Researchers discover new COVID-19 variation in New Mexico population

By Sarah Bliss-Carpenter, UNM Center for Advanced Research Computing.

Daryl Domman, assistant professor at The University of New Mexico Center for Global Health, and Darrell Dinwiddie, assistant professor in the UNM Department of Pediatrics, have discovered a novel variant of the SARS-CoV-2 virus among COVID-19-positive samples in New Mexico.

The two have been working with the New Mexico Department of Health and other health officials to sequence the genomes of coronavirus samples from across the state, as well as those from other regions of the Rocky Mountains. A new variant named the “Pelican Lineage” has been observed in New Mexican samples dating back to December 2020.

Health scientists around the world have been coordinating their efforts to understand the coronavirus by uploading the genomic data they collect to an online platform called GISAID. After noticing an unfamiliar mutation at the 677P site of the genetic sequence in several of his SARS-CoV-2 samples, Domman turned to GISAID to see if anyone else had found a similar variant.

Domman reports, “It was very early on a Saturday morning when I was combing through this data. I saw the mutation and then I immediately went to this GISAID data to see where else this might be popping up.” Domman found that researcher Jeremy Kamil, associate professor of Microbiology and Immunology at Louisiana State University in Shreveport, had uncovered the same mutation in COVID-19 samples from Louisiana.

While there is no clinical evidence to suggest that this new variant has made the virus more deadly or contagious, there is reason to suspect that the mutation could offer an evolutionary advantage. The first reason for this suspicion is that the 677P mutation affects the spike protein of the virus. A spike protein is, as Domman says, the “molecular handshake that occurs between the virus and the human cell.” This protein is essential to the virus’s ability to connect with and infect a host; because of this, it is the part of a virus that is typically targeted by our own immune cells. A mutation in this part of the SARS-CoV-2 genome has the potential to make infection easier for the virus.

The second cause for concern is that the mutation appears to be the result of convergent evolution. Convergent evolution is a term used to describe how multiple populations can independently develop the same beneficial trait through the process of natural selection. Mutations at the 677 position have been found in seven separate lineages of SARS-CoV-2 spread across at least 20 US states so far. These lineages did not inherit the mutation from a common ancestor; they acquired the same trait via separate paths of evolution. While researchers aren’t able to say how or if the 677P mutation helps SARS-CoV-2 survive or spread, the number of times that the same trait has cropped up in separate variants suggests that it may be somehow useful to the virus.

Of the New Mexican COVID-19 samples dating back to December 2020, about 11% of them contain the 677P mutation. This number seems to be holding steady.

The data generated by this project is sequenced and stored using UNM Center for Advanced Research Computing resources. Genomic sequencing requires an immense amount of computing power—far more than what a personal computer is capable of handling.

“We literally could not do it without CARC. It has been absolutely fundamental and crucial to utilize the supercomputing facility to process all of this genomic data. We are generating results at an enormous pace and it’s a lot of data. The folks at CARC have just been incredible in terms of providing us the computational resources, which is a free service to the university, which is an amazing thing. They are also very accommodating our ever-increasing demand for space,” Domman explains, adding, “They’ve really underpinned our ability to provide this data back to New Mexico.”

Domman and Dinwiddie, along with the New Mexico Department of Health (NM DOH), have been analyzing COVID-19 samples since the spring of 2020 as a part of the Centers for Disease Control and Prevention’s SPHERES program. Because of their efforts along with NM DOH, the State of New Mexico has the seventh-highest rate of SARS-CoV-2 sample sequencing in the country. Nationally, only about 0.3% of positive samples are sequenced; in New Mexico, that rate is over 1%. Domman and Dinwiddie hope to bring New Mexico’s genomic sequencing rate to over 5% of samples.

The key to New Mexico’s success may be the extensive coordination of local health entities. Domman and Dinwiddie have been working in concert with physicians, TriCore Reference Laboratories, NM DOH, the Los Alamos National Laboratory, and others. Domman comments, “Here in New Mexico I think we’ve had this amazing opportunity for all of our major public health entities and diagnostic centers to come together as one unit.”

Currently, this work is being funded primarily by a Pilot Award from the UNM Clinical & Translational Science Center along with fellowship funding. Domman and Dinwiddie are hoping to further their research using funds from multiple sources.

Moving forward, Domman stresses the importance of sustained measures to slow the spread of COVID-19. He reminds us, “The virus will continue to mutate. This is just a fact of viruses, you know, they do this. It is important to note that one of the best things that we can do in terms of ensuring that our vaccines remain effective is reducing case counts because potentially every single new case is an opportunity for the virus to pick up a beneficial mutation.” The public is urged to continue wearing masks and socially distancing to prevent future viral mutations.

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