Pinoy scientists trace COVID-19 source in PH via genome sequencing; virus mutation seen

Kristine Sabillo, ABS-CBN News

Posted at Jul 31 2020 05:57 PM | Updated as of Jul 31 2020 07:10 PM

A medical personnel wears a new pair of gloves during the mega swabbing of Grab driver-partners and deliver riders event at the Quezon Memorial Circle on July 30, 2020. George Calvelo, ABS-CBN


MANILA — Filipino scientists are now trying to trace the source of coronavirus disease (COVID-19) in the country, in a bid to get a clearer picture of the outbreak.

Through gene or genome sequencing, a process of decoding the genomes that make up an organism’s DNA or RNA, types of nucleic acid that store genetic information, scientists can determine the dominant COVID-19 strain. 

Dr. Cynthia Saloma, executive director of the Philippine Genome Center (PGC) in the University of the Philippines, told ABS-CBN News that since the start of the outbreak, they have been sequencing samples from hundreds of patients.

Of the samples they sequenced, they were able to complete 6 whole genome sequences, which they submitted to the GISAID, which is the main source of genomic data on SARS-CoV-2 and other viruses. Alongside the Research Institute for Tropical Medicine’s 7 whole genome sequences, the Philippines was able to submit 13 in total.

After several tests, scientists determined that nearly half of the completed genome sequences had virus DNA similar to those seen in Diamond Princess, a cruise ship forced to dock in Japan in February after more than 700 of its passengers contracted COVID-19.

“Yung sampling namin is very small but out of the 13 marami talaga Diamond Princess. At least 6 siguro. And sa Shanghai not so many. Sa palagay ko meron ding Europe doon,” she said when asked about the source of the virus.

(Our sampling is very small but out of the 13, many are from the Diamond Princess. At least 6. And those from Shanghai are not so many. I think there were also some from Europe.)

Saloma explained that certain mutations in the gene sequence allow them to identify the source country of a specific strain of the virus. She said they were also able to identify certain variations in the gene sequence that only patients in the Philippines shared.

She added that the patients they tested in March who were infected with the virus strain that is similar to those from the Diamond Princess cruise ship did not have any recent travel history, which meant they contracted COVID-19 in their community.

While more than 400 Filipino crew members were repatriated to the Philippines, they were tested in Japan and even underwent another 14-day quarantine in New Clark City. Only two tested positive during the quarantine.

It is still unclear how the virus from Diamond Princess could have spread in other parts of the Philippines although the World Health Organization said then that the additional quarantine period for the repatriates was a “good decision” since “the disease may develop (later on).”

Saloma said that based on the gene sequence of the samples, the strain from the Diamond Princess originated in China, reached Japan, then the Philippines and India — countries where many crew members of the ship are from. 

The PGC is now hoping to get additional funding from the Department of Science and Technology to expand their gene sequencing efforts to see the "virus diversity" and to determine how the virus evolved locally.

“We wanted to test and to sequence both the archived and luma na ba (old samples). At nagci-cirulate pa around the Philippines (And those still circulating around the Philippines),” she said. 

DOMINANT STRAIN AND MUTATION

Scientists also saw a pattern from the July samples they sequenced, somehow confirming studies that D614G, or simply known as “G,” a new variant of a single amino acid in the virus’ spike area, has become more common. 

“We are able to test for example na sa July ang karamihan sa samples na nasequence ay yung D614G na mutation,” Saloma said.

(We were able to test in July and most of the samples we tested had the D614G mutation.)

Reports claim that the G variant has “dominated” the COVID-19 outbreak in Chicago and other parts of the world.

Saloma explained a mutation was not always a bad thing; it can be harmless or even make a virus less infectious.

“Meron naman lumalabas while it is infectious it does not make your hospital stay longer. Hindi naman associated with severity,” she said. 

(There are studies saying that while it is infectious, it does not make your hospital stay longer. It is not associated with severity.)

Saloma also warned that the dominance of the G variant may also be because of “submission bias” because particular countries are flooding data banks with their sequences.

“We want to see if that is the case,” she said.

EFFECT ON VACCINES

Gene sequencing was how scientists in China identified the SARS-CoV-2. And their release of its genetic sequence allowed the rest of the world to develop their own test kits.

With the continued spread of COVID-19 — 17 million people infected worldwide, there is increasing interest in the insights that gene sequencing can give.

Public health expert Dr. Susan Mercado told ABS-CBN News on Tuesday that to survive, viruses mutate or evolve. And it is important to see if a virus is mutating to ensure that the vaccines being developed are still effective.

“Kasi kung ang gagamitin mong strain ay nagbago at gumawa kayo ng bakuna para sa isang strain lamang, hindi natin matitiyak kung ang bakuna ay magiging epektibo sa isang strain,” she said.

(Because if you made a vaccine based on one strain only and that strain mutated, we cannot be sure if the vaccine can still be effective for another strain.)

Saloma said many of the vaccines were developed based on the genetic sequence of SARS-CoV-2’s spike region so many are monitoring if there will be mutations there.

GENE SEQUENCING FOR DIAGNOSTICS

Besides additional funding for their research, Saloma said they are hoping that the Philippine government will soon consider using gene sequencing to diagnose individuals if they have COVID-19.

She said there are now machines that can run tests that are competitive in price with the polymerase chain reaction (PCR) tests, which the DOH considers the gold standard for COVID-19 testing.

For almost the same price, she said they can test a person and learn where the virus strain comes from.

“That would be very very informative to epidemiologists pati sa mga nagcocontact tracing. Ma-compare mo pa ang sequence ng mag-neighbor sa isang community,” she said.

(That would be very very informative for epidemiologists and those who do contact tracing. You can even compare the gene sequence of neighbors in a community.)