DAVAO CITY (MindaNews / 08 August) — At least 30 cases of the highly transmissible Delta variant of SARS-Cov-2, the virus that causes COVID-19, have been reported in three of six regions in Mindanao as of August 6 but like in the first months of detecting COVID-19 in Mindanao last year, detection of the variants is slow as specimens have to be sent to Manila for whole genome sequencing (WGS).
But local government officials are on a proactive mode, already assuming that the Delta variant, first detected in India, is present and spreading in their areas.
“We need to already assume conservatively nga nia na gyud ang Delta variant sa dakbayan” (that the Delta variant is really here in the city), Cagayan de Oro Mayor Oscar Moreno said in his daily virtual presser on Saturday. Cagayan de Oro logged the most number of Delta variant cases among Mindanao’s 33 cities with 21 out of 30.
The city received the results of the WGS in three batches, the first involving five Delta variant cases, the second eight and on August 6, another eight.
Unlike the first two batches when these were confirmed in two barangays and mostly within a family only, the locations of the third batch are “generally scattered,” Moreno said.\
Dr. Rachel Joy Pasion, head of the Department of Health (DOH)-Davao’s Regional Epidemiology Surveillance Unit, told a virtual presser on August 2 that the “Delta variant is really here” and since the cases were found to have no history of travel, “we should consider it a local transmission.”
The DOH central office on August 5 announced 116 additional Delta variant cases (B.1.617.2), three of them in Mindanao: two in the Davao region (Region 11) and one in the Zamboanga Peninsula (Region 9). Earlier, the DOH reported 18 cases in Mindanao.
Nationwide as of August 5, the number of Delta variant cases had reached 331, the DOH central office reported. Out of this number, 21 are in Mindanao but this rose to 30 on August 6 with the report of the City Health Office in Cagayan de Oro of eight more cases and the Ipil COVID-19 Task Force in Zamboanga Sibugay of one case.
Of the 30 Delta variant cases as of August 6 in Mindanao, 22 were detected in Region 10 or Northern Mindanao (21 in Cagayan de Oro City and one in Gingoog City); six in the Davao region (four in Davao City, one in Tagum City and one in Davao del Sur) and two in the Zamboanga Peninsula (one in Zamboanga City and one in Ipil, Zamboanga Sibugay).
From Mindanao to Manila and back
All cases have been reported to have recovered from COVID-19 but found to have tested positive for the Delta variant only when the DOH central office and the UP PGC sent the results of the WGS.
Asked during a virtual presser on August 2 why the variant cases had been reported to have recovered by the time they were announced to have been been stricken with the Delta variant, Dr. Pasion replied that WGS “is a very tedious job to do.”
She explained that it takes the Philippine Genome Center (PGC) at the University of the Philippines campus in Diliman, Quezon City, about two days for validation of the specimen and five to seven days to process. She said there is a one-week turnaround time and that does not include the shipment to Quezon City of the specimens as well as other factors like availability of kits.
The UP PGC processes all specimens from all over the country, Pasion said.
In the early days of COVID-19 last year, swab specimens from Mindanao were sent to the Regional Institute of Tropical Medicine (RITM) in Manila for the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) test. It took a few weeks before the state-run Southern Philippines Medical Center (SPMC) in Davao City became a subnational laboratory where specimens from the Davao region and other parts of Mindanao were sent for RT-PCR testing.
This year, in detecting variants, specimens from Mindanao are sent to UP PGC in Diliman, initially taking about a month before the results are released although the more recent cases have been released in less than a month.
The DOH has been reiterating its PDITR strategies to fight COVID-19. PDITR stands for Prevention, Detection, Isolation, Treatment and Reintegration.
A slow-paced detection of a variant whose transmissibility is fast-paced, affects the other aspects of the PDITR.
Pasion said they are closely monitoring the Delta variant because “it rapidly takes off and spreads between people more efficiently among other variants of concern.”
Dr. Maria Van Kerkhove, lead epidemiologist and COVID-19 technical lead of the World Health Organization had earlier explained that the Delta variant has certain mutations that allow the virus to adhere to human cells more easily and that experts are also seeing a higher viral load in individuals infected.
The Delta variant, which has spread to 132 countries as of July 30, is “dangerous and the most transmissible SARS-CoV-2 virus to date.”
“There are some laboratory studies that suggest that there’s increase replication in some of the modelled human airway systems”, she added.
There is a PGC inside the campus of UP Mindanao in this city which launched its on-site sequencing facility in June to detect cases of variants and Pasion said sending specimens there “can really save us time” and “real time ang results ng UP Mindanao if ever maka–process sila.”
But Pasion said specimens are still sent to PGC in UP Diliman because “only PGC (in Diliman) can do the whole genome sequencing.”
She said PGC Mindanao is still “on a research phase and they said they will notify if nasa final planning na sila for whole genome sequencing for surveillance.”
Pasion said UP Mindanao “partnered with a private agency so they can have this research type of whole genome sequencing but right now kulang pa manpower, kulang pa yung resources (it still lacks manpower and resources).
She said they are “in close coordination” with UP Mindanao as well as SPMC so their laboratories can be capacitated for whole genome sequencing for surveillance in the region.
Pasion assured that they are doing everything “so we can fast-track” the process so that PGC Mindanao can process the specimens in the region and neighboring regions.
On the third week of June, PGC Mindanao received a total of 23 specimens from three COVID-19 laboratories in Mindanao to detect variants — Cotabato Regional and Medical Center in Cotabato City, Davao de Oro Provincial Hospital in Montevista town, and the Department of Health in Northern Mindanao.
Dr. Lyre Anni Murao, a professor of virology at UP Mindanao and concurrent director of PGC Mindanao then said that the genome sequencing at the PGC Mindanao is a pilot project in collaboration with Accessible Genomics, Research Institute for Tropical Medicine (RITM) and University of Glasgow, but is not yet part of the biosurveillance program of the DOH, which is being undertaken by the PGC in Diliman.
She said the collaborative project with RITM and the University of Glasgow “aims to operationalize genomic surveillance and inform responses across the Philippines. The report will serve as a baseline data in Mindanao for SARS-CoV2 variants.”
Murao added that the RITM “will be responsible to relay all information that we get from the study to DOH, and then DOH will be the one to take care of the release of this information.”
Sequencing for research
MindaNews asked Murao on August 4 on the status of PGC Mindanao given the presence of Delta variant cases in Mindanao, but she did not reply to the queries.
Instead, her office sent a press release posted July 19 on the website of UP in Diliman titled “PGC Mindanao engages in a collaborative SARS-COV-2 genomics study using a portable sequencing platform.”
It said PGC Mindanao “partnered with Accessible Genomics, the University of Glasgow, and COVID-19 laboratories in Mindanao to engage in a research project that will investigate the dynamics of SARS-CoV-2 spread in selected hospitals and communities of the region.”
It said viral RNA collected from COVID-19 patients in some laboratories and hospitals in Mindanao “will be sequenced by PGC Mindanao” using the MinION, a portable genetic sequencer donated by Accessible Genomics, which will also serve as “a learning experience for the Center as it prepares to expand its omics facility and services.”
It said results from the sequencing “will solely be used for research purposes to subsequently aid local hospitals and communities in COVID-19 prevention and control.”
According to the press release, the technology has been validated to produce SARS-CoV-2 consensus sequences with the same accuracy as other sequencing platforms and its low start-up cost is an advantage for research laboratories that are just establishing their own sequencing projects.
The DOH, the UP-PGC and UP National Institute of Health have an ongoing bio-surveillance program to detect SARS-CoV-2 variants in the Philippines.
High capital expenditure
The PGC in Diliman uses Illumina NovaSeq 6000 for its 750 weekly sequencing output and NextSeq550 for the 350 sample runs.
“These high throughput sequencing equipment capable of 3,000 Gb and 120 Gb sequencing outputs, respectively, require high capital expenditure for equipment acquisition and consequently high startup and annual maintenance costs. They are suited for large-scale surveillance which is conducted by health agencies in order to inform and guide public health authorities,” the press release said.
It added that the global genomic surveillance of SARS-CoV-2 is used to “monitor the characteristics and movements of the virus, including the emergence of new variants that may spread more easily, cause more severe disease, or may escape from immune recognition” as the information culled “can help guide authorities and researchers to improve public health measures and medical interventions for COVID-19.”
MindaNews asked Murao that if manpower and resources were problems PGC Mindanao was facing, as mentioned by Pasion, “how can the national government or the private sector help you especially now when your services are badly needed?” She sent no reply.
PGC Mindanao was launched in 2019 as a satellite facility of PGC in Diliman, hosted by UP Mindanao, set up through a seed fund worth P40 million state of the art equipment from the Department of Science and Technology-Philippine Council for Health Research and Development.
Preparing for Delta
In Cotabato City, Mayor Cynthia Guiani said the city government has been preparing for the Delta variant even as no case has so far been reported.
In a video message to her constituents on August 1, Guiani said “it is just a matter of time before this deadly variant enters our city.”
Guani said they are “aggressively campaigning for vaccination against COVID-19” and are hopeful to achieve herd immunity by the “end of this year.”
Pasion said “no single strategy is enough to protect our people” but stressed the observance of minimum public health protocols as well as vaccination.
As of August 5, only 320,938 residents in the five-province, six-city Davao region have been fully vaccinated. This accounts for only 6.1% of its 5.2 million population.
Treat as Delta
Dr. Michelle Schlosser, spokesperson of the Davao City COVID-19 Task Force, said “collaborative effort” is needed alongside observance of minimum health protocols and vaccination.
“All of us should battle this together,” she said in a virtual presser on August 2.
Schlosser said that in their July 31 meeting with the DOH-Davao to strengthen contact-tracing, it was agreed upon that specimens with cycle threshold of less than 30 would be submitted for whole genome sequencing but “from now on,” specimens falling within the cycle threshold criteria, “even if wala pa pong result from the genome sequencing, we will be treating that case as Delta para po outright ma contact trace na natin at isolate ang close contacts even before results come to us because medyo matagal ang turnaround of results ng whole genome sequencing.”
“We will be doing that para mas mabilis ang ating pag isolate and mitigate the risk of spread sa variant,” Schlosser said. (Carolyn O. Arguillas / MindaNews)