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

1.Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182, 1295–1310 (2020).CAS  Article  Google Scholar  2.Baum, A. et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science 369, 1014–1018 (2020).ADS  CAS  Article  Google Scholar  3.Van Egeren, D. et al. Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein. PLOS ONE 16, e0250780 (2021).Article  Google Scholar  4.Abdool Karim, S. S. & de Oliveira, T. New SARS-CoV-2 variants—clinical, public health, and vaccine implications. N. Engl. J. Med. 6, 67 (2021). Google Scholar  5.Davies, N. G. et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science https://doi.org/10.1126/science.abg3055 (2021).Article  PubMed  PubMed Central  Google Scholar  6.Tada, T. et al. Decreased neutralization of SARS-CoV-2 global variants by therapeutic anti-spike protein monoclonal antibodies. bioRxiv https://doi.org/10.1101/2021.02.18.431897 (2021).Article  PubMed  PubMed Central  Google Scholar  7.Tegally, H. et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv https://doi.org/10.1101/2020.12.21.20248640 (2020).Article  PubMed  PubMed Central  Google Scholar  8.Sabino, E. C. et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. The Lancet 397, 452–455 (2021).CAS  Article  Google Scholar  9.Kemp, S. A. et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature https://doi.org/10.1038/s41586-021-03291-y (2021).Article  PubMed  PubMed Central  Google Scholar  10.Choi, B. et al. Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host. N. Engl. J. Med. 383, 2291–2293 (2020).Article  Google Scholar  11.Valesano, A. L. et al. Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts. bioRxiv https://doi.org/10.1101/2021.01.19.427330 (2021).Article  PubMed  PubMed Central  Google Scholar  12.Baang, J. H. et al. Prolonged severe acute respiratory syndrome coronavirus 2 replication in an immunocompromised patient. J. Infect. Dis. 223, 23–27 (2021).CAS  Article  Google Scholar  13.Truong, T. T. et al. Persistent SARS-CoV-2 infection and increasing viral variants in children and young adults with impaired humoral immunity. medRxiv https://doi.org/10.1101/2021.02.27.21252099 (2021).Article  PubMed  PubMed Central  Google Scholar  14.Avanzato, V. A. et al. Case study: Prolonged infectious SARS-CoV-2 Shedding from an asymptomatic immunocompromised individual with cancer. Cell 183, 1901-1912.e9 (2020).CAS  Article  Google Scholar  15.Rueca, M. et al. Compartmentalized replication of SARS-Cov-2 in upper vs. lower respiratory tract assessed by whole genome quasispecies analysis. Microorganisms 8, 66 (2020).Article  Google Scholar  16.Ramazzotti, D. et al. VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns 2, 100212 (2021).Article  Google Scholar  17.Jary, A. et al. Evolution of viral quasispecies during SARS-CoV-2 infection. Clin. Microbiol. Infect. https://doi.org/10.1016/j.cmi.2020.07.032 (2020).Article  PubMed  PubMed Central  Google Scholar  18.Capobianchi, M. R. et al. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy. Clin. Microbiol. Infect. 26, 954–956 (2020).CAS  Article  Google Scholar  19.Armero, A., Berthet, N. & Avarre, J.-C. Intra-host diversity of SARS-Cov-2 should not be neglected: Case of the state of Victoria, Australia. Viruses 13, 133 (2021).CAS  Article  Google Scholar  20.Xu, Y. et al. Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence. J. Genet. Genomics 47, 610–617 (2020).Article  Google Scholar  21.Popa, A. et al. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Sci. Transl. Med. 12, 66 (2020).Article  Google Scholar  22.Lythgoe, K. A. et al. SARS-CoV-2 within-host diversity and transmission. Science https://doi.org/10.1126/science.abg0821 (2021).Article  PubMed  PubMed Central  Google Scholar  23.Pfefferle, S. et al. SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany. Clin. Microbiol. Infect. 27(130), e5-130.e8 (2021). Google Scholar  24.James, S. E. et al. High resolution analysis of transmission dynamics of Sars-Cov-2 in two major hospital outbreaks in South Africa leveraging intrahost diversity. medRxiv https://doi.org/10.1101/2020.11.15.20231993 (2020).Article  PubMed  PubMed Central  Google Scholar  25.Shen, Z. et al. Genomic diversity of severe acute respiratory syndrome-coronavirus 2 in patients with coronavirus disease 2019. Clin. Infect. Dis. 71, 713–720 (2020).CAS  Article  Google Scholar  26.Wang, D. et al. Population bottlenecks and intra-host evolution during human-to-human transmission of SARS-CoV-2. Front. Med. 8, 66 (2021).ADS  CAS  Google Scholar  27.Goyal, A., Reeves, D. & Schiffer, J. T. Early super-spreader events are a likely determinant of novel SARS-CoV-2 variant predominance. medRxiv https://doi.org/10.1101/2021.03.23.21254185 (2021).Article  PubMed  PubMed Central  Google Scholar  28.Wölfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020).ADS  Article  Google Scholar  29.Focosi, D. & Maggi, F. Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. Rev. Med. Virol. https://doi.org/10.1002/rmv.2231 (2021).Article  PubMed  PubMed Central  Google Scholar  30.Grint, D. J. et al. Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February. Euro Surveill 26, 66 (2021).Article  Google Scholar  31.Grabowski, F., Preibisch, G., Giziński, S., Kochańczyk, M. & Lipniacki, T. SARS-CoV-2 variant of concern 202012/01 has about twofold replicative advantage and acquires concerning mutations. Viruses 13, 66 (2021).Article  Google Scholar  32.Cele, S. et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature https://doi.org/10.1038/s41586-021-03471-w (2021).Article  PubMed  Google Scholar  33.Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7.. bioRxiv https://doi.org/10.1101/2021.01.25.428137 (2021).Article  PubMed  PubMed Central  Google Scholar  34.Widera, M. et al. Bamlanivimab does not neutralize two SARS-CoV-2 variants carrying E484K in vitro. medRxiv https://doi.org/10.1101/2021.02.24.21252372 (2021).Article  Google Scholar  35.Shen, X. et al. Neutralization of SARS-CoV-2 variants B.1.429 and B.1.351. N. Engl. J. Med. 6, 66 (2021). Google Scholar  36.Garcia-Beltran, W. F. et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. medRxiv https://doi.org/10.1101/2021.02.14.21251704 (2021).Article  PubMed  PubMed Central  Google Scholar  37.Madhi, S. A. et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 vaccine against the B.1.351 variant. N. Engl. J. Med. 6, 66 (2021). Google Scholar  38.Kissler, S. M. et al. Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2. medRxiv https://doi.org/10.1101/2021.02.16.21251535 (2021).Article  PubMed  PubMed Central  Google Scholar  39.Domingo, E. & Perales, C. Viral quasispecies. PLoS Genet 15, e1008271 (2019).CAS  Article  Google Scholar  40.CDC. COVID-19 Quarantine and Isolation. Centers for Disease Control and Prevention https://www.cdc.gov/coronavirus/2019-ncov/your-health/quarantine-isolation.html (2021).41.CDC. Ending Isolation and Precautions for People with COVID-19: Interim Guidance. Centers for Disease Control and Prevention https://www.cdc.gov/coronavirus/2019-ncov/hcp/duration-isolation.html (2021).42.Marks, M. et al. Transmission of COVID-19 in 282 clusters in Catalonia, Spain: A cohort study. Lancet Infect. Dis. 6, 66 (2021). Google Scholar  43.CDC. COVID-19 and Your Health. Centers for Disease Control and Prevention https://www.cdc.gov/coronavirus/2019-ncov/if-you-are-sick/end-home-isolation.html (2020).44.van Kampen, J. J. A. et al. Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19). Nat. Commun. 12, 267 (2021).Article  Google Scholar  45.La Scola, B. et al. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. Eur. J. Clin. Microbiol. Infect. Dis. https://doi.org/10.1007/s10096-020-03913-9 (2020).Article  PubMed  PubMed Central  Google Scholar  46.Rhee, C., Kanjilal, S., Baker, M. & Klompas, M. Duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity: When is it safe to discontinue isolation?. Clin. Infect. Dis. https://doi.org/10.1093/cid/ciaa1249 (2020).Article  PubMed Central  Google Scholar  47.Rodríguez-Grande, C. et al. Inference of active viral replication in cases with sustained positive reverse transcription-PCR results for SARS-CoV-2. J. Clin. Microbiol. 59, 66 (2021).Article  Google Scholar  48.Dimcheff, D. E. et al. SARS-CoV-2 total and subgenomic RNA viral load in hospitalized patients. medRxiv https://doi.org/10.1101/2021.02.25.21252493 (2021).Article  PubMed  PubMed Central  Google Scholar  49.Lavine, J. S., Bjornstad, O. N. & Antia, R. Immunological characteristics govern the transition of COVID-19 to endemicity. Science 371, 741–745 (2021).ADS  CAS  Article  Google Scholar  50.Herbeck, J. T. et al. Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS 26, 193–205 (2012).Article  Google Scholar  51.Watanabe, T. & Kawaoka, Y. Pathogenesis of the 1918 pandemic influenza virus. PLoS Pathog. 7, 66 (2011). Google Scholar  52.Marshall, I. D. & Fenner, F. Studies in the epidemiology of infectious myxomatosis of rabbits. V. Changes in the innate resistance of Australian wild rabbits exposed to myxomatosis. J. Hyg. (Lond.) 56, 288–302 (1958).CAS  Article  Google Scholar  53.Kerr, P. J. et al. Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype. PNAS https://doi.org/10.1073/pnas.1710336114 (2017).Article  PubMed  PubMed Central  Google Scholar  54.Best, S. M. & Kerr, P. J. Coevolution of host and virus: the pathogenesis of virulent and attenuated strains of myxoma virus in resistant and susceptible European rabbits. Virology 267, 36–48 (2000).CAS  Article  Google Scholar  55.Karlin, S. A First Course in Stochastic Processes (Academic Press, 1966).56.Li, Q. et al. Prolonged shedding of severe acute respiratory syndrome coronavirus 2 in patients with COVID-19. Emerg. Microb. Infect. 9, 2571–2577 (2020).CAS  Article  Google Scholar  57.Bar-On, Y. M., Flamholz, A., Phillips, R. & Milo, R. SARS-CoV-2 (COVID-19) by the numbers. eLife 9, 66 (2020).Article  Google Scholar  Page 2 Scientific Reports (Sci Rep) ISSN 2045-2322 (online)
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