Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage

Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies

(2022) Aude Jary et al.   Viruses-Basel

Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies

(2022) Masaud Shah et al.   Frontiers in Immunology

Two years of SARS-CoV-2 infection (2019–2021): structural biology, vaccination, and current global situation

(2022) Waqar Ahmad et al.   The Egyptian Journal of Internal Medicine

Differences in environmental stability among SARS-CoV-2 variants of concern: Both Omicron BA.1 and BA.2 have higher stability

(2022) Ryohei Hirose et al.   CLINICAL MICROBIOLOGY AND INFECTION

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

(2022) Matthew McCallum et al.   SCIENCE

The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

(2022) Michael Worobey et al.   SCIENCE

Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape

(2022) Zhennan Zhao et al.   Nature Communications

Clinical severity of Omicron subvariants BA.1, BA.2, and BA.5 in a population‐based cohort study in British Columbia, Canada

(2022) Shannon L. Russell et al.   JOURNAL OF MEDICAL VIROLOGY

SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines

(2021) Xiaoying Shen et al.   Cell Host & Microbe

Sixteen novel lineages of SARS-CoV-2 in South Africa

(2021) Houriiyah Tegally et al.   NATURE MEDICINE

On the origin and evolution of SARS-CoV-2

(2021) Devika Singh et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Mutation rates and selection on synonymous mutations in SARS-CoV-2

(2021) Nicola De Maio et al.   Genome Biology and Evolution

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon

(2021) Rita Feghali et al.   PeerJ

The SARS-CoV-2 Spike variant D614G favors an open conformational state

(2021) Rachael A. Mansbach et al.   Science Advances

Novel and emerging mutations of SARS-CoV-2: Biomedical implications

(2021) Elmira Mohammadi et al.   BIOMEDICINE & PHARMACOTHERAPY

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

(2021) Sarah P. Otto et al.   CURRENT BIOLOGY

Emergence of SARS-CoV-2 variant B.1.575.2 containing the E484K mutation in the spike protein in Pamplona (Spain) May-June 2021

(2021) Camino Trobajo-Sanmartín et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SARS-CoV-2 variants, spike mutations and immune escape

(2021) William T. Harvey et al.   NATURE REVIEWS MICROBIOLOGY

Guidance for Implementing COVID-19 Prevention Strategies in the Context of Varying Community Transmission Levels and Vaccination Coverage

(2021) Athalia Christie et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool

(2021) Áine O’Toole et al.   Virus Evolution

Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database

(2021) Maria Zelenova et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

(2021) Changshuo Wei et al.   Journal of Genetics and Genomics

Impact of the SARS-CoV-2 pandemic and first lockdown on pregnancy monitoring in France: the COVIMATER cross-sectional study

(2021) Alexandra Doncarli et al.   BMC Pregnancy and Childbirth

The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape

(2021) Dandan Tian et al.   Frontiers in Immunology

Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil

(2021) Filipe Romero Rebello Moreira et al.   Virus Evolution

Whole-Genome Sequences of SARS-CoV-2 Isolates from the Dominican Republic

(2021) R. Paulino-Ramirez et al.   Microbiology Resource Announcements

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

(2020) Sara Cleemput et al.   BIOINFORMATICS

Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China

(2020) Aiping Wu et al.   Cell Host & Microbe

Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2

(2020) Xingguang Li et al.   JOURNAL OF MEDICAL VIROLOGY

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Identification of a novel coronavirus causing severe pneumonia in human

(2020) Li-Li Ren et al.   CHINESE MEDICAL JOURNAL

Phylogenetic network analysis of SARS-CoV-2 genomes

(2020) Peter Forster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4+ T cell count

(2020) Wu Menghua et al.   AIDS Research and Therapy

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

(2020) Maciej F. Boni et al.   Nature Microbiology

Seroprevalence of Specific Antibodies against SARS-CoV-2 from Hotspot Communities in the Dominican Republic

(2020) Robert Paulino-Ramirez et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Phylogenetic and phylodynamic analyses of SARS-CoV-2

(2020) Qing Nie et al.   VIRUS RESEARCH

Coronapp : A web application to annotate and monitor SARS‐CoV‐2 mutations

(2020) Daniele Mercatelli et al.   JOURNAL OF MEDICAL VIROLOGY

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic Story

(2013) Israel Pagán et al.   PLoS One

Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System

(2012) Israel Pagán et al.   PLoS Pathogens

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission

(2009) R. L. Graham et al.   JOURNAL OF VIROLOGY

Broadening of Neutralization Activity to Directly Block a Dominant Antibody-Driven SARS-Coronavirus Evolution Pathway

(2008) Jianhua Sui et al.   PLoS Pathogens