Intra-Host Evolution Provides for the Continuous Emergence of SARS-CoV-2 Variants
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Abstract
New SARS-CoV-2 variants can potentially disrupt ongoing public health measures and vaccine efforts. Still, little is known regarding how frequently new viral variants emerge and under what circumstances.
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SciScore for 10.1101/2021.05.08.21256775: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
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: We detected the following sentences addressing limitations in the study:There are limitations to this study. First, it is a single center study biased towards patients with severe clinical disease rather than a population-based sample. This contrasts with the majority of SARS-CoV-2 infected persons, who do not require hospitalization. Second, many participants did not have enough viral RNA at time points …
SciScore for 10.1101/2021.05.08.21256775: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
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: We detected the following sentences addressing limitations in the study:There are limitations to this study. First, it is a single center study biased towards patients with severe clinical disease rather than a population-based sample. This contrasts with the majority of SARS-CoV-2 infected persons, who do not require hospitalization. Second, many participants did not have enough viral RNA at time points subsequent to baseline for NGS to yield complete genome coverage. This was expected as in most cases, viral RNA is detectable by swab of the nasopharyngeal cavity (NP-swab) 2-3 days before onset of symptoms (pre-symptomatic), but rapidly disappears within 5 days after clinical symptom onset17,33-36. The genome copy numbers reported here are consistent with a report of 35 RT-QPCR positive specimens that were collected at >10 days after symptom onset, and that failed to yield infectious virus upon culture 25,37,38. Control experiments established that complete genome coverage and confident SNV detection was possible down to a limit of 7 pfu/ml; however, it is possible that persistent intra-host replication predominanty leads to the accumulation of fragmented viral genomes or debilitated viral particles with low transmission potential as the intra-host selection pressures differ from the selection pressures that lead to increased transmissibility between hosts. In sum, this study suggests that widely divergent SARS-CoV-2 variants, including VOC, will continually emerge spontaneously as long as there is significant community infection (often stipulat...
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.
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