SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection

Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, Si H-R, Zhu Y, Li B, Huang C-L, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Worobey M, Levy JI, Malpica Serrano LM, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, et al. The Huanan market was the epicenter of SARS-CoV-2 emergence. 2022.

Google Scholar 

Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, et al. SARS-CoV-2 emergence very likely resulted from at least two zoonotic events. 2022.

Google Scholar 

Shuaib M, Adroub S, Mourier T, Mfarrej S, Zhang H, Esau L, Alsomali A, Alofi FS, Ahmad AN, Shamsan A, et al. Impact of the SARS-CoV-2 nucleocapsid 203K/204R mutations on the inflammatory immune response in COVID-19 severity. Genome Med. 2023;15:54.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M, Amoako DG, Everatt J, Bhiman JN, Scheepers C, et al. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet. 2022;399:437–46.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Menni C, Valdes AM, Polidori L, Antonelli M, Penamakuri S, Nogal A, Louca P, May A, Figueiredo JC, Hu C, et al. Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observational study from the ZOE COVID Study. Lancet. 2022;399:1618–24.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ong SWX, Chiew CJ, Ang LW, Mak TM, Cui L, Toh M, Lim YD, Lee PH, Lee TH, Chia PY, et al. Clinical and Virological Features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern: A Retrospective Cohort Study Comparing B.1.17 (Alpha), B.1.351 (Beta), and B.1.6172 (Delta). Clin Infect Dis. 2022;75:e1128–36.

Article  PubMed  Google Scholar 

Denison MR, Graham RL, Donaldson EF, Eckerle LD, Baric RS. Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity. RNA Biol. 2011;8:270–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moeller NH, Shi K, Demir O, Belica C, Banerjee S, Yin L, Durfee C, Amaro RE, Aihara H: Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proc Natl Acad Sci U S A. 2022;119:e2106379119.

Prince T, Dong X, Penrice-Randal R, Randle N, Hartley C, Goldswain H, Jones B, Semple MG, Baillie JK, Openshaw PJM, et al. Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages. mSphere. 2022;7:e0091321.

Article  PubMed  Google Scholar 

Goldswain H, Dong X, Penrice-Randal R, Alruwaili M, Shawli GT, Prince T, Williamson MK, Raghwani J, Randle N, Jones B, et al. The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection. Genome Biol. 2023;24:47.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dudouet P, Colson P, Aherfi S, Levasseur A, Beye M, Delerce J, Burel E, Lavrard P, Bader W, Lagier JC, et al. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding. Sci Rep. 2022;12:18721.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jary A, Leducq V, Malet I, Marot S, Klement-Frutos E, Teyssou E, Soulie C, Abdi B, Wirden M, Pourcher V, et al. Evolution of viral quasispecies during SARS-CoV-2 infection. Clin Microbiol Infect. 2020;26:1560 e1561–1560 e1564.

Article  Google Scholar 

Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O'Toole Á, Southgate J, Johnson R, Jackson B, Nascimento FF, et al. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell. 2021;184:64–75.

Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile TP, Wang Y, Baum A, Diehl WE, Dauphin A, Carbone C, et al. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell. 2020;83:739–51.

Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, Andersson M, Otecko N, Wise EL, Moore N, et al. SARS-CoV-2 within-host diversity and transmission. Science. 2021;372:eabg0281.

Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, Zhou Z, Yang J, Zhong J, Yang D, et al. Genomic Diversity of Severe Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease 2019. Clin Infect Dis. 2020;71:713–20.

Article  CAS  PubMed  Google Scholar 

Gallichotte EN, Quicke KM, Sexton NR, Fitzmeyer E, Young MC, Janich AJ, Dobos K, Pabilonia KL, Gahm G, Carlton EJ, et al. Early Adoption of Longitudinal Surveillance for SARS-CoV-2 among Staff in Long-Term Care Facilities: Prevalence. Virologic and Sequence Analysis Microbiol Spectr. 2021;9:e0100321.

Article  PubMed  Google Scholar 

Ge Y, Martinez L, Sun S, Chen Z, Zhang F, Li F, Sun W, Chen E, Pan J, Li C, et al. COVID-19 Transmission Dynamics Among Close Contacts of Index Patients With COVID-19: A Population-Based Cohort Study in Zhejiang Province. China JAMA Intern Med. 2021;181:1343–50.

Article  CAS  PubMed  Google Scholar 

Khanh NC, Thai PQ, Quach HL, Thi NH, Dinh PC, Duong TN, Mai LTQ, Nghia ND, Tu TA, Quang N, et al. Transmission of SARS-CoV 2 During Long-Haul Flight. Emerg Infect Dis. 2020;26:2617–24.

Letizia AG, Ramos I, Obla A, Goforth C, Weir DL, Ge Y, Bamman MM, Dutta J, Ellis E, Estrella L, et al. SARS-CoV-2 Transmission among Marine Recruits during Quarantine. The New Engl J Med. 2020;383:2407–16.

Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. 2022;603:679–86.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kemp SA, Collier DA, Datir RP, Ferreira I, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2021;592:277–82.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, Ellaby N, Gallagher E, Groves N, Jackson B, et al. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. 2022.

Google Scholar 

Ison MG, Gubareva LV, Atmar RL, Treanor J, Hayden FG. Recovery of drug-resistant influenza virus from immunocompromised patients: a case series. J Infect Dis. 2006;193:760–4.

Article  CAS  PubMed  Google Scholar 

Walter KS, Kim E, Verma R, Altamirano J, Leary S, Carrington YJ, Jagannathan P, Singh U, Holubar M, Subramanian A, et al. Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference. Open Forum Infect Dis. 2023;10:ofad001.

Article  PubMed  PubMed Central  Google Scholar 

Lovestad AH, Jorgensen SB, Handal N, Ambur OH, Aamot HV. Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole-genome sequencing. J Hosp Infect. 2021;111:107–16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang PY, Wu TS, Cheng CW, Chen CJ, Huang CG, Tsao KC, Lin CS, Chung TY, Lai CC, Yang CT, et al. A hospital cluster of COVID-19 associated with a SARS-CoV-2 superspreading event. J Microbiol Immunol Infect. 2022;55:436–44.

Article  CAS  PubMed  Google Scholar 

Mele-Casas M, Launes C, de Sevilla MF, Hernandez-Garcia M, Pons-Tomas G, Bassat Q, Fumado V, Fortuny C, Garcia-Miquel A, Bonet-Carne E, et al. Low transmission of SARS-CoV-2 derived from children in family clusters: An observational study of family households in the Barcelona Metropolitan Area. Spain PLoS One. 2022;17:e0277754.

Article  CAS  PubMed  Google Scholar 

Li C, Ji F, Wang L, Wang L, Hao J, Dai M, Liu Y, Pan X, Fu J, Li L, et al. Asymptomatic and Human-to-Human Transmission of SARS-CoV-2 in a 2-Family Cluster, Xuzhou. China Emerg Infect Dis. 2020;26:1626–8.

Article  CAS  PubMed  Google Scholar 

Bendall EE, Paz-Bailey G, Santiago GA, Porucznik CA, Stanford JB, Stockwell MS, Duque J, Jeddy Z, Veguilla V, Major C, et al. SARS-CoV-2 Genomic Diversity in Households Highlights the Challenges of Sequence-Based Transmission Inference. mSphere. 2022;7:e0040022.

Article  PubMed  Google Scholar 

Hare D, Gonzalez G, Dean J, McDonnell K, Carr MJ, De Gascun CF. Genomic epidemiological analysis of SARS-CoV-2 household transmission. Access Microbiol. 2021;3:000252.

Article  CAS  PubMed  PubMed Central  Google Scholar 

De Marco C, Marascio N, Veneziano C, Biamonte F, Trecarichi EM, Santamaria G, Leviyang S, Liberto MC, Mazzitelli M, Quirino A, et al. Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Infect Genet Evol. 2022;99:105253.

Article  PubMed  PubMed Central  Google Scholar 

Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, Greninger AL, Bloom JD. Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat. Virus Evol. 2022;8:veac052.

Article  PubMed

留言 (0)

沒有登入
gif