Lagging COVID-19 genomic surveillance poses risk as schools prepare to reopen

COSACO: Health Dept. must tackle data access issue

By Pedro Correa Henry

Twitter: @pete_r_correa

Special to The Star

The Community Health Coalition (COSACO by its Spanish acronym) on Monday called for the island Department of Health to take immediate action on the delay in the flow of genomic sequences from suppliers such as the Centers for Disease Control and Prevention (CDC) so that local public health organizations can keep better track of the spread of the delta variant.

COSACO’s call comes as the non-profit organization released an executive report showing that the island’s genomic sequencing efforts have decreased to 1.8% in the midst of a coronavirus case increase.

COSACO Executive Director Danilo Trinidad Pérez-Rivera told The STAR that the genomic sequencing in Puerto Rico was up to 2.8% due to the efforts of institutions such as Ponce Health Sciences University and Central Caribbean University, which, under the helm of former Municipal Case Investigation and Contact Tracing System (SMICRC by its Spanish initials) chief Fabiola Cruz, collaborated with Yale University to strengthen efforts in providing samples and sequencing coronavirus variants in Puerto Rico along with the CDC.

However, Pérez-Rivera said, those institutions should “work as supplements” to the Health Department and urged the commonwealth agency to lead the way and speak up to the CDC, as the delay in data and sample deliveries from the federal agency can take up to four months.

“This is a real problem,” he said. “We can’t wait for four months for those sequencing samples to arrive. It should arrive as soon as possible so the Department of Health finally recognizes that if they open up schools on Aug. 5, as they have planned, they’re repeating the same mistake that happened back in March and led us to an [COVID-19] outbreak in April.”

“It’s the same mistake again, getting the same [result], that schools probably have to shut down, undermining [public health leaders’] public trust again, and that’s the problem,” Pérez-Rivera added. “There is a lot of accusation here that independent organizations are the ones raising their voices and undermining the trust in the Department of Health, and I totally disagree; those who undermine trust in the department are the officials themselves who refuse to do the job well.”

The coalition stated in its report that “it is key that we achieve a random [genomic sequencing] coverage of 10% [of confirmed COVID-19 cases] in order to feel confident in the data and the conclusions they can supply.”

“Back when we had certain control because the delta variant was not under full community transmission, it was easier to achieve that 10% coverage because if I had 100 cases [per week], I had to sequence just 10 samples,” Pérez-Rivera said. “But what starts to happen when you go up to 400, 800, or 1,000 cases [weekly]? We are already close to 1,000 cases per week, which means that I have to pay for at least 100 sequences.”

Meanwhile, the coalition confirmed that the delta variant phenomenon “is a fact in Puerto Rico, representing 90% of the samples sequenced in the past month, producing a strong and clear rebound that is no longer possible to ignore.”

“One thing we learned in these spaces is that these variants are taking advantage of the infectious niche of early childhood with an opportunity to spread dynamically through the population,” the COSACO chief said. “I’m putting in a little bit of personification, but we know that this is not a decision, that these [coronavirus] mutations are random, but they are random because they are forced [to mutate] according to the conditions in which we find ourselves with the population.”

“We are in a position where, one, we are not so stringent with children, we don’t see a child out there being scolded because he is wearing his mask inappropriately; we are quite lenient. And two, children are not infected as severely, so there are more asymptomatic cases in this population than in the aging population,” Perez-Rivera added. “So these conditions are conducive to these variants of interest, particularly making the setting like K-12 education one of high risk because people infected in this setting don’t necessarily recognize their infection, they go back to their nuclear family, where many of those children are cared for by their grandparents.”

At press time, Gov. Pedro Pierluisi Urrutia said that given the “significant increase” in confirmed coronavirus cases, unvaccinated islanders must get their shots as “vaccination is the solution.”

“No one here wants to return to the days of restrictions and a curfew,” he said. “I am relying on the cooperation of our people to achieve the immunity that will help us defeat this pandemic.”

Pierluisi stressed that scientific evidence “is clear and convincing that the vast majority of the people who are becoming infected, who are being hospitalized and who are dying are unvaccinated people, people with other diseases or with compromised immune systems.”

He also urged the use of face masks “in enclosed spaces where not everyone is vaccinated.”