Genomic analysis of the SARS-CoV-2 variants circulated in the Philippines, 2020-2024

Abstract

Purpose: Genomic sequencing has been an invaluable tool to determine the evolution of SARS-CoV-2. In the present study, we provided a comprehensive description of the SARS-CoV-2 variants circulated in the Philippines.

Methods: The dataset from the human COVID-19 infections was acquired by downloading the sequences and their associated metadata spanning from March 2020 to April 2024. Then, we executed several filtering criteria to acquire the final dataset for the Philippine samples and performed spatial distribution analysis and phylogenetic tree construction of the reported SARS-CoV-2 sequences.

Results: A total of 16,679,203 SARS-CoV sequences were obtained, of which 17,393 (0.10 %) were sampled in the Philippines. Western Visayas reported the highest SARS-CoV-2 sequences (21.33 %), while the Bangsamoro Autonomous Region in Muslim Mindanao reported the least (0.48 %). The phylogenetic tree revealed the evolution of the detected SARS-CoV-2 variants circulating in the Philippines with 19 A as the first reported case (based on the GISAID submission), and 24 A (JN.1) as the currently circulating variant. Omicron variants have dominated the Philippines with 21 L (Omicron, BA.2) having 5102 cases (29.33 %), followed by 22B (BA.5) having 2184 cases (12.57 %). Using Pearson's Chi-square test of independence, we showed that there is a significant association between the age-groups and gender with the detection years.

Conclusion: Altogether, this analysis showed the updated epidemiological trends of the reported SARS-CoV-2 variants in the Philippines. This increases the importance of conducting surveillance on viral infectious diseases such as COVID-19 to provide the scope and trajectory of viral spread in a country.

Keywords: COVID-19; Epidemiology; Philippines; SARS-CoV-2 variants.

Fig. 1

Spatial distribution of SARS-CoV-2 sequences in the Philippines.

Fig. 2

Maximum-likelihood phylogenetic tree based on the complete genome of Philippine SARS-CoV-2 sequences with their emergence date. The red squares represent the bootstrap values at each node present in some branch at >95 %. The distance scale of this phylogenetic tree is 0.0005. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)