23 SARS-CoV-2 strains circulating in the Philippines

By Angela Betsaida B. Laguipo, BSNReviewed by Aimee MolineuxOct 1 2020

The coronavirus disease (COVID-19) pandemic continues to ravage the globe, with more than 33.88 million cases and more than a million deaths. One of the countries with skyrocketing cases in the past two months is the Philippines, which reported more than 311,000 confirmed cases, the highest in Southeast Asia.

In a new study published on the medRxiv* preprint server, scientists reported coding of complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains in the Philippines.

Antipolo City, Philippines - March 31, 2020: A volunteer stands guard at the entrance of a public market to spray alcohol to hands and ensure the use of face mask during the COVID-19. Image Credit: junpinzon / Shutterstock

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

COVID-19 in the Philippines

The country reports surging COVID-19 cases, spreading across the country since January when the first two cases of the infection were reported.

By March, due to the increasing number of cases, the government imposed an enhanced community quarantine spanning the entire Luzon region. As the months passed by, the National Capital Region (NCR), where Manila is located, has been placed in general community quarantine to allow the reopening of businesses and impose regulations to limit the movement of people in the area.

As most of the country lifted lockdown orders, increasing cases were were reported, prompting the government to implement localized lockdowns in affected areas.  

From the more than 311,000 confirmed cases, 5,504 have died.

The World Health Organization (WHO) reports that as of September 29, of the number of cases reported in the country, 55 percent are male and the most affected group were those between 20 and 29 years old, followed by those who are 30 to 39 years old. These age groups are the working class in the country, making them at a high risk of contracting the virus.

Of the total number of cases, 53 percent of cases were reported in the NCR, followed by the CALABARZON region (17 percent), Central Visayas region (7 percent), and Central Luzon (5 percent). Of the more than 5,000 deaths, 61 percent are males, with the most affected age group aged 60 to 68 years old, followed by those who are more than 70 years old. The NCR also reports the highest number of deaths (49 percent).

The study

A team of researchers at the Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences in Bangkok, Thailand, the University of the Philippines Manila, and V. Luna Medical Center, Armed Forces of the Philippines Health Service Command aimed to determine and isolate the different strains of the ravaging SARS-CoV-2 in the country.

The research team obtained the genome sequences from nasopharyngeal and oropharyngeal swabs from patients who tested positive for COVID-19 between April and July 2020. The patients tested positive for COVID-19 via the reverse transcription-polymerase chain reaction (RT-PCR) test. The team used QIAamp viral RNA Mini kit (Qiagen) to extract the viral RNA and used as a template for amplicon sequencing using ARTIC SARS-CoV-2 V3 primers.

What the study found

The strain details and mutations showed that 20/23 genomes collected between June and July were classified under clade G.R./lineage B.1.1, a major lineage frequently found in Europe and has spread across the globe. Further, two genomes found between July 6 and 7 were placed under clade G.R./lineage B.1.1.28, which were found in Brazil (89 percent), the United Kingdom (8 percent), and China (2 percent).

A single genome was also found and classified under clade O/lineage B.6, a global lineage mostly seen in Singapore and India. The team also reported that none of the sequences in GISAID, which was accessed on August 22 and collected in June, contained the D614G mutation, the most prevalent variant across the globe, and has been tied to higher viral RNA levels and titers of pseudoviruses.

“Mutation analysis showed the presence of the D614G mutation in the spike protein in 22 of 23 genomes,” the authors wrote in the paper.

However, lineage B.1.1 containing the D614G mutation was observed in samples collected in June. The lineages B.6, B.1.1, and B1.1.28 are the ones present in the Philippines, with the latter as the one first reported in the country.

The team also noted that all patients in the study had no history of travel outside the country and contracted the virus in the National Capital Region (NCR), Region 3, and Region 4A. All the patients were infected due to community transmission.

Some of these lineages may have been introduced to the country by travelers or repatriates who came from other countries. Also, the D614G mutation surpasses the original SARS-CoV-2 strain in terms of prevalence across the globe, which may explain the sudden surge of cases in the Philippines.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources