Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines

Li, Y.-T. et al. (2022) Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines. Virus Evolution, 8(2), veac078. (doi: 10.1093/ve/veac078) (PMID:36090771) (PMCID:PMC9452094)

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Abstract

The Omicron SARS-CoV-2 variant led to a dramatic global epidemic wave following detection in South Africa in November, 2021. The Omicron lineage BA.1 was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, whilst 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 lineage BA.2 underwent sustained transmission in the country, with an estimated emergence around November 18th, 2021 [95% highest posterior density: November 6-28th], whilst despite multiple introductions BA.1 transmission remained limited. These results suggest the Philippines was one of the earliest areas affected by BA.2, and reiterate the importance of whole-genome sequencing for monitoring outbreaks.

Item Type:Articles
Additional Information:The work is supported by the UK Research and Innovation Global effort on COVID-19 (MR/V035444/1) and Wellcome (207569/Z/17/Z). JH is funded by the Medical Research Council (MC_UU_12014/12).
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Daldry, Mr Simon and Brunker, Dr Kirstyn and Hughes, Dr Joseph and Hampson, Professor Katie and Li, Mr Yao-Tsun
Authors: Li, Y.-T., Polotan, F. G. M., Sotelo, G. I. S., Alpino, A. P. A., Dolor, A. Y. M., Tujan, M. A. A., Gomez, M. R. R., Onza, O. J. T., Chang, A. K. T., Bautista, C. T., Carandang, J. C., Yangzon, M. S. L., Pangilinan, E. A. R., Mantaring, R. J. Q., Telles, A. J. E., Egana, J. M. C., Endozo, J. J. S., Cruz, R. P. S., Tablizo, F. A., Yap, J. M. C., Maralit, B. A., Ayes, M. E. C., de la Paz, E. M. C., Saloma, C. P., Lim, D. R., Dancel, L. L. M., Uy-Lumandas, M., Medado, I. A. P., Dizon, T. J. R., Hampson, K., Daldry, S., Hughes, J., and Brunker, K.
College/School:College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
Journal Name:Virus Evolution
Publisher:Oxford University Press
ISSN:2057-1577
ISSN (Online):2057-1577
Published Online:19 August 2022
Copyright Holders:Copyright © 2022 The Authors
First Published:First published in Virus Evolution 8(2): veac078
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
312279Implementing genomic surveillance to support SARS-CoV-2 control and mitigation strategies in the PhilippinesKirstyn BrunkerMedical Research Council (MRC)MR/V035444/1Institute of Biodiversity, Animal Health and Comparative Medicine
301620The Science of Rabies EliminationKatie HampsonWellcome Trust (WELLCOTR)207569/Z/17/ZInstitute of Biodiversity, Animal Health and Comparative Medicine