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.


This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Cite as

Li, Y., Polotan, F., Sotelo, G., Alpino, A., Dolor, A., Tujan, M., Gomez, M., Onza, O., Chang, A., Bautista, C., Carandang, J., Yangzon, M., Pangilinan, E., Mantaring, R., Telles, A., Egana, J., Endozo, J., Cruz, R., Tablizo, F., Yap, J., Maralit, B., Ayes, M., de la Paz, E., Saloma, C., Lim, D., Dancel, L., Uy-Lumandas, M., Medado, I., Dizon, T., Hampson, K., Daldry, S., Hughes, J. & Brunker, K. 2022, 'Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines', Virus Evolution, article no: veac078. https://dx.doi.org/10.1093/ve/veac078

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Last updated: 26 August 2022
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