink farming province. Hence, exposure of SARS-CoV-2 from wildlife or infected animals to humans by contact and consumption are more likely to have taken place in 2019, a year when China was experiencing the worst effects of the ASFV pandemic.

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