Healing Snakes With Supercomputers

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A picture of a Columbian red-tailed boa.

Advay Shindikar, SDSC Communications, contributed to this story.

Just like humans, snakes can get sick. Specifically, reptarenaviruses can lead snakes to devastating health problems like Boid Inclusion Body Disease (BIBD), which has no cure. Thanks to an ACCESS allocation on Bridges-2 at the Pittsburgh Supercomputing Center (PSC), Dr. Mohamed Abouelkhair, an immunology and virology assistant professor at the University of Tennessee Veterinary Medical Center, has recently identified and molecularly characterized the complete genome sequence of a reptarenavirus found in a Colombian red-tailed boa.

He and his team accomplished the identification portion of their study using a method for constructing genomes from many DNA fragments called de novo assembled.

A Columbian red-tailed boa coiled over a tree branch,
A Columbian red-tailed boa

“Using advanced metagenomics sequencing with our ACCESS allocation on Bridges-2, we discovered that the Colombian Red-Tailed Boa in this study carried the University of Giessen virus (UGV-1) S or S6 (UGV/S6) segment and L genotype 7. The prevalence of the UGV/S6 genotype, in line with prior research findings, hints at potential advantages it holds over other genotypes,” said Abouelkhair, a veterinarian board-certified in virology and immunology. “This finding opens new avenues for understanding the evolutionary dynamics of reptarenaviruses and holds promise for targeted interventions to mitigate their impact on snake populations.”

Abouelkhair said that the first comprehensive conservation assessment of reptiles found that 21.1% of the animals were classed as vulnerable, endangered or critically endangered. 

“The situation with reptiles at this status is significantly more than birds, of which 13.6% are threatened – this is largely because we lack information about these viruses in snakes, both in the United States and globally, ” Abouelkhair explained. “Our study used the ACCESS allocation on Bridges-2 to fill this gap by using an advanced metagenomics sequencing approach.” 

Our research using ACCESS allowed us to contribute to our knowledge of viral pathogens in snakes. Monitoring and understanding these viruses are essential for the well-being of both captive and wild snake populations. It can also aid in developing ways to diagnose and intervene in case of infections, ultimately contributing to the conservation of these reptilian species. By unraveling the mysteries surrounding viral pathogens in snakes, we can better safeguard the health and conservation of reptiles, as well as mitigate potential risks to human health.

–Dr. Mohamed Abouelkhair, University of Tennessee Veterinary Medical Center.

“The allocation of ACCESS supercomputing resources played a pivotal role in our research by facilitating intricate analyses and computations on the metagenomic data of the reptarenavirus,” Abouelkhair said. “Leveraging the supercomputer’s immense processing power, we were able to perform complex tasks such as identifying the virus variant, assembling genomic sequences and phylogenetic analysis. This capability was crucial for handling large datasets efficiently and extracting meaningful insights – allowing us to unravel important details about the reptarenavirus genetic makeup in the Colombian red-tailed boa.” 

Dr. Mohamed Abouelkhair in his lab performing tests.
Dr. Mohamed Abouelkhair of the University of Tennessee Veterinary Medical Center plans to next use ACCESS resources to delve deeper into the evolutionary history, molecular epidemiology, and biological properties of reptarenaviruses in various snake species – not just boas. Credit: Dr. Mohamed Abouelkhair

He said that Bridges-2 significantly expedited the team’s research process – enabling a more thorough understanding of the virus’s genetic makeup.

“Understanding these viruses is crucial for snake conservation, aiding in diagnosis, intervention and protection of vulnerable species,” he said. “Our study also offers insights for future research on the evolution and properties of these viruses in various snake species.” 

The study was published in an article entitled Molecular characterization of a reptarenavirus detected in a Colombian Red-Tailed Boa in the Virology Journal.


Project Details

Resource Provider Institution(s): Pittsburgh Supercomputing Center (PSC)
Affiliations: University of Tennessee Veterinary Medical Center
Funding Agency: NSF
Grant or Allocation Number(s): AGR220002

The science story featured here was enabled by the ACCESS program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.

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