Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Wang, Daxi; Wang, Yanqun; Sun, Wanying; Lu, Zengjun; Ji, Jingkai; Zhang, Zhaoyong; Cheng, Xinyi; Li, Yimin; Xiao, Fei; Zhu, Airu; Zhong, Bei; Ruan, Si-Min; Li, Jian Dong; Ren, Peng; Ou, Zhihua; Xiao, Minfeng; Li, Min; Deng, Ziqing; Huang, Zhong; Li, Fuqiang; Wang, Wenjing; Zhang, Yong‐Wei; Chen, Weijun; Zhu, Shida; Xu, Xun; Jin, Xin; Zhao, Jingxian; Zhong, Nanshan; Zhang, Wenwei; Zhao, Jincun; Li, Junhua; Xu, Yonghao

doi:10.3389/fmed.2021.585358

Cited by 33 publications

(26 citation statements)

References 28 publications

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“…So far, efforts to understand how transmission shapes the evolution of SARS-CoV-2 have mainly focused on small household events or nosocomial pairs [3][4][5][6][7]. Such studies point to a narrow transmission bottleneck that significantly reduces viral genetic diversity at the start of each infection [3,4,[6][7][8]. While exact estimates of the bottleneck range from 1 to 15 virions, it is clear that a limited number of virions initiate most human infections.…”

Section: Introductionmentioning

confidence: 99%

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

Hannon

Roychoudhury

Xie

et al. 2022

Preprint

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The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a SARS-CoV-2 outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.

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Section: Introductionmentioning

confidence: 99%

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

Hannon

Roychoudhury

Xie

et al. 2022

Preprint

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“…Consistent with this bottleneck, sequencing studies have provided conflicting results with respect to the ability of intrahost variants to transmit and establish new SARS-CoV-2 lineages that have the potential to transmit widely. While a number of studies have shown this to be the case [21][22][23][24] , other studies have not been able to demonstrate transmission of viral lineages derived from intrahost evolution 11,25,26 . The stochasticity in inter-host transmission of specific viral lineages is compounded by the overdispersed nature of SARS-CoV-2 spread, where most onward transmission originates from a small number of individuals.…”

mentioning

confidence: 99%

Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure

Egeren

Novokhodko

Stoddard³

et al. 2021

Sci Rep

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The rapid emergence and expansion of novel SARS-CoV-2 variants threatens our ability to achieve herd immunity for COVID-19. These novel SARS-CoV-2 variants often harbor multiple point mutations, conferring one or more evolutionarily advantageous traits, such as increased transmissibility, immune evasion and longer infection duration. In a number of cases, variant emergence has been linked to long-term infections in individuals who were either immunocompromised or treated with convalescent plasma. In this paper, we used a stochastic evolutionary modeling framework to explore the emergence of fitter variants of SARS-CoV-2 during long-term infections. We found that increased viral load and infection duration favor emergence of such variants. While the overall probability of emergence and subsequent transmission from any given infection is low, on a population level these events occur fairly frequently. Targeting these low-probability stochastic events that lead to the establishment of novel advantageous viral variants might allow us to slow the rate at which they emerge in the patient population, and prevent them from spreading deterministically due to natural selection. Our work thus suggests practical ways to achieve control of long-term SARS-CoV-2 infections, which will be critical for slowing the rate of viral evolution.

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“…In the review there were 2 studies discussed the COVID 19 genotypes. The work of Ramaiah and Arumugaswami (2020) and of Wang et al 2021. The nCoV genotype have been evolved from a bat-CoV by accumulating non-synonymous mutations, indels, and recombination events.…”

Section: Resultsmentioning

confidence: 99%

Evolution of Coronavirus in Human Population: An Integrative Review

Lu¹,

Caballes²

2021

IJRP

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Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Cited by 33 publications

References 28 publications

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure

Evolution of Coronavirus in Human Population: An Integrative Review

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