Sequence result release: March 6 - 10, 2023

VARIANT DISTRIBUTION OVER TIME

Figure 1. Samples sequenced from the Philippines, collected from June 2022 onwards.

Figure 1 above shows the proportion of variants sequenced by the University of the Philippines - Philippine Genome Center (UP-PGC) Main, Visayas, and Mindanao, Research Institute for Tropical Medicine (RITM), San Lazaro Hospital (SLH), and Southern Philippines Medical Center (SPMC) with collection dates from June 2022 onwards.

After the observed increase in the number and proportion of the BA.5 sub-lineage of Omicron since July 2022, different Omicron subvariants under monitoring that were previously and are currently being flagged by the World Health Organization (WHO) or European Centre for Disease Prevention and Control (ECDC) (ie. BA.2.3.20, XBB) have been on a continuous uptrend starting September 2022. From the month of February onwards, the BA.2.3.20 subvariant was the most detected variant, comprising 46.01% of samples sequenced with assigned lineages, followed by the XBB subvariant (31.90%).

Note that the graph above must be interpreted with caution due to sampling biases brought about by factors such as changes in testing protocols and other logistical issues. Moreover, as we continue sequencing samples, the proportion of each variant may vary over time.

WGS RESULTS releases on March 6 - 10, 2023

Table 1. Cumulative count and percentage of sequenced Omicron subvariants and their respective classification under the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC).

^aIncludes all descendant sub-lineages (e.g. BA.2.75 counts indicated in the table comprise of  all descendent  sub-lineages, including BN.1 and CH.1.1 cases)
^bOmicron-Omicron Recombinant XBF share the same spike as BA.2.75 and is monitored under BA.2.75 lineages by ECDC
^cTotal number of samples with assigned lineages

On 15 March 2023, the World Health Organization (WHO) announced that moving forward, Greek letters will only be assigned to Variants of Concern (VOC), while Variants of Interest (VOI) will be referred to labels using established scientific nomenclature systems (e.g. Pango tool, Nextstrain).

Below are the updated working definitions per variant classification. The full technical report can be found here.

1. Variant of interest (VOI) - A SARS-CoV-2 variant with genetic changes that are predicted or known to affect variant characteristics (e.g. transmissibility, antibody evasion, virulence). Identified to have a growth advantage over other circulating variants in more than one WHO region showing an increasing prevalence and number of cases over time or other epidemiological impacts that suggest an emerging risk to global public health.
2. Variant Under Monitoring (VUM) - A SARS-CoV-2 variant with genetic changes that are suspected to affect virus characteristics and early signals of growth advantage relative to other circulating variants. Epidemiological impact remains unclear and additional monitoring is required to reassess risk of the variant.
3. Variant of Concern (VOC) - Meets the definition of a VOI (see no. 1) and meets at least one of the following criteria, when compared to other variants:

a. Detrimental change in clinical disease severity; OR

b. Change in COVID-19 epidemiology causing substantial impact on the ability of health systems to provide care to COVID-19 patients or other illnesses, thus, requiring major public health interventions; OR

c. Significant decrease in effectiveness of available vaccines in protecting against severe disease.

Meanwhile, as of 3 March 2023, the European Centre for Disease Prevention and Control (ECDC) has de-escalated BA.2, BA.4, and BA.5 from its list of SARS-CoV-2 VOC since these parental lineages are no longer in circulation. Similarly, as of March 9, 2023, two Omicron subvariants, namely BA.2.3.20 and BF.7, have also been de-escalated from the list of variants under monitoring by the ECDC. For tracking purposes, the de-escalated variants (i.e. BA.4, BA.5, BA.2.3.20) will continue to be locally monitored by the Department. Meanwhile, BA.2.75, BQ.1 (a subvariant of BA.5), XBB, and XBB.1.5 (a subvariant of XBB) are still classified as VOIs, and XBC, BN.1 (a subvariant of BA.2.75), and CH.1.1 (a subvariant of BA.2.75) are still classified as VUMs.

Table 2. Distribution of recently sequenced samples by San Lazaro Hospital (SLH), Research Institute for Tropical Medicine (RITM), and the University of the Philippines - Philippine Genome Center (UP-PGC) Main, Visayas, and Mindanao released last March 6 - 10, 2023.

NOTE: Variants reported above include their own subvariants or sub-lineages. Case counts per variant may change over time due to the continuous updates in the PANGO tool (lineage assigning application).

Out of the recent 798 samples sequenced by UP-PGC last March 6 - 10, 2023: 264 (33.08%) were classified as BA.5 (including three BQ.1 cases and one BF.7 case), 259 (32.46%) as BA.2.3.20, 72 (9.02%) as XBB (including ten XBB.1.5 cases), 28 as XBC (3.51%), four (0.50%) as BA.2.75 (including two BN.1 cases and one CH.1.1 case), three (0.38%) as BA.4, and 81 (10.15%) as other Omicron sublineages.

All additional BA.5 cases were local cases from all regions except Region 10 and BARMM while additional BA.2.3.20 cases were from all regions except Region 8. Among recently detected XBB cases, one was classified as a Returning Overseas Filipino (ROF) while the rest were local cases from Regions 1, 3, 4A, 4B, 5, 6, 7, 11, 12, CAR, and NCR. Meanwhile, detected XBC cases were all local cases from Regions 1, 7, 10, 11, and 12. Similarly, all BA.2.75 cases were local cases from Regions 11, CAR, and NCR. Lastly, all additional BA.4 cases were local cases from Regions 4A, 11, and 12.

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Note: For additional references and information on the COVID-19 variants you can access the links below:
European Centre for Disease Control Monitoring:
European Centre for Disease Prevention and Control - SARS-CoV-2 variants of concern as of 9 March 2023

World Health Organization Monitoring:
World Health Organization - Tracking SARS-CoV-2 variants