SARS-CoV-2 variants in the making: Sequential intrahost evolution and forward transmissions in the context of persistent infections
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, to our knowledge, no direct evidence of subsequent transmission and stepwise adaptation is available.
Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins.
Our findings demonstrate that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome during persistent infection in more than one host, and also document ongoing transmission of these novel variants. There is an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.
Article activity feed
-
-
SciScore for 10.1101/2022.05.25.22275533: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: The Mount Sinai Pathogen Surveillance Program (MS-PSP): Residual nasopharyngeal and anterior nares (AN) swab specimens were collected after completion of the diagnostic process, as part of the Mount Sinai Pathogen Surveillance Program (IRB approved HS#13-00981). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Molecular SARS-CoV-2 diagnostics: SARS-CoV-2 molecular diagnostic testing was performed in the Molecular Microbiology Laboratories of the MSHS Clinical Laboratory by nucleic acid amplification tests (NAAT) that have been validated for nasopharyngeal, anterior … SciScore for 10.1101/2022.05.25.22275533: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: The Mount Sinai Pathogen Surveillance Program (MS-PSP): Residual nasopharyngeal and anterior nares (AN) swab specimens were collected after completion of the diagnostic process, as part of the Mount Sinai Pathogen Surveillance Program (IRB approved HS#13-00981). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Molecular SARS-CoV-2 diagnostics: SARS-CoV-2 molecular diagnostic testing was performed in the Molecular Microbiology Laboratories of the MSHS Clinical Laboratory by nucleic acid amplification tests (NAAT) that have been validated for nasopharyngeal, anterior nares swabs and saliva specimens. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Briefly, Vero-E6 cells expressing TMPRSS2 were cultured in Dulbecco’s Modified Eagle Medium containing 10% heat-inactivated fetal bovine serum and 1% Minimum Essential Medium (MEM) Amino Acids Solution, supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, 100 μg/ml normocin, and 3 μg/ml puromycin. Vero-E6suggested: None200ul of viral transport media from the nasopharyngeal or anterior nares swab specimen was added to Vero-E6-TMPRSS2 cells in culture media supplemented with 0.5 μg/ml Amphotericin B. Vero-E6-TMPRSS2suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-