LATEST COVID-19 BIOSURVEILLANCE REPORT

Sequence result release: November 21 - 24, 2022

VARIANT DISTRIBUTION OVER TIME

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

After the observed increase in the number and proportion of the BA.5 sublineage of Omicron since July 2022, the different Omicron subvariants under monitoring flagged by the World Health Organization (WHO) (ie. BA.2.3.20, XBB) have been on a continuous uptrend starting September 2022.

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 November 21-24, 2022

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

WHO labelLineageaCount (Percent to Total)Classification
WHO
As of October 12, 2022
ECDC
As of November 24, 2022
OmicronBA.2.3.203,485 (7.29%)VOC-subvariant under monitoringN/A
OmicronBA.2.7535 (0.07%)VOC-subvariant under monitoringVOI
OmicronBA.4324 (0.68%)BA.4.6 - VOC-subvariant under monitoringVOC
OmicronBA.512,559 (26.28%)VOC-subvariant under monitoringVOC
OmicronBQ.1b16 (0.03%)N/AVOI
OmicronXBB684 (1.43%)VOC-subvariant under monitoringVariant under Monitoring
N/AXBC532 (1.11%)N/ANone

aIncludes all descendant sub-lineages
bBQ.1 is a BA.5 sub-lineage currently reported under BA.5

NOTES (Following WHO definition)

  1. Variant of interest (VOI) - A SARS-COV-2 variant with genetic changes that are predicted or known to alter virus characteristics (ie. transmissibility, disease severity, immune escape, diagnostic or therapeutic escape).
  2. Variant of concern (VOC) - A SARS-CoV-2 variant meeting the definition of a VOI (see 1) with clear evidence available to support significant impact on transmissibility, severity, and/or immune evasion at a degree of global public health significance.
  3. VOC-subvariant under monitoring - A SARS-CoV-2 variant belonging to a currently circulating VOC (according to phylogenetic analysis) showing signals of transmission advantage compared to other circulating VOC lineages and has additional genetic changes known or suspected to confer change in epidemiology or fitness advantage.

At present, of the currently circulating variants, only Omicron and its subvariants have been identified by the WHO as variants of concern (VOC) and under monitoring. Alpha, Beta, Gamma, and Delta variants are now labeled as previously circulating VOCs. Meanwhile, ECDC classifies BA.5 as a VOC, BA.2.75 and BQ.1 (a subvariant of BA.5) as VOIs, and XBB as a variant under monitoring (VUM). To date, there is no VOC among the circulating subvariants in the country as these sub-variants have not yet been assigned their own WHO label and will be tracked under Omicron until sufficient evidence arises, showing that their virus characteristics are significantly different from the VOC they belong to.

 

Table 2. Distribution of recently sequenced and reclassified samples by the University of the Philippines - Philippine Genome Center (UP-PGC) Main, Visayas, and Mindanao, and Southern Philippines Medical Center (SPMC) released last November 21 - 24, 2022.

RegionOmicronXBC*DeltaNo lineage assignedTotal
BA.2.3.20*BA.4*BA.5*XBB*Other Omicron sublineagesTotal
Local3531191332853445366648
18000080019
264031068101382
32300102400125
51300001300114
68802858183107191
7330425163302187
1131791939373382
120010010001
4A2300102420228
4B0001010001
CAR7802308300689
CARAGA0000001001
NCR20007027001138
Incoming International Traveler0020020002
ROF0020020002
Total3531211332853645366650

NOTE: Variants reported above include their own sub-variants 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 650 samples sequenced by the UP-PGC and SPMC last November 21 - 24, 2022: 353 (54.31%) were classified as Omicron BA.2.3.20, one (0.15%) was as BA.4, 21 (3.23%) as BA.5 (including 2 classified as BQ.1, a subvariant of BA.5),  133 (20.46%) as XBB, 45 (6.92%) as XBC, and 28 (4.31%) as other Omicron subvariants. In addition, three (0.46%) were identified as Delta variant cases with collection dates in August 2021. These were samples sequenced during the retrospective sequencing run of SPMC.

All additional BA.2.3.20 cases were local cases from 10 regions, namely Regions 1, 2, 3, 4A, 5, 6, 7, 11, CAR, and NCR. Meanwhile, of the 21 BA.5 cases, 19 were local cases from Regions 2, 6, 7, 11, 12, and CAR, and the remaining two (2) cases were ROFs. Among these, two (2) were local BQ.1 cases coming from Regions 2 and 7. All 133 XBB and 45 XBC cases were local cases coming from Regions 2, 3, 4A, 4B,  6, 7, 11, CAR, CARAGA, and NCR.

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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 10 November 2022

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