Gene sequencing of COVID-19 samples in PH show different ‘lineages’ from China, other countries

Kristine Sabillo, ABS-CBN News

Posted at Aug 19 2020 04:26 PM

MANILA — The Research Institute for Tropical Medicine (RITM) on Wednesday said that its initial study of samples of SARS-CoV-2, the virus that causes COVID-19, showed that that there are different “lineages” of the virus currently spreading in the country.

In a statement, the RITM said there were multiple strains of the virus causing the disease in the Philippines, including those that trace their origins back to China, where the pandemic began, other countries in Asia Pacific, and parts of Europe and North America.

“The viral genomes that have been sequenced so far by RITM and PGC (Philippine Genome Center) represent a very small picture of SARS-CoV-2 transmission in the country. The sequencing results, however, suggest that from January to July 2020, there were multiple introductions of different SARS-CoV-2 lineages and strains in the country,” the RITM said in a media release.

Gene or genome sequencing is a process of decoding the genomes that make up an organism’s DNA or RNA, types of nucleic acid that store genetic information. Sequencing enabled scientists to identify the SARS-CoV-2. It is also being used to monitor different mutations of the virus.

Back in July, the PGC revealed to ABS-CBN News that a dominant variant of the COVID-19 virus was detected in the Philippines, although scientists said more studies need to be done before drawing any conclusion.

According to the RITM, a total of 17 whole genome sequences from the Philippines were shared with the Global Initiative on Sharing All Influenza Data or GISAID Initiative, an open-access database that enables rapid sharing of sequencing data to contribute to the global response to epidemics and pandemics.

A total of five lineages were identified based on these sequences, which were from the months of January, March and June.

RITM said that the five lineages were: A, B, B.1, B.1.1, and B.6. 

“Lineages A and B were the original strains from China. Lineages B.1 and B.1.1 are associated with the outbreaks in Italy and other European countries. Lineage B.6 was also detected in India, UK, North America, Australia, and Singapore,” RITM said.

RITM data showed that the first three cases of COVID-19 in the Philippines — all Chinese tourists — were of Lineage A and B, the original strains from China.

Meanwhile, some COVID-19 patients from the National Capital Region and Laguna who did not have travel history had a variant of the virus that is similar to the lineages that spread in Europe.

“Almost all sequences from samples collected in March belonged to Lineage B.6. Only two of the cases had traveled from Japan and South Korea while the rest of the cases had no recent history of travel outside the country at the time of sample collection,” RITM said.

The RITM explained that among the most recent Philippine samples belong to Lineage B.1.1 and had the so-called dominant D614G mutation that has been linked to increased transmission efficiency. The mutation was also detected in 7 more samples collected in June and July in NCR and Laguna.

Source: RITM

The institute said this is why the country needs to use gene sequencing on more COVID-19 samples in the country to “provide clearer insight as to how the virus is spreading within the local communities, and help health authorities have a better understanding of what mitigation and control measures are necessary.”

“Previous epidemics and pandemics have shown that mutations in pathogen genomes may generate new viral strains that cause more severe disease or to spread more easily from person to person,” it said.

“By limiting the introduction of new strains into the country, we may not only help reduce the spread of infections, but also prevent new potentially, more virulent and/or infectious strains from coming into the country,” the RITM added.

The RITM also said there is a need to strengthen surveillance and control measures at the country’s ports of entry.

It said the ongoing gene sequencing of the RITM is funded by the Department of Health and is in collaboration with the University of Glasgow.

The DOH also said on Tuesday that while this is new information, “regardless of what variant is causing community transmission, the preventive measures to protect the public against contracting COVID-19 are the same.”

It advised the public to continue wearing face masks, practicing physical distancing and proper hygiene.

As of Wednesday, over 173,000 COVID-19 cases have been recorded in the country, with 2,795 deaths and 113,481.