Genome sequencing for COVID-19 positive samples takes time

MANILA, Philippines — The Department of Health (DOH) explained on Thursday that the process of subjecting COVID-19 positive samples to genome sequencing takes time so that results on whether collected specimens are positive for new variants are not immediately released.

Health Undersecretary Maria Rosario Vergeire said the public should understand that there is a turnaround period between COVID-19 testing, sequencing, and the publishing of the full genome sequencing results.

“Samples are carefully selected to provide the best yield of the sequencing efforts. Thus, not all RT-PCR (reverse transcription-polymerase chain reaction) positive samples qualify for WGS (whole genome sequencing), and it takes about a week to complete WGS,” she said in a statement when asked if the supposedly slow release of genome sequencing results was to blame for the increase in COVID-19 cases being recorded recently.

“Selection alone to see if the RT PCR samples are viable (CT threshold below 30), arranging transportation, and other operational concerns also take time. But we are doing the best we can to facilitate this WGS where it is needed the most,” she added.

Vergeire noted that, after the United Kingdom announced a new variant of concern of the SARS-CoV-2 virus in December, the Philippines began to strengthen its entire genome sequence at the beginning of January.

She reiterated that while variants may contribute or aggravate a case increase, it is the practice or non-practice of minimum public health standards that determines whether people are at risk of being infected with the virus.

READ: Increase of COVID-19 cases also due to non-compliance with health protocols — DOH

The DOH reported on Thursday 3,749 new cases of COVID-19, bringing the total number of coronavirus cases in the Philippines to 47,769. The total number of coronavirus cases in the country, which cover active cases, recoveries, and deaths, is now at 607,048.

So far, the 3,749 fresh cases are the highest number of additional COVID-19 infections that breached the 3,000-mark this year. The DOH again started reporting over 3,000 new coronavirus cases per day last March 5, although it reported over 2,000 cases on Tuesday and Wednesday.

The country has so far detected a total of 118 cases of the B.1.1.7 variant from the United Kingdom and 58 cases of the B.1.351 variant from South Africa.

READ: Metro Manila has highest number of COVID-19 variant cases in PH

According to DOH, the UK variant demonstrated higher transmissibility, while the pattern of mutations for the South African variant “suggests higher transmissibility and may have an impact on vaccine efficacy.”

Meanwhile, there are also 85 cases of mutations with “potential clinical significance.” These are the N501Y mutation that is linked to increased transmissibility of the virus, and the E484K, which may have a potential effect on vaccines’ efficacy.

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