Literature DB >> 33659260

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

Daxi Wang1,2, Yanqun Wang3, Wanying Sun1,2,4, Lu Zhang3,5, Jingkai Ji1,2, Zhaoyong Zhang3, Xinyi Cheng1,2,6, Yimin Li3, Fei Xiao7, Airu Zhu3, Bei Zhong8, Shicong Ruan9, Jiandong Li1,2,4, Peidi Ren1,2, Zhihua Ou1,2, Minfeng Xiao1,2, Min Li1,2,4, Ziqing Deng1,2, Huanzi Zhong1,2,10, Fuqiang Li1,2,11, Wen-Jing Wang1,11, Yongwei Zhang1, Weijun Chen4,12, Shida Zhu1,13, Xun Xu1,14, Xin Jin1, Jingxian Zhao3, Nanshan Zhong3, Wenwei Zhang1, Jincun Zhao3,5, Junhua Li1,2,6, Yonghao Xu3.   

Abstract

The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.
Copyright © 2021 Wang, Wang, Sun, Zhang, Ji, Zhang, Cheng, Li, Xiao, Zhu, Zhong, Ruan, Li, Ren, Ou, Xiao, Li, Deng, Zhong, Li, Wang, Zhang, Chen, Zhu, Xu, Jin, Zhao, Zhong, Zhang, Zhao, Li and Xu.

Entities:  

Keywords:  SARS-CoV-2; evolution; human to human transmission; intra-host variation; population bottleneck

Year:  2021        PMID: 33659260      PMCID: PMC7917136          DOI: 10.3389/fmed.2021.585358

Source DB:  PubMed          Journal:  Front Med (Lausanne)        ISSN: 2296-858X


  21 in total

1.  HISAT: a fast spliced aligner with low memory requirements.

Authors:  Daehwan Kim; Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2015-03-09       Impact factor: 28.547

Review 2.  Matters of Size: Genetic Bottlenecks in Virus Infection and Their Potential Impact on Evolution.

Authors:  Mark P Zwart; Santiago F Elena
Journal:  Annu Rev Virol       Date:  2015-11       Impact factor: 10.431

3.  Virological assessment of hospitalized patients with COVID-2019.

Authors:  Roman Wölfel; Victor M Corman; Wolfgang Guggemos; Michael Seilmaier; Sabine Zange; Marcel A Müller; Daniela Niemeyer; Terry C Jones; Patrick Vollmar; Camilla Rothe; Michael Hoelscher; Tobias Bleicker; Sebastian Brünink; Julia Schneider; Rosina Ehmann; Katrin Zwirglmaier; Christian Drosten; Clemens Wendtner
Journal:  Nature       Date:  2020-04-01       Impact factor: 49.962

4.  Reconciling disparate estimates of viral genetic diversity during human influenza infections.

Authors:  Katherine S Xue; Jesse D Bloom
Journal:  Nat Genet       Date:  2019-09       Impact factor: 38.330

5.  Quantifying influenza virus diversity and transmission in humans.

Authors:  Leo L M Poon; Timothy Song; Roni Rosenfeld; Xudong Lin; Matthew B Rogers; Bin Zhou; Robert Sebra; Rebecca A Halpin; Yi Guan; Alan Twaddle; Jay V DePasse; Timothy B Stockwell; David E Wentworth; Edward C Holmes; Benjamin Greenbaum; Joseph S M Peiris; Benjamin J Cowling; Elodie Ghedin
Journal:  Nat Genet       Date:  2016-01-04       Impact factor: 38.330

6.  Stochastic processes constrain the within and between host evolution of influenza virus.

Authors:  John T McCrone; Robert J Woods; Emily T Martin; Ryan E Malosh; Arnold S Monto; Adam S Lauring
Journal:  Elife       Date:  2018-05-03       Impact factor: 8.140

7.  Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples.

Authors:  Minfeng Xiao; Xiaoqing Liu; Jingkai Ji; Min Li; Jiandong Li; Lin Yang; Wanying Sun; Peidi Ren; Guifang Yang; Jincun Zhao; Tianzhu Liang; Huahui Ren; Tian Chen; Huanzi Zhong; Wenchen Song; Yanqun Wang; Ziqing Deng; Yanping Zhao; Zhihua Ou; Daxi Wang; Jielun Cai; Xinyi Cheng; Taiqing Feng; Honglong Wu; Yanping Gong; Huanming Yang; Jian Wang; Xun Xu; Shida Zhu; Fang Chen; Yanyan Zhang; Weijun Chen; Yimin Li; Junhua Li
Journal:  Genome Med       Date:  2020-06-30       Impact factor: 11.117

8.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937

9.  Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses.

Authors:  Everett Clinton Smith; Nicole R Sexton; Mark R Denison
Journal:  Annu Rev Virol       Date:  2014-06-02       Impact factor: 10.431

10.  Structural basis of receptor recognition by SARS-CoV-2.

Authors:  Jian Shang; Gang Ye; Ke Shi; Yushun Wan; Chuming Luo; Hideki Aihara; Qibin Geng; Ashley Auerbach; Fang Li
Journal:  Nature       Date:  2020-03-30       Impact factor: 49.962

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  12 in total

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

Authors:  William W Hannon; Pavitra Roychoudhury; Hong Xie; Lasata Shrestha; Amin Addetia; Keith R Jerome; Alexander L Greninger; Jesse D Bloom
Journal:  Virus Evol       Date:  2022-06-16

2.  When might host heterogeneity drive the evolution of asymptomatic, pandemic coronaviruses?

Authors:  Kenichi W Okamoto; Virakbott Ong; Robert Wallace; Rodrick Wallace; Luis Fernando Chaves
Journal:  Nonlinear Dyn       Date:  2022-06-20       Impact factor: 5.741

3.  Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.

Authors:  Katarina M Braun; Gage K Moreno; Peter J Halfmann; Emma B Hodcroft; David A Baker; Emma C Boehm; Andrea M Weiler; Amelia K Haj; Masato Hatta; Shiho Chiba; Tadashi Maemura; Yoshihiro Kawaoka; Katia Koelle; David H O'Connor; Thomas C Friedrich
Journal:  PLoS Pathog       Date:  2021-02-26       Impact factor: 7.464

4.  Computational characterization of inhaled droplet transport to the nasopharynx.

Authors:  Saikat Basu
Journal:  Sci Rep       Date:  2021-03-23       Impact factor: 4.379

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

Authors:  Debra Van Egeren; Alexander Novokhodko; Madison Stoddard; Uyen Tran; Bruce Zetter; Michael S Rogers; Diane Joseph-McCarthy; Arijit Chakravarty
Journal:  Sci Rep       Date:  2021-11-19       Impact factor: 4.379

6.  Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.

Authors:  Pilar Gallego-García; Nair Varela; Nuria Estévez-Gómez; Loretta De Chiara; Iria Fernández-Silva; Diana Valverde; Nicolae Sapoval; Todd J Treangen; Benito Regueiro; Jorge Julio Cabrera-Alvargonzález; Víctor Del Campo; Sonia Pérez; David Posada
Journal:  Virus Evol       Date:  2022-02-04

7.  Intra-host evolution during SARS-CoV-2 prolonged infection.

Authors:  Carolina M Voloch; Ronaldo da Silva Francisco; Luiz G P de Almeida; Otavio J Brustolini; Cynthia C Cardoso; Alexandra L Gerber; Ana Paula de C Guimarães; Isabela de Carvalho Leitão; Diana Mariani; Victor Akira Ota; Cristiano X Lima; Mauro M Teixeira; Ana Carolina F Dias; Rafael Mello Galliez; Débora Souza Faffe; Luís Cristóvão Pôrto; Renato S Aguiar; Terezinha M P P Castiñeira; Orlando C Ferreira; Amilcar Tanuri; Ana Tereza R de Vasconcelos
Journal:  Virus Evol       Date:  2021-09-29

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

Authors:  William W Hannon; Pavitra Roychoudhury; Hong Xie; Lasata Shrestha; Amin Addetia; Keith R Jerome; Alexander L Greninger; Jesse D Bloom
Journal:  bioRxiv       Date:  2022-02-09

9.  Characteristics of SARS-CoV-2 transmission in a medium-sized city with traditional communities during the early COVID-19 epidemic in China.

Authors:  Yang Li; Hao-Rui Si; Yan Zhu; Nan Xie; Bei Li; Xiang-Ping Zhang; Jun-Feng Han; Hong-Hong Bao; Yong Yang; Kai Zhao; Zi-Yuan Hou; Si-Jia Cheng; Shuan-Hu Zhang; Zheng-Li Shi; Peng Zhou
Journal:  Virol Sin       Date:  2022-01-25       Impact factor: 6.947

10.  Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes.

Authors:  Ankit K Pathak; Gyan Prakash Mishra; Bharathram Uppili; Safal Walia; Saman Fatihi; Tahseen Abbas; Sofia Banu; Arup Ghosh; Amol Kanampalliwar; Atimukta Jha; Sana Fatma; Shifu Aggarwal; Mahesh Shanker Dhar; Robin Marwal; Venkatraman Srinivasan Radhakrishnan; Kalaiarasan Ponnusamy; Sandhya Kabra; Partha Rakshit; Rahul C Bhoyar; Abhinav Jain; Mohit Kumar Divakar; Mohamed Imran; Mohammed Faruq; Divya Tej Sowpati; Lipi Thukral; Sunil K Raghav; Mitali Mukerji
Journal:  Nucleic Acids Res       Date:  2022-02-22       Impact factor: 16.971

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