A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.

In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge.

Role of admission rapid antigen testing (RATs) for COVID-19 on patients transferred from acute hospitals to a postacute rehabilitation setting.

Background: Rapid antigen tests (RATs) are suitable for point-of-care testing, require no laboratory time, and give immediate results. However, are RATs useful for detecting asymptomatic COVID-19 infection when compared with polymerase chain reaction (PCR) testing in health care settings?

Methods: RAT testing was carried out on all new admissions without a history of confirmed COVID-19 infection within 3 months of admission. PCR testing was carried out on all patients with a positive RAT for confirmation purposes.

Evaluating the risk of SARS-CoV-2 reinfection with the Omicron or Delta variant in Wales, UK.

Recent studies suggest an increased risk of reinfection with the SARS-CoV-2 Omicron variant compared with previous variants, potentially due to an increased ability to escape immunity specific to older variants, high antigenic divergence of Omicron from earlier virus variants as well as its altered cell entry pathway. The present study sought to investigate epidemiological evidence for differential SARS-CoV-2 reinfection intervals and incidence rates for the Delta versus Omicron variants within Wales. Reinfections in Wales up to February 2022 were defined using genotyping and whole genome sequencing.

Movement behavior in a dominant ungulate underlies successful adjustment to a rapidly changing landscape following megafire.

Background: Movement plays a key role in allowing animal species to adapt to sudden environmental shifts. Anthropogenic climate and land use change have accelerated the frequency of some of these extreme disturbances, including megafire. These megafires dramatically alter ecosystems and challenge the capacity of several species to adjust to a rapidly changing landscape.