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Alexander Lucaci

@aglucaci.bsky.social

Postdoctoral Associate @ Weill Cornell Medicine. PhD in Bioinformatics from Temple University

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Alexander Lucaci@aglucaci.bsky.social · 2y ago

journals.asm.org/doi/10.1128/...

Pathogen genomic surveillance and the AI revolution | Journal of Virology

Genomic pathogen sequencing during the COVID-19 pandemic highlighted the critical role of surveillance in understanding the persistence of SARS-CoV-2 in the human population despite high levels of protective immunity and the effect of the changing circulating variants on public health, advising policymakers and informing vaccine design. With nearly 20 million SARS-CoV-2 genomes currently available in the GISAID database, the sequencing effort since 2020 has surpassed those of other viruses, followed by less than half a million influenza virus genomes (GISAID) and less than 50,000 HIV-1 genomes (GenBank) all collected over several decades. The almost real-time resolution of circulating SARS-CoV-2 variants allowed scientists to readily detect and characterize genome changes corresponding to the virus’s functional and antigenic evolution in humans and anthroponosis events to other animals. This phenotypic change was apparent from the outset of the pandemic, with genomic surveillance revealing the first “functional” substitution, D614G (1, 2), and first significant antigenic substitution, N439K (3), both changes in the virus’s Spike entry glycoprotein. In addition to such point mutations creating variants with altered phenotypic properties, the global sequencing effort uncovered several mechanisms this new human virus used to maintain its circulation in the population: recurring indel mutations generating new variants, e.g., deletion H69/V70 (4); independent occurrence of the same amino acid substitutions at the same site in different variants (convergence) (5, 6); the emergence of variants of concern associated with multiple beneficial mutations through saltation-like evolution linked to chronic infections (7, 8); and bringing novel sets of mutations together in one variant (recombination) (9, 10), which can have a combinatory beneficial effect for the virus (positive epistasis) (11).

journals.asm.org

Richard Neher@neher.io · 2y ago

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome: [1/N] www.biorxiv.org/content/10.1...

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure

RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...

biorxiv.org

Jeremy M. Brown@jembrown.bsky.social · 2y ago

Applications are now open for the 2025 Workshop on Molecular Evolution (MOLE) at the Marine Biological Laboratory in *beautiful* Woods Hole, MA! More info here: molevolworkshop.github.io Apply here: www.mbl.edu/education/ad... Application deadline: Jan. 29th Workshop dates: May 22nd - June 1st

Workshop on Molecular Evolution | Marine Biological Laboratory

The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetic...

mbl.edu