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UnknownIntegrated population clustering and genomic epidemiology with PopPIPE.
Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due to their variable gene content and order, reference-free methods offer more sensitive d...
S-EPMC12038005 | biostudies-literature
UnknownA manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

Background

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia ...
S-EPMC5902842 | biostudies-literature
UnknownDevelopment of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus.
The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, t...
S-EPMC9603838 | biostudies-literature
UnknownDevelopment of an amplicon-based sequencing approach in response to the global emergence of mpox.
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox inf...
S-EPMC10263305 | biostudies-literature
UnknownA large-scale study across the avian clade identifies ecological drivers of neophobia.
Neophobia, or aversion to novelty, is important for adaptability and survival as it influences the ways in which animals navigate risk and interact with their environments. Across individuals, species and other taxonomic levels, neophobia is known to vary considerably, but our understanding of the w...
S-EPMC12520376 | biostudies-literature
UnknownChanges in atherosclerotic cardiovascular disease risk over time among people living with HIV.

Objective

To describe changes in atherosclerotic cardiovascular disease (ASCVD) risk over time among people living with HIV (PLHIV).

Methods

We used data from the TREAT Asia HIV Observational Database (TAHOD) and the Australian HIV Observational Database (AHOD). Five-year ASCVD risk w...
S-EPMC10984948 | biostudies-literature
UnknownSARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway.
Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid...
S-EPMC9352574 | biostudies-literature
UnknownGenomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning.
Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student m...
S-EPMC9296497 | biostudies-literature
UnknownA second update on mapping the human genetic architecture of COVID-19.
Not available
S-EPMC10482689 | biostudies-literature
UnknownInvestigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.

Background

The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discha...
S-EPMC9997060 | biostudies-literature
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