Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover model to the viral circulation model

Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

(2021) Kathy Leung et al.   Eurosurveillance

Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia

(2021) Supaporn Wacharapluesadee et al.   Nature Communications

Emergence of Bat-Related Betacoronaviruses: Hazard and Risks

(2021) Roger Frutos et al.   Frontiers in Microbiology

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

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

Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2

(2020) Zhixin Liu et al.   JOURNAL OF MEDICAL VIROLOGY

Cross‐species transmission of the newly identified coronavirus 2019‐nCoV

(2020) Wei Ji et al.   JOURNAL OF MEDICAL VIROLOGY

Early phylogenetic estimate of the effective reproduction number of SARS‐CoV‐2

(2020) Alessia Lai et al.   JOURNAL OF MEDICAL VIROLOGY

Outbreak of pneumonia of unknown etiology in Wuhan, China: The mystery and the miracle

(2020) Hongzhou Lu et al.   JOURNAL OF MEDICAL VIROLOGY

Statement in support of the scientists, public health professionals, and medical professionals of China combatting COVID-19

(2020) Charles Calisher et al.   LANCET

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

HIV-1 did not contribute to the 2019-nCoV genome

(2020) Chuan Xiao et al.   Emerging Microbes & Infections

No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2

(2020) Shan-Lu Liu et al.   Emerging Microbes & Infections

On the origin and continuing evolution of SARS-CoV-2

(2020) Xiaolu Tang et al.   National Science Review

The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

(2020) B. Coutard et al.   ANTIVIRAL RESEARCH

Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection

(2020) Junwen Luan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

(2020) Yong-Zhen Zhang et al.   CELL

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein

(2020) Hong Zhou et al.   CURRENT BIOLOGY

Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak

(2020) Tao Zhang et al.   CURRENT BIOLOGY

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

(2020) D. Paraskevis et al.   INFECTION GENETICS AND EVOLUTION

Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy

(2020) Gianguglielmo Zehender et al.   JOURNAL OF MEDICAL VIROLOGY

Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1

(2020) Chengxin Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Early dynamics of transmission and control of COVID-19: a mathematical modelling study

(2020) Adam J Kucharski et al.   LANCET INFECTIOUS DISEASES

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

(2020) Tommy Tsan-Yuk Lam et al.   NATURE

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

Transmission of SARS-CoV-2 in Domestic Cats

(2020) Peter J. Halfmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2

(2020) Jianzhong Shi et al.   SCIENCE

How related is SARS-CoV-2 to other coronaviruses?

(2020) Nanhua Chen et al.   VETERINARY RECORD

Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?

(2020) Ping Liu et al.   PLoS Pathogens

Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism

(2020) Houcemeddine Othman et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Origins of SARS‐CoV‐1 and SARS‐CoV‐2 are often poorly explored in leading publications

(2020) John Wenzel   CLADISTICS

Natural transmission of bat-like SARS-CoV-2PRRA variants in COVID-19 patients

(2020) Yik Chun Wong et al.   CLINICAL INFECTIOUS DISEASES

SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020

(2020) Nadia Oreshkova et al.   Eurosurveillance

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

(2020) Timokratis Karamitros et al.   JOURNAL OF CLINICAL VIROLOGY

Coronavirus rips through Dutch mink farms, triggering culls

(2020) Martin Enserink   SCIENCE

Wuhan coronavirus hunter Shi Zhengli speaks out

(2020) Jon Cohen   SCIENCE

Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

(2020) Roman Matyášek et al.   Genes

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

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

COVID-19: The Conjunction of Events Leading to the Coronavirus Pandemic and Lessons to Learn for Future Threats

(2020) Roger Frutos et al.   Frontiers in Medicine

COVID-19: Time to exonerate the pangolin from the transmission of SARS-CoV-2 to humans

(2020) Roger Frutos et al.   INFECTION GENETICS AND EVOLUTION

Characterization of codon usage pattern in SARS-CoV-2

(2020) Wei Hou   Virology Journal

Confronting models with data: the challenges of estimating disease spillover

(2019) Paul C. Cross et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

(2019) Ping Liu et al.   Viruses-Basel

Do we need a Global Virome Project?

(2019) Olga Jonas et al.   Lancet Global Health

The Global Virome Project

(2018) Dennis Carroll et al.   SCIENCE

Bats, Coronaviruses, and Deforestation: Toward the Emergence of Novel Infectious Diseases?

(2018) Aneta Afelt et al.   Frontiers in Microbiology

Pathways to zoonotic spillover

(2017) Raina K. Plowright et al.   NATURE REVIEWS MICROBIOLOGY

A single mutation in the prM protein of Zika virus contributes to fetal microcephaly

(2017) Ling Yuan et al.   SCIENCE

Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus

(2017) Ye Chen et al.   Oncotarget

Discrete stochastic analogs of Erlang epidemic models

(2017) Wayne M. Getz et al.   Journal of Biological Dynamics

1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

(2016) Michael Worobey et al.   NATURE

Mathematical models to characterize early epidemic growth: A review

(2016) Gerardo Chowell et al.   Physics of Life Reviews

A Unified Framework for the Infection Dynamics of Zoonotic Spillover and Spread

(2016) Giovanni Lo Iacono et al.   PLoS Neglected Tropical Diseases

Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft

(2016) Xing-Yi Ge et al.   VIROLOGICA SINICA

Using Stable Isotopes to Infer the Impacts of Habitat Change on the Diets and Vertical Stratification of Frugivorous Bats in Madagascar

(2016) Kim E. Reuter et al.   PLoS One

Viral quasispecies

(2015) Raul Andino et al.   VIROLOGY

Middle East Respiratory Syndrome Coronavirus Quasispecies That Include Homologues of Human Isolates Revealed through Whole-Genome Analysis and Virus Cultured from Dromedary Camels in Saudi Arabia

(2014) T. Briese et al.   mBio

Influenza surveillance in Europe: establishing epidemic thresholds by the Moving Epidemic Method

(2012) Tomás Vega et al.   Influenza and Other Respiratory Viruses

Sequential Adaptive Mutations Enhance Efficient Vector Switching by Chikungunya Virus and Its Epidemic Emergence

(2011) Konstantin A. Tsetsarkin et al.   PLoS Pathogens

Proteolytic Activation of the Spike Protein at a Novel RRRR/S Motif Is Implicated in Furin-Dependent Entry, Syncytium Formation, and Infectivity of Coronavirus Infectious Bronchitis Virus in Cultured Cells

(2009) Y. Yamada et al.   JOURNAL OF VIROLOGY

A226V mutation in virus during the 2007 chikungunya outbreak in Kerala, India

(2008) N. P. Kumar et al.   JOURNAL OF GENERAL VIROLOGY

Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice

(2008) M. M. Becker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA