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

Dialogues in health Pub Date : 2024-09-12 DOI:10.1016/j.dialog.2024.100193

Arnie Dimaano , Kiana Dominique Carreon , Giselle Sophia Camaya , Irvin Rondolo , Jarel Elgin Tolentino

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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.

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2020-2024 年菲律宾流行的 SARS-CoV-2 变种的基因组分析

目的基因组测序是确定 SARS-CoV-2 演变的重要工具。方法通过下载 2020 年 3 月至 2024 年 4 月期间的序列及其相关元数据，获得人类 COVID-19 感染的数据集。结果共获得16,679,203个SARS-CoV序列，其中17,393个（0.10%）在菲律宾采样。西米沙鄢报告的 SARS-CoV-2 序列最多（21.33%），而棉兰老穆斯林邦萨摩洛自治区报告的最少（0.48%）。系统发生树揭示了在菲律宾流行的已检测到的 SARS-CoV-2 变种的演变过程，其中 19 A 是第一个报告的病例（根据 GISAID 提交的资料），24 A（JN.1）是目前流行的变种。欧米克隆变种在菲律宾占主导地位，其中 21 L（欧米克隆，BA.2）有 5102 个病例（占 29.33%），其次是 22B（BA.5），有 2184 个病例（占 12.57%）。通过皮尔逊卡方检验（Pearson's Chi-square test of independence），我们发现年龄组和性别与检测年份之间存在显著关联。这增加了对 COVID-19 等病毒性传染病进行监测的重要性，以提供病毒在一个国家的传播范围和轨迹。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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