Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota
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Abstract
SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two variants, Alpha and Iota, by integrating genomic surveillance data to estimate the effective reproduction number (R t ) of the variants. We use Connecticut, United States, in which Alpha and Iota co-circulated in 2021. We find that the R t of these variants were up to 50% larger than that of other variants. We then use phylogeography to show that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of Alpha were larger than those resulting from Iota introductions. By monitoring the dynamics of individual variants throughout our study period, we demonstrate the importance of routine surveillance in the response to COVID-19.
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SciScore for 10.1101/2021.07.01.21259859: (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
Software and Algorithms Sentences Resources Ethics: Yale University: The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599). Human Research Protection Programsuggested: NoneWe visualized these data using Prism v. Prismsuggested: (PRISM, RRID:SCR_005375)Using BWA-MEM v. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)We have previously shown that temporal estimates inferred … SciScore for 10.1101/2021.07.01.21259859: (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
Software and Algorithms Sentences Resources Ethics: Yale University: The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599). Human Research Protection Programsuggested: NoneWe visualized these data using Prism v. Prismsuggested: (PRISM, RRID:SCR_005375)Using BWA-MEM v. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)We have previously shown that temporal estimates inferred using TreeTime agree with those inferred from BEAST for B.1.1.710, and we assumed this would also be the case for B.1.526*. BEASTsuggested: (BEAST, RRID:SCR_010228)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 were some limitations to the epidemiological findings we have presented. First, we were not able to directly measure the secondary attack rates of individuals infected with B.1.1.7 or one of the B.1.526* sublineages. Collecting this information requires extensive contact tracing and sequencing of all secondary infections that are not available in Connecticut. Instead, we assumed that biases introduced by the method we employed in this study would be systematic across SARS-CoV-2 lineages so that estimates of the relative transmissibility of B.1.1.7 and B.1.526* would be unaffected. Second, we used a small subset of publicly available SARS-CoV-2 genomes for our phylodynamic analyses to make them computationally tractable. Incorporating a small proportion of available data into our analyses may have introduced biases, but by demonstrating the reproducibility of our findings with independent replicates (Supplemental Fig. 3), we substantially mitigated this issue. Finally, the scope of our study was limited to Connecticut and, in some cases, New York City, which may impinge upon the generalizability of our findings. However, our objective was to directly compare the fitness of B.1.1.7 and B.1.526*, and Connecticut is one of few locations with a robust genomic surveillance infrastructure where these variants emerged concurrently. Here, we present a framework that uses genomic data to estimate the effective reproduction number of individual virus lineages as a measure of relat...
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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