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Links for 2022-06-01

  • Intrahost evolution and forward transmission of a novel SARS-CoV-2 Omicron BA.1 subvariant

    This is an incredible pre-print — “We describe a persistent SARS-CoV-2 Omicron BA.1 infection in an immuno-compromised individual during a 12-week period, and document the accumulation of eight additional amino acid substitutions in the already antigenically-distinct Omicron BA.1 spike protein.” A SARS-CoV-2 variant evolving in a single person in real time!

    Persistent SARS-CoV-2 infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. It has been speculated that the emergence of antigenically diverse SARS-CoV-2 variants such as the Omicron variant may be the result of intra-host viral evolution driven by suboptimal immune responses, which must be followed by forward transmission. However, while intrahost evolution has been documented, to our knowledge no direct evidence of subsequent forward transmission is available to date. Here we describe the emergence of an Omicron BA.1 sub-lineage with 8 additional amino acid substitutions within the spike (E96D, L167T, R346T, L455W, K458M, A484V, H681R, A688V) in an immune-compromised host along with evidence of 5 forward transmission cases. Our findings show that the Omicron BA.1 lineage can further diverge from its exceptionally mutated genome during prolonged SARS-CoV-2 infection; highlighting an urgent need to employ therapeutic strategies to limit duration of infection and spread in vulnerable patients.

    (tags: variants sars-cov-2 covid-19 evolution papers preprints immunocompromise viruses omicron)

  • Docker build cache sharing on multi-hosts with BuildKit and buildx

    decent speed improvements by sharing a layer cache between hosts

    (tags: docker building compilation ci tweaks containers)

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