High-resolution epidemiological landscape from~ 290,000 SARS-CoV-2 genomes from Denmark

MP Khurana, J Curran-Sebastian… - Nature …, 2024 - nature.com
Vast amounts of pathogen genomic, demographic and spatial data are transforming our
understanding of SARS-CoV-2 emergence and spread. We examined the drivers of …

Durability and breadth of neutralisation following multiple antigen exposures to SARS-CoV-2 infection and/or COVID-19 vaccination

AP Underwood, C Sølund, C Fernandez-Antunez… - …, 2023 - thelancet.com
Background Given the importance of vaccination against severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) in the prevention of severe coronavirus disease 2019 (COVID …

Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha

B Faucher, CE Sabbatini, P Czuppon… - Nature …, 2024 - nature.com
SARS-CoV-2 variants of concern (VOCs) circulated cryptically before being identified as a
threat, delaying interventions. Here we studied the drivers of such silent spread and its …

Benchmarking long‐read sequencing strategies for obtaining ASV‐resolved rRNA operons from environmental microeukaryotes

CK Overgaard, M Jamy, S Radutoiu… - Molecular Ecology …, 2024 - Wiley Online Library
The use of short‐read metabarcoding for classifying microeukaryotes is challenged by the
lack of comprehensive 18S rRNA reference databases. While recent advances in high …

SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics

AM Rice, EP Troendle, SJ Bridgett, B Firoozi Nejad… - Genome Medicine, 2024 - Springer
Background Ireland's COVID-19 response combined extensive SARS-CoV-2 testing to
estimate incidence, with whole genome sequencing (WGS) for genome surveillance. As an …

[HTML][HTML] Real-time estimates of the emergence and dynamics of SARS-CoV-2 variants of concern: A modeling approach

N Gozzi, M Chinazzi, JT Davis, K Mu, AP y Piontti… - Epidemics, 2024 - Elsevier
The emergence of SARS-CoV-2 variants of concern (VOCs) punctuated the dynamics of the
COVID-19 pandemic in multiple occasions. The stages subsequent to their identification …

A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary

E Ari, BM Vásárhelyi, G Kemenesi, GE Tóth… - Virus …, 2022 - academic.oup.com
Retrospective evaluation of past waves of the severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) epidemic is key for designing optimal interventions against …

NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from Nanopore and Illumina data

SA Fuchs, L Hülse, T Tamayo, S Kolbe-Busch… - Msystems, 2024 - journals.asm.org
Genomic surveillance enables the early detection of pathogen transmission in healthcare
facilities and contributes to the reduction of substantial patient harm. Fast turnaround times …

Routes of importation and spatial dynamics of SARS-CoV-2 variants during localized interventions in Chile

B Gutierrez, JLH Tsui, G Pullano, M Mazzoli… - PNAS …, 2024 - academic.oup.com
Human mobility is strongly associated with the spread of SARS-CoV-2 via air travel on an
international scale and with population mixing and the number of people moving between …

Exploring the Spatial Distribution of Persistent SARS-CoV-2 Mutations-Leveraging mobility data for targeted sampling

R Spott, MW Pletz, C Fleischmann-Struzek, A Kimmig… - medRxiv, 2024 - medrxiv.org
Given the rapid cross-country spread of SARS-CoV-2 and the resulting difficulty in tracking
lineage spread, we investigated the potential of combining mobile service data and fine …