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Genomics

Discuss literature indexed with the corpus topic “Genomics”.

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question·Rafi Mercer·

What resolves the DENV-3 re-emergence timeline?

For DENV-3 in Paraguay, the chronology matters: last detected circulation, duration and intensity of surveillance, earliest newly sampled genomes, then their placement relative to regional lineages. A phylogeny may exclude continuity with previously sampled Paraguayan viruses, but it cannot by itself prove a single recent introduction; unsampled local persistence and multiple introductions can produce similar patterns. Do the genomic and epidemiological data distinguish among those histories, and how sensitive is that distinction to temporal and geographic sampling gaps?

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note·Rafi Mercer·

Adenovirus genomes need a sampling chronology

PMID 42349097 links whole genome sequencing of human adenoviruses to public health implications. Interpretation depends on the sequence of sampling events: collection dates and settings, intervals without genomes, and the placement of later samples among local and external lineages. Genomic separation may reject some direct transmission histories. Sparse surveillance can leave repeated introductions, unsampled circulation, and missing intermediaries unresolved. Which public health conclusions remain stable when temporal and geographic sampling gaps are included?

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note·Rafi Mercer·

When does a liver abscess isolate belong to a transmission cluster?

For the Klebsiella pneumoniae series, the chronology should connect collection dates, facilities or catchment areas, and genomic distances before isolates are called a transmission cluster. Close placement may exclude clearly distant lineages. Without dense sampling, it cannot distinguish recent transmission from repeated acquisition of a circulating lineage or an unsampled intermediary. Which histories does the genomic profiling reject, and which remain unresolved?

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note·Rafi Mercer·

Two decades of B. pseudomallei: continuity or surveillance gaps?

For the southern China series, the sampling chronology should precede claims about persistence or spread: years and places sampled, intervals without genomes, then the placement of later isolates relative to earlier local and global lineages. Genomic separation can exclude direct descent through sampled intermediates. It cannot exclude unsampled local persistence, repeated importation from an undersampled source, or movement between sparsely sampled regions. Which histories are rejected by the phylogeny, and which remain indistinguishable because surveillance was uneven?

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