Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France

Estimates of SARS-CoV-2 Omicron Variant Severity in Ontario, Canada

(2022) Ana Cecilia Ulloa et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

(2022) Raquel Viana et al.   NATURE

Deltacron: the story of the variant that wasn’t

(2022) Freda Kreier   NATURE

Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study

(2022) Tommy Nyberg et al.   LANCET

Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

(2022) Rebecca J. Rockett et al.   Nature Communications

Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection

(2022) Filipe Zimmer Dezordi et al.   Microbial Genomics

Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing

(2022) Patricia Combes et al.   CLINICAL MICROBIOLOGY AND INFECTION

Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021

(2021) Alexandre Gaymard et al.   Eurosurveillance

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response

(2021) Rong Liu et al.   Scientific Reports

Patterns of within-host genetic diversity in SARS-CoV-2

(2021) Gerry Tonkin-Hill et al.   eLife

A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples

(2021) Tiantian Liu et al.   iScience

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

(2021) James J. Davis et al.   Microbiology Spectrum

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

(2020) Caroline Charre et al.   Virus Evolution

Improved Indel Detection in DNA and RNA via Realignment with ABRA2

(2019) Lisle E Mose et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Unified representation of genetic variants

(2015) Adrian Tan et al.   BIOINFORMATICS

Why do RNA viruses recombine?

(2011) Etienne Simon-Loriere et al.   NATURE REVIEWS MICROBIOLOGY