Labeling variants called key in battle
Experts tell lawmakers sequencing critical to effort
The many COVID-19 variants that have been spreading around the globe and here in Massachusetts could have ramifications for the state’s economic reopening and vaccination efforts, but first the Bay State needs to get a better snapshot of how prevalent these mutants are, experts told lawmakers Tuesday.
The U.S. Centers for Disease Control and Prevention has identified five unique mutations of the COVID-19 virus as “variants of concern,” meaning there’s evidence that these circulating strains could be more conta
gious, cause more severe disease, or blunt the efficacy of treatments and vaccines.
As of Saturday, the CDC said a sampling of positive COVID-19 results had identified 1,100 cases in Massachusetts of the B.1.1.7 variant first found in the United Kingdom, making up 5.26% of the 20,915 cases the federal agency identified across the country. The B.1.351 variant first identified in South Africa was identified in 12 Massachusetts cases sequenced, 2.65% of the 453 nationwide cases, and the P.1 variant that originated in Brazil was found in 102 Massachusetts samples — just more than 20% of the cases found in the country and more than any state other than Florida.
But only about 1.4% of all positive coronavirus cases from Massachusetts undergo the genomic sequencing that can determine whether they were caused by a viral variation, Dr. Bronwyn MacInnis, the director of pathogen genomic surveillance in the Infectious Disease and Microbiome Program at the Broad Institute of MIT and Harvard, said.
“Statistically, we think we need about 5% of cases to be sequenced to be able to identify variants of concern with confidence that are circulating in our community and, moreover, to identify emerging threats — the kind of unknown unknowns that we should be paying attention to,” she said.
MacInnis told lawmakers on the COVID-19 and Emergency Preparedness and Management Committee and the Committee on Public Health, which jointly pulled together a roster of local doctors, scientists and researchers Tuesday to discuss variants, that the Broad Institute is significantly ramping up its sequencing capabilities with the help of the state and federal government.
She said the institute has been sequencing between 100 and 200 samples per week but is “at the beginning of a very steep upward trend in our capacity.” This week, the Broad will sequence about 1,000 samples, and it aims to be sequencing about 4,000 samples per week by the end of April.
“That, together with the sources of data that are coming from the other largescale testing facilities and other academic and public health efforts, will really help to improve the picture,” MacInnis said. Dr. Nahid Bhadelia, an infectious diseases physician and medical director of the Special Pathogens Unit at Boston Medical Center, said her teams at Boston University and BMC have been sequencing all positive test results since January, about 50 to 100 each week. She said they have the capacity to sequence three times that number.
Dr. Paul Biddinger, director of Massachusetts General Hospital’s Center for Disaster Medicine and the head of Gov. Charlie Baker’s vaccine advisory group, said he thinks Massachusetts needs to bring the Broad, BMC and others under the umbrella of a public-private partnership that is tasked with launching a topflight sequencing and surveillance program.
“Massachusetts is, compared to many states in the country, doing well on sequencing, but I think probably most all of us who are testifying today would agree we need more. We need more capability for testing and for sequencing specifically. And we need a comprehensive statewide approach,” Biddinger said. “This is hard — sequencing is much, much, much harder than testing. You need expertise, you need equipment to do it well. And you need resources to design a comprehensive strategy.”