Thread by @freedman04

[THREAD] P.3 SARS-CoV-2 variant first detected in the Philippines

I've been meaning to tweet about this but I've been staying away from social media for quite sometime now. Since news are catching up, here's a thread to avoid misconceptions on the topic.

1. A preprint describing the initial 33 cases of this variant has already been posted in medRxiv on March 03, 2021. For those who are interested in the more technical aspects of the analysis, here's a link to the preprint:

doi.org/10.1101/2021.0…

2. The first case of this variant was detected in our Feb. 04 sequencing run and we identified several more during the Feb. 11 batch, prompting us to flag the then possibly new virus variant. We have since detected this variant in all subsequent sequencing runs.

3. The variant shares a number of mutations with other variants of concern (B.1.1.7, B.1.351, P.1). These mutations -- E484K, N501Y, P681H -- have been associated with increased transmissibility and immune escape (lower vaccine efficacy).

4. Another mutation, a 3-amino acid deletion in the spike protein positions 141 to 143 was also observed. This is adjacent to a deletion at position 144 seen in B.1.1.7 viruses. Deletions in this region of the spike protein have also been implicated in immune escape mechanisms.

5. Therefore, the combination of mutations observed in this variant, which is different from those of other known variants of concern, warrants further studies to determine their collective effects on rate of viral transmission, disease severity, and vaccine efficacy.

6. This variant was initially classifed as B.1.1.28, the parent lineage of the P.1 variant of concern. However, our analysis revealed that the variant we initially designated as PHL-B.1.1.28 in the preprint forms a separate cluster from other B.1.1.28 and P.1 viruses.

7. This observed clustering provides further evidence that it is indeed an emergent lineage and was recently officially recognized as P.3, an alias of B.1.1.28.3, alluding to its shared ancestry with B.1.1.28 viruses. Note that P.1 is also an alias for B.1.1.28.1.

8. The observed clustering also suggests that the mutations shared by P.1 and P.3 viruses were acquired independently, not P.1 evolving to P.3. This may occur in chronic infections or during continued, uninterrupted transmission that allows the virus to evolve from host to host.

9. Based on current distribution, majority of the P.3 cases were from Central Visayas, with a few cases in NCR and other regions. However, due to non-representative sampling, we cannot determine the extent and frequency of its spread throughout the country as of the moment.

10. Interestingly, the collection dates of the P.3 samples coincide with a period of sharp increase in COVID-19 cases in Central Visayas. Although this surge may be due to increased mobility post holiday, the contribution of the variant to this surge cannot be discounted.

11. As of now, P.3 is not as prevalent as other variants of concern. Only two international cases, 1 from Germany and 1 from Japan (from a Filipino traveller), have been reported so far. However, the mutations seen in P.3 poses potential public health risks.

12. Thus, we recommend that P.3 cases be treated in a manner similar to other variants of concern in terms of quarantine, contact tracing, and other management strategies to curb its spread not only within the country but also globally.

13. Efforts have been initiated to further investigate the P.3 variant, spearheaded by an interdisciplinary team of researchers from various UP units to provide valuable biological, clinical and epidemiological insights to help control this and other future variants. #ParaSaBayan