Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines
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Abstract
The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021–January 2022, while other Omicron lineages, including BA.2, accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only the BA.2 lineage underwent sustained transmission in the country, with an estimated emergence around 18 November 2021 (95 per cent highest posterior density: 6–28 November), while despite multiple introductions, BA.1 transmission remained limited. These results suggest that the Philippines was one of the earliest areas affected by BA.2 and reiterate the importance of whole genome sequencing for monitoring outbreaks.
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SciScore for 10.1101/2022.05.30.22275783: (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 Sequence data preparation: To compile all available genomic data from the Philippines and fit the domestic isolates in the context of global virus transmission, all SARS-CoV-2 sequences and metadata were downloaded from GISAID on February 15th, 2022 (EpiCoV, https://www.gisaid.org). https://www.gisaid.orgsuggested: (GISAID, RRID:SCR_018279)A time-scaled phylogeny was inferred using BEAST v10.4 (Suchard et al. 2018) facilitated by the BEAGLE library v3.1 for better computational performance (Ayres et al. 2019). BEASTsuggested: (BEAST, RRID:SCR_010228)Statistical correlation between … SciScore for 10.1101/2022.05.30.22275783: (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 Sequence data preparation: To compile all available genomic data from the Philippines and fit the domestic isolates in the context of global virus transmission, all SARS-CoV-2 sequences and metadata were downloaded from GISAID on February 15th, 2022 (EpiCoV, https://www.gisaid.org). https://www.gisaid.orgsuggested: (GISAID, RRID:SCR_018279)A time-scaled phylogeny was inferred using BEAST v10.4 (Suchard et al. 2018) facilitated by the BEAGLE library v3.1 for better computational performance (Ayres et al. 2019). BEASTsuggested: (BEAST, RRID:SCR_010228)Statistical correlation between locations of isolation and the phylogeny was detected by BaTS v0.9 with 1000 posterior trees subsampled from the MCMC process (Parker et al. 2008). BaTSsuggested: NoneResults from OddPub: Thank you for sharing your code.
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.
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