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Biology subjects

Papalambros, L.

Publications and source records attributed to Papalambros, L..

2 recordsLinked to original sources

H5N5 virus transmission is driven by repeated cross-Atlantic introductions and transmission among high latitude seabirds

In November 2025, the first global H5N5 infection was reported in a person in Washington State. Previously, these viruses had only been detected in seabirds and shorebirds near the Atlantic Ocean, suggesting potentially distinct ecology from dominant H5N1 strains. Using 354 global H5N5 genomes, we show that H5N5 viruses have been carried by high latitude seabirds and shorebirds across the Atlantic at least 9 times, with introductions more frequent in the fall and spring. We reconstruct a plausible path of cross-continental movement via Arctic or sub-Arctic regions, followed by a year of cryptic circulation prior to human spillover. These data show that H5N5 viruses have undergone far more intercontinental movements than previously recognized, and exhibit host and geographic patterns that are fundamentally distinct from dominant H5N1 lineages. The distinct host ecology, geography, and movement, paired with the capacity to infect a person, suggest that enhanced surveillance may be warranted.

evolutionary biology↗

In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. The low diversity within-hosts and strong genetic linkage among genomic sites make accurately detecting positive selection difficult. Longitudinal sampling is a powerful method for detecting selection that has seldom been used for SARS-CoV-2. Here we combine longitudinal sampling with replicate sequencing to increase the accuracy of and lower the threshold for variant calling. We sequenced 577 specimens from 105 individuals from a household cohort primarily during the BA.1/BA.2 variant period. There was extremely low diversity and a low rate of divergence. Specimens had 0-12 intrahost single nucleotide variants (iSNV) at >0.5% frequency, and the majority of the iSNV were at frequencies <2%. Within-host dynamics were dominated by genetic drift and purifying selection. Positive selection was rare but highly concentrated in spike. Two individuals with BA.1 infections had S:371F, a lineage defining substitution for BA.2. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 14 loci with 7 in spike, including S:448 and S:339. We also detected significant genetic hitchhiking between synonymous changes and nonsynonymous iSNV under selection. The detectable immune-mediated selection may be caused by the relatively narrow antibody repertoire in individuals during the early Omicron phase of the SARS-CoV-2 pandemic. As both the virus and population immunity evolve, understanding the corresponding shifts in SARS-CoV-2 within-host dynamics will be important.

microbiology↗