Virus evolution affected early COVID-19 spread

  1. Derek Corcoran
  2. Mark C. Urban
  3. Jill Wegrzyn
  4. Cory Merow

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Abstract

As the SARS-Cov-2 virus spreads around the world afflicting millions of people, it has undergone divergent genetic mutations. Although most of these mutations are expected to be inconsequential, some mutations in the spike protein structure have been hypothesized to affect the critical stage at which the virus invades human cells, which could affect transmission probability and disease expression. If true, then we expect an increased growth rate of reported COVID-19 cases in regions dominated by viruses with these altered proteins. We modeled early global infection dynamics based on clade assignment along with other demographic and meteorological factors previously found to be important. Clade, but not variant D614G which has been associated with increased viral load, enhanced our ability to describe early COVID-19 growth dynamics. Including clade identity in models significantly improved predictions over earlier work based only on weather and demographic variables. In particular, higher proportions of clade 19A and 19B were negatively correlated with COVID-19 growth rate, whereas higher proportions of 20A and 20C were positively correlated with growth rate. A strong interaction between the prevalence of clade 20C and relative humidity suggests that the impact of clade identity might be more important when coupled with certain weather conditions. In particular, 20C an 20A generate the highest growth rates when coupled with low humidity. Projections based on data through April 2020 suggest that, without intervention, COVID-19 has the potential to grow more quickly in regions dominated by the 20A and 20C clades, including most of South and North America.

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    SciScore for 10.1101/2020.09.29.20202416: (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:
    Some limitations of our study are important to recognize when interpreting the results. First, genomic information remains limited, and although we analyzed 9000+ genomes, sample size issues remain important (6). In particular, the number of cases available for the estimation of the proportion of each clade or variant in a given polity at a particular point in time was sometimes low. The number of cases within a polity ranged from 1 to 110, with a median of 21. However, we performed a sensitivity analysis, removing polities with fewer than five cases, and demonstrated that removing polities with low numbers of samples resulted in qualitatively similar results, with the exception of a flatter response for clade 19B (Figure S5). To further test our analysis, we developed another, sensitivity analysis, we generated 95% multinomial confidence intervals for the clades proportions following (Sison and Glaz 1995) and made 100 replications of analysis selecting randomly for each polity the lower upper or estimate, and generated a new analysis with that. As was the case with the prior sensitivity analysis, the results were very similar with clade 19B again being the only one differing by having a flatter response (Figure S7). A related caveat is that the flexibility of BRTs allows for the possibility of overfitting to potentially idiosyncratic trends in clade prevalence. To address overfitting, we took two steps. First, we used replicated, balanced cross-validation to produce an ensem...

    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.

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  2. Version published to 10.1101/2020.09.29.20202416 on medRxiv