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

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.

Keywords: Philippines; SARS-CoV-2; genomic epidemiology.

Figure 1.

SARS-CoV-2 infections during the Omicron variant epidemic wave in the Philippines. (A) Total numbers of cases reported (bar chart) in the country and numbers of cases identified from ROFs (line) based on the case information data from the Department of Health, Philippines. (B) Proportions of variant sequences among available SARS-CoV-2 sequences as of 15 February 2022. The classification was based on the software Pangolin version 2022-02-02. (C) Numbers of available Omicron lineage sequences as of 15 February 2022. Numbers below 100 are annotated (coloured by lineage) above the bars. The BA.1 and BA.2 categories here contain the descending lineages assigned by Pangolin, e.g. BA.1 includes the BA.1.1 lineage. X-axis labels indicate the epidemiological week defined by the US-CDC (Centers for Disease Control), which corresponds to the ISO (International Organization for Standardization) week starting on Sunday.

Figure 2.

Phylogenetic relationship of SARS-CoV-2 Omicron variants isolated in the Philippines. (A) Time-scaled tree was inferred by TreeTime using Omicron variant genome sequences isolated in the Philippines and from the global database. The blue and orange tips indicate the BA.1 and BA.2 lineage viruses, respectively, isolated in the Philippines, whereas the white tips indicate the viruses isolated in the other countries. Long branches descending from the common ancestor of BA.1 and BA.2 are shortened. (B) Average genetic divergence of viruses isolated in the Philippines. Error bars represent 95 per cent bootstrap percentiles. (C) Distribution of time intervals from tMRCA to the isolation time. The time intervals were calculated based on pairs of Philippine taxa on the time-scaled tree (A); for each pair, the larger time difference was recorded.

Figure 3.

Introduction of the BA.2 lineage in the Philippines. The time-scaled tree was inferred by BEAST using BA.2 genomes isolated in the Philippines along with the genomes of early global BA.2 viruses. The estimated tMRCAs with 95 per cent HPD illustrated by the grey area are aligned with the phylogenetic tree. Tips are coloured according to the location of isolation. Red shades for viruses isolated in the Philippines indicate the three island groups in the country.