Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

CARING pCO2 Data Report. FIGURE-CARING cruise 21-30 Jul 2022

During the FIGURE-CARING cruise (https://doi.org/10.17600/18002940) on board the RV/Atlantic Explorer (21-30 Jul 2022), continuous underway measurements of pCO2 were taken by means of an autonomous General Oceanics LI-COR 7000 pCO2 system (measurement method IR), located in an air-conditioned laboratory (RV/AE End Lab). Raw data were automatically stored to be calibrated and QCd for outliers a posteriori by BIOS CARING project collaborators (M. Enright, N. Bates), following the method by Pierrot et al. (2009). As part of the post-processing, pCO2 data were merged with position, barometric pressure, and underway temperature and salinity data, and flagged following the WOCE flagging code (2=Good, 3=Questionable). Further details on the water sampling/storage procedure can be found in the cruise report (Benavides and Carracedo, 2022; https://doi.org/10.13155/96692). Further details on the processing steps by parameter are indicated in this data report. The corresponding datafile is provided as a CSV file, and parameter metadata as a TXT file (Carracedo et al., 2022, https://doi.org/10.17882/96728)

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic phylogenomic efforts to compile a phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. © 2009 Macmillan Publishers Limited. All rights reserved

Reference genome sequence of the model plant Setaria

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