In collaboration with Nathan Grubaugh, researchers at the Yale Center for Genomic Analysis are at the forefront of the fight against COVID-19.
Yash Roy, co-photographer
Due to the disruptive nature of the pandemic, the Yales Center for Genomic Analysis has taken on the responsibility of sequencing samples from positive COVID-19 cases in Yale and Southern Connecticut communities.
YCGA is at the forefront of genomic testing in the state and nation, providing physicians at the Yale New Haven Health System with targeted information on plans for treating patients with cancer and autoimmune disease. The center houses Nate Grubaugh’s laboratory, which currently specializes in a Yale SARS-CoV-2 surveillance initiative. The initiative is responsible for sequencing approximately 10 percent of COVID-19 tests, which currently translate to approximately 190 tests, within the Yale New Haven Hospital system each week.
“We did not set up the weekly sequencing routine until January 2021,” Grubaugh said. “Then we really started to increase our efforts … we were able to capture a kind of heyday of varieties, which was the spring of 2021, where there was alpha, beta, gamma, theta, iota, epsilon, and then we caught Delta under over in the summer, and then apparently Omicron last winter. “
Grubaugh said he first worked with Yale epidemiology researcher Anne Wyllie on SalivaDirect project. During this process, his laboratory split up and began working on genomic testing when it became clear that sequencing of positive samples would be necessary to effectively combat COVID-19.
Grubaugh’s lab also worked with the NBA and NFL to sequence the SARS-CoV-2 virus to help both leagues gain a deeper understanding of transmission within their facilities.
“Before the advent of variants, it was more about looking at dispersal patterns and an outbreak study,” Grubaugh said. That changed when alpha appeared in the UK in late 2020. And it was pretty clear that this would hit the US, and we did not have a systematic program to monitor for new SARS-CoV-2 variants. ”
According to Grubaugh, his laboratory and Yale’s were the primary sequencers of the virus at the beginning of the sequencing in Connecticut. In recent months, however, the CDC has overtaken his laboratory in sequencing in the state.
Grubaugh told News that to sequence, his lab analyzes about 30,000 nucleotides of information and turns them into strings of letters and numbers with the Pangolin computer program. The data is then uploaded to both his lab’s website as well as a weekly Thursday twitter thread, where he provides updates on which strains of the virus are prevalent in southern Connecticut.
“Every Friday, we receive samples from Nate’s laboratory,” said Bony De Kumar, director of operations at the Yale Center for Genome Analysis. “We then sequence them and return the results to Nate’s lab by Wednesday. And they analyze and report those sequences. And then all variant detections, which is Omicron or Delta.”
YCGA has three different sequencers, two that provide 8.8 billion readings when run in a 48-hour cycle, and another sequencer that sequences larger chunks of genomic code.
De Kumar told the news that YCGA can produce up to 27 terabytes of information per week, including COVID-19 sequence data.
“The Yale Center for Genome Analysis is a full-service facility dedicated to providing RNA expression profiling,” the YCGA website said. “DNA genotyping and high-throughput sequencing use advanced technology, and the resource is open to both Yale and other non-profit organizations.”
Recently, more than half of the samples have been identified as the newer strain of the Omicron variant, BA 2.