tags: groupthink

Center for Viral Evolution (CVE)

Viruses are as old as life itself, infecting everything from bacteria to humans. Since the very beginning, viruses have left an indelible imprint on the human genome, human history, and medical research. SARS-CoV-2, the viral pathogen responsible for the COVID-19 pandemic, is just the latest in a long line of highly impactful human pathogens, including smallpox, Influenza A virus (IAV) and HIV-1. By some estimates, close to 30% of human proteins are involved in combating viral infections.

Viral pathogens, especially RNA viruses such (HIV-1, IAV, SARS-CoV-2), mutate very quickly, with some viruses generating every possible single-nuclotide mutation in each new viral generation. Immune reponses, antiviral drugs, competition between viral strains, transmission between species and hosts create some of strongest evolutionary forces that have been reported in evolutionary biology. Viruses are also some of the most sequenced organisms in existence (e.g. ~15M SARS-CoV-2 genomes have been sequenced in 2020-2022).

The mission of the Center for Viral Evolution at Temple University is to

1. Create computational and statistical learning approaches for the analysis of genomic data from rapidly evolving viral pathogens.
2. Develop scalable software tools for processing large volumes of viral sequence data and deliver actionable and interpretable results.
3. Apply these tools and techniques to learn how past viral evolution informs their present ability to adapt to our responses, and predict likely future paths viruses may take.

Examples of CVE success

1. Software tools (e.g. HyPhy and Datamonkey) and statistical methods for studying natural selection, recombination, and other evolutionary features of viral genomes are "gold-standard" tools (>10000 citations), and have been relied upon by the research community to study every significant human and animal pathogen. For example, in 2020-2022 the Datamonkey server ran well over 20,000 analyses submitted by researchers worldwide on SARS-CoV-2 data for free, enabling "real-time" research to help combat the pandemic.

2. Our team has developed methods and tools powering national and international public health efforts to reduce HIV-1 tranmsssion and advance towards its eventual eradication by tracking clusters of transmission in the US (Secure HIV-TRACE, used by the US CDC) and other countries (e.g., Mexico).

3. Since early 2020, members of CVE have been very active in SARS-CoV-2 research, leading or contributing to studies on

   • Rapid (within two weeks) analysis of the potential impact of many mutations in the Omicron genome on its fitness and transmissibility.
   • The origin and selection on key variants of conern (beta, gamma, omicron)
   • Analytical tools (RASCL, Stanford CoV-RDB) for studying the evolution of viral variants and tracking the importance of individual mutations.
   • Approaches to predict near-term evolution of viral variants
   • Investigations into viral origins and ancestral sequences.

4. Members of CVE have lead or contributed to research on related Coronaviruses that infect animals or have jumped between animals and humans

   • Detection of selection in a Canine Coronavirus associated with the jump from dogs to humans.
   • Characterization of selection in Feline Coronaviruses associated with increased pathogenicity within host.

5. Computational approaches to improve vaccine design, and understand the development of drug resistance.