Evolution of the viral genomes of SARS-CoV-2 in association with the changes in local condition: a genomic epidemiological study of a suburban city of Japan

COVID-19 in Japan, January–March 2020: insights from the first three months of the epidemic

(2022) Natsuko Imai et al.   BMC INFECTIOUS DISEASES

Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021

(2022) Kathleen Subramoney et al.   JOURNAL OF MEDICAL VIROLOGY

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

(2022) Houriiyah Tegally et al.   NATURE MEDICINE

Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5

(2022) Izumi Kimura et al.   CELL

Characterization of SARS-CoV-2 Omicron BA.4 and BA.5 isolates in rodents

(2022) Ryuta Uraki et al.   NATURE

Ebola virus disease

(2020) Shevin T. Jacob et al.   Nature Reviews Disease Primers

COVID-19, SARS and MERS: are they closely related?

(2020) N. Petrosillo et al.   CLINICAL MICROBIOLOGY AND INFECTION

Cluster infections play important roles in the rapid evolution of COVID-19 transmission: a systematic review

(2020) Tao Liu et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

(2020) Davide F. Robbiani et al.   NATURE

Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein

(2020) Seth J. Zost et al.   NATURE MEDICINE

Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

(2020) Philip J. M. Brouwer et al.   SCIENCE

Applying lessons from the Ebola vaccine experience for SARS-CoV-2 and other epidemic pathogens

(2020) Jayanthi Wolf et al.   npj Vaccines

Characteristics of SARS-CoV-2 and COVID-19

(2020) Ben Hu et al.   NATURE REVIEWS MICROBIOLOGY

Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020

(2020) Jiratchaya Puenpa et al.   Scientific Reports

Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2

(2020) Alexandra Popa et al.   Science Translational Medicine

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

(2020) Ana da Silva Filipe et al.   Nature Microbiology

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

OUP accepted manuscript

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popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH