The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Article Cell Biology

Serosurvey for SARS-CoV-2 among blood donors in Wuhan, China from September to December 2019

Le Chang et al.

Summary: By studying blood donors in Wuhan from September to December 2019, it was found that there were no SARS-CoV-2 specific antibodies existing before 2020, indicating no evidence of COVID-19 transmission in Wuhan before December 2019.

PROTEIN & CELL (2023)

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Article Evolutionary Biology

Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination

Spyros Lytras et al.

Summary: The study suggests that horseshoe bats in southern China and Southeast Asia are likely the reservoir species for the proximal animal ancestor of SARS-CoV-2. The research also reveals recent geographic movement and cocirculation of these viruses' ancestors. However, a direct proximal ancestor to SARS-CoV-2 has not been sampled yet, highlighting the need for more wildlife sampling to determine the exact origins, intermediate species involved in transmission, and the diversity of related sarbecoviruses that pose a high risk for future spillovers.

GENOME BIOLOGY AND EVOLUTION (2022)

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Article Biochemistry & Molecular Biology

Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza

Mahan Ghafari et al.

Summary: High-throughput sequencing allows rapid genome sequencing during outbreaks, providing insight into pathogen evolution dynamics. Evolutionary analyses over short timescales are challenging due to the time-dependent nature of evolutionary rate estimates. The study on SARS-CoV-2 and pH1N1 influenza found that inferred evolutionary parameters decline over time, with growth rates and emergence dates stable after 4 months. Terminal branches exhibit elevated substitution rates, correlated with purifying selection generating time dependency in evolutionary parameters.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

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Article Multidisciplinary Sciences

SARS-CoV-2 infection in free-ranging white-tailed deer

Vanessa L. Hale et al.

Summary: Research shows that free-ranging white-tailed deer in northeast Ohio, USA are highly susceptible to SARS-CoV-2 infection, potentially enabling the virus to be transmitted in wildlife, opening up new pathways for evolution.

NATURE (2022)

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Article Multidisciplinary Sciences

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

Sarah Temmam et al.

Summary: SARS-CoV-2-like bat viruses that are potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula, and they can enter human cells through the hACE2 pathway, indicating the need for further understanding of the origin of the epidemic.

NATURE (2022)

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Article Multidisciplinary Sciences

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Suresh V. Kuchipudi et al.

Summary: White-tailed deer, particularly in Iowa, have been found to be susceptible to SARS-CoV-2 infection and show evidence of human-to-deer transmission. This discovery highlights the need for a One Health approach to better understand the ecology, molecular evolution, and dissemination of the virus.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Biochemical Research Methods

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity

Marcos A. Caraballo-Ortiz et al.

Summary: This study developed a method called TopHap that uses common variant positions to determine spatiotemporally common haplotypes and builds their phylogeny in a fraction of the computational time of traditional methods. Applying TopHap to 68,057 SARS-CoV-2 genomes produced an evolutionary tree of major haplotypes that was consistent with other traditional analyses. The study also evaluated alternative roots of the SARS-CoV-2 phylogeny and discovered that the earliest sampled genomes likely evolved from the most recent common ancestor through four mutations. Additionally, applying TopHap to over 1 million SARS-CoV-2 genomes reconstructed the most comprehensive evolutionary relationships of major variants, confirming the 68KG phylogeny and providing evolutionary origins of major and recent variants of concern.

BIOINFORMATICS (2022)

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Article Medicine, General & Internal

Transmission of SARS-CoV-2 delta variant (AY.127) from pet hamsters to humans, leading to onward human-to-human transmission: a case study

Hui-Ling Yen et al.

LANCET (2022)

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Article Evolutionary Biology

Accuracy in Near-Perfect Virus Phylogenies

Joel O. Wertheim et al.

Summary: Phylogenetic trees based on real-world data often contain short branches with few substitutions per site, leading to partially resolved trees and low accuracy. However, accuracy can still be high even with common short branches if it is defined in terms of the rate of discovering false splits. The expected false positive rate in a near-perfect parameter space is lower than 1/3, and this result holds for maximum parsimony and maximum likelihood methods.

SYSTEMATIC BIOLOGY (2022)

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Article Multidisciplinary Sciences

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

Michael Worobey et al.

Summary: This article demonstrates that the SARS-CoV-2 virus originated from the Huanan Seafood Wholesale Market in Wuhan, China, where susceptible animals were sold in late 2019, and SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live animals.

SCIENCE (2022)

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Article Infectious Diseases

Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: a retrospective observational study

Fang Li et al.

LANCET INFECTIOUS DISEASES (2021)

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Article Biochemistry & Molecular Biology

Assessing Uncertainty n the Rooting of the SARS-CoV-2 Phylogeny

Lenore Pipes et al.

Summary: Research on the rooting of the SARS-CoV-2 phylogeny shows that methods based on molecular clock tend to place the root in the B clade, while outgroup rooting methods tend to place it in the A clade. However, these results are statistically incompatible, and none of the methods provide strong statistical support for the placement of the root in any specific edge of the tree. This suggests that phylogenetic evidence alone is unlikely to identify the origin of the SARS-CoV-2 virus, cautioning against strong inferences about the early spread of the virus based solely on this evidence.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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Article Multidisciplinary Sciences

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Louis du Plessis et al.

Summary: The study analyzed the genetic lineage structure of the early UK COVID-19 epidemic through genomic sampling, identifying that virus lineages introduced before the national lockdown tended to be larger and more dispersed. After the lockdown, lineage importation and regional diversity decreased, while lineage elimination depended on lineage size. The research emphasizes the impact of genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

SCIENCE (2021)

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Article Virology

Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution

Jeremy Ratcliff et al.

Summary: Members of the APOBEC family exhibit antiviral activities in mammalian cells through lethal editing of the genomes of various viruses, including RNA viruses like coronaviruses. APOBEC-like C-*U transitions are significantly overrepresented in the SARS-CoV-2 genome sequences during the COVID-19 pandemic, which may leave evolutionary imprints on coronavirus genomes. This process may lead to homoplasy and amino acid sequence changes in viral proteins, potentially explaining global depletion of C and excess of U bases in human seasonal coronavirus genomes.

VIROLOGY (2021)

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Article Multidisciplinary Sciences

Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

Claudia Alteri et al.

Summary: The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Using whole genome sequencing, researchers found multiple virus introductions into the region with transmission occurring before the first case was detected.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Independent infections of porcine deltacoronavirus among Haitian children

John A. Lednicky et al.

Summary: Since 2003, coronaviruses have caused three major epidemics, including the ongoing SARS-CoV-2 pandemic. The emergence of coronaviruses in human species has been associated with zoonotic transmissions from animal reservoirs, emphasizing the propensity of such pathogens to spill over and adapt to new species.

NATURE (2021)

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Editorial Material Multidisciplinary Sciences

Dissecting the early COVID-19 cases in Wuhan

Michael Worobey

SCIENCE (2021)

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Article Multidisciplinary Sciences

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands

Lu Lu et al.

Summary: In the first wave of the COVID-19 pandemic, SARS-CoV-2 was detected in mink farms in April 2020, leading to infections in minks and farm workers. The virus spread rapidly between mink farms, with a significant mutation in the Spike protein. Movement of people and distance between farms were significant predictors in viral dissemination between farms.

NATURE COMMUNICATIONS (2021)

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Article Biology

Estimating the reproductive number R0 of SARS-CoV-2 in the United States and eight European countries and implications for vaccination

Ruian Ke et al.

Summary: The rapid spread of SARS-CoV-2 from a regional outbreak to a global pandemic necessitated high levels of intervention efforts to mitigate or contain the exponential epidemic growth. The early epidemic grew at exponential rates between 0.18 and 0.29/day, emphasizing the importance of effective control measures.

JOURNAL OF THEORETICAL BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic

Sudhir Kumar et al.

Summary: Global sequencing of SARS-CoV-2 genomes has uncovered the genetic variants that contribute to its early evolutionary history and global spread. A likely common ancestor of SARS-CoV-2 was identified, showing that the virus had spread worldwide months before the first reported cases in China. The same coronavirus lineage dominated North America in 2020, while Europe and Asia saw multiple replacements of predominant strains.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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Article Genetics & Heredity

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Yatish Turakhia et al.

Summary: UShER is an efficient method that aids in real-time analysis of viral evolution during the COVID-19 pandemic by facilitating the addition of new SARS-CoV-2 genome sequences onto the existing phylogeny. The unprecedented accumulation of viral genome sequences is leading to a new era of 'genomic contact tracing' using viral genomes to trace local transmission dynamics. UShER addresses the challenge of placing new sequences onto the already large viral phylogeny, thus improving the speed of phylogenetic placement and data visualization for real-time contact tracing.

NATURE GENETICS (2021)

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Article Biology

Speed and strength of an epidemic intervention

Jonathan Dushoff et al.

Summary: Disease modellers have historically focused more on the strength of an epidemic, but speed is also an important factor. A new speed-based paradigm has been developed to provide complementary insights for research. When evaluating the effectiveness of disease intervention measures, the speed-based paradigm may offer a clearer view of the situation.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2021)

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Article Multidisciplinary Sciences

Timing the SARS-CoV-2 index case in Hubei province

Jonathan Pekar et al.

Summary: The study found that SARS-CoV-2 may have emerged in Hubei province, China between mid-October and mid-November 2019. The dynamics of the virus before discovery showed that over two-thirds of SARS-CoV-2-like zoonotic events would self-limit, without causing a pandemic. The study highlights shortcomings in current zoonosis surveillance methods.

SCIENCE (2021)

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Article Biochemistry & Molecular Biology

Emergence of an early SARS-CoV-2 epidemic in the United States

Mark Zeller et al.

Summary: The COVID-19 epidemic in the U.S. was initially undetected due to inadequate testing. New Orleans experienced an early outbreak related to Mardi Gras, with one introduction of SARS-CoV-2 leading to most of the early transmission. Genomic data showed SARS-CoV-2 was present in New Orleans before Mardi Gras, and the festival significantly accelerated transmission.

CELL (2021)

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Review Biochemistry & Molecular Biology

The origins of SARS-CoV-2: A critical review

Edward C. Holmes et al.

Summary: This article critically reviews the current scientific evidence to help clarify the origin of SARS-CoV-2. Recent debate has centered around two competing ideas: a laboratory escape scenario and zoonotic emergence.

CELL (2021)

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Article Biochemistry & Molecular Biology

Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic

Jesse D. Bloom

Summary: The study reveals that a data set containing early Wuhan epidemic SARS-CoV-2 sequences deleted from the NIH's Sequence Read Archive has been recovered and analyzed, suggesting that the sequences from Huanan Seafood Market do not fully represent the early viruses in Wuhan. It is suggested that the progenitor of known SARS-CoV-2 sequences likely had three mutations making it more similar to bat coronavirus relatives than the market viruses.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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Article Biology

Challenges in control of COVID-19: short doubling time and long delay to effect of interventions

Lorenzo Pellis et al.

Summary: Early assessments of COVID-19 growth rate were uncertain due to limited data, but as cases were recorded in multiple countries, more reliable inferences could be made. Physical distancing interventions typically did not show impact until at least 9 days after implementation, during which time confirmed cases could grow eightfold. Precise estimates of the time-sensitive basic reproduction number R-0 were found to be less critical than temporal patterns for initiating interventions.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2021)

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Article Multidisciplinary Sciences

Animal sales from Wuhan wet markets immediately prior to the COVID-19 pandemic

Xiao Xiao et al.

Summary: The study documents the sale of 47,381 individuals from 38 species in Wuhan's markets, noting the absence of pangolins and bats which supports the theory that they are not the source of the COVID-19 pandemic. China implemented a temporary ban on wildlife trade and a permanent ban on eating and trading terrestrial wild animals to protect human health, address past inconsistencies, and benefit global biodiversity conservation and animal welfare.

SCIENTIFIC REPORTS (2021)

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Article Microbiology

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Katarina M. Braun et al.

Summary: The study shows that within-host diversity of SARS-CoV-2 is low and transmission bottlenecks are narrow, with most infections founded by very few viruses. Within-host variants are rarely transmitted, even within the same household, and are seldom detected along phylogenetically linked infections within the broader community. This suggests that most variation generated within-host is lost during transmission.

PLOS PATHOGENS (2021)

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Article Microbiology

Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA

Peter Simmonds et al.

Summary: The study found a preponderance of C->U transitions in diverse mammalian RNA viruses, suggesting a potential RNA editing process driving this phenomenon. The presence of genome scale RNA secondary structure was significantly associated with C->U/U->C transition asymmetries, indicating a possible RNA structure dependence of sites targeted for C->U mutations. These C->U mutations accounted for a significant portion of standing sequence variability of structured viruses, potentially driving their sequence diversification and longer-term evolution.

PLOS PATHOGENS (2021)

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Article Microbiology

Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers

Takayuki Murata et al.

Summary: This study evaluated the infectivity of SARS-CoV-2 in nasopharyngeal samples from asymptomatic carriers during a COVID-19 outbreak, finding that asymptomatic carriers can shed viable virus until 7 days after the initial positive PCR test. The crossing point (Cp) value of RT-PCR was associated with virus viability and may serve as a predictive factor. These findings highlight the potential role of asymptomatic carriers in transmission.

MSPHERE (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus)

Jeffrey C. Chandler et al.

Summary: Research indicates that white-tailed deer in the United States have been exposed to SARS-CoV-2, with 40% of samples testing positive for antibodies. This suggests that human infections of the novel coronavirus may have an impact on wildlife.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Multidisciplinary Sciences

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Bas B. Oude Munnink et al.

Summary: Animal experiments have shown that various animals can be infected by SARS-CoV-2, with evidence of animal-to-human transmission within mink farms. Investigation into mink farm outbreaks revealed that the virus was initially introduced by humans and has since evolved, causing transmission between mink farms. Despite enhanced biosecurity measures and culling, transmission occurred between farms in three large clusters with unknown modes of transmission, resulting in a high percentage of infections among mink farm residents and employees.

SCIENCE (2021)

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Article Medicine, General & Internal

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

Roujian Lu et al.

LANCET (2020)

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Article Medicine, General & Internal

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

Chaolin Huang et al.

LANCET (2020)

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Letter Infectious Diseases

An interactive web-based dashboard to track COVID-19 in real time

Ensheng Dong et al.

LANCET INFECTIOUS DISEASES (2020)

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Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

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Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

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Article Multidisciplinary Sciences

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

Peng Zhou et al.

NATURE (2020)

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Article Medicine, General & Internal

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia

Qun Li et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Article Multidisciplinary Sciences

The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak

Matteo Chinazzi et al.

SCIENCE (2020)

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Article Medicine, General & Internal

Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study

Li-Li Ren et al.

CHINESE MEDICAL JOURNAL (2020)

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Article Critical Care Medicine

Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study

Xiaobo Yang et al.

Lancet Respiratory Medicine (2020)

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Article Multidisciplinary Sciences

Phylogenetic network analysis of SARS-CoV-2 genomes

Peter Forster et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2)

Ruiyun Li et al.

SCIENCE (2020)

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Article Medicine, General & Internal

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Fei Zhou et al.

LANCET (2020)

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Article Multidisciplinary Sciences

Viral and host factors related to the clinical outcome of COVID-19

Xiaonan Zhang et al.

NATURE (2020)

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Letter Biochemistry & Molecular Biology

The proximal origin of SARS-CoV-2

Kristian G. Andersen et al.

NATURE MEDICINE (2020)

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Article Biochemistry & Molecular Biology

Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China

Joseph T. Wu et al.

NATURE MEDICINE (2020)

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Article Microbiology

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

Andrew Rambaut et al.

NATURE MICROBIOLOGY (2020)

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Article Microbiology

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

Maciej F. Boni et al.

NATURE MICROBIOLOGY (2020)

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Article Microbiology

Rampant C -> U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

P. Simmonds

MSPHERE (2020)

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Article Multidisciplinary Sciences

The effect of large-scale anti-contagion policies on the COVID-19 pandemic

Solomon Hsiang et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Reconstruction of the full transmission dynamics of COVID-19 in Wuhan

Xingjie Hao et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak

Tsuyoshi Sekizuka et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

The challenges of modeling and forecasting the spread of COVID-19

Andrea L. Bertozzi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

Cryptic transmission of SARS-CoV-2 in Washington state

Trevor Bedford et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Disease burden and clinical severity of the first pandemic wave of COVID-19 in Wuhan, China

Juan Yang et al.

NATURE COMMUNICATIONS (2020)

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Article Immunology

Susceptibility of Raccoon Dogs for Experimental SARS-CoV-2 Infection

Conrad M. Freuling et al.

EMERGING INFECTIOUS DISEASES (2020)

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Article Immunology

High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2

Steven Sanche et al.

EMERGING INFECTIOUS DISEASES (2020)

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Article Computer Science, Software Engineering

TreeSwift: A massively scalable Python tree package

N. Moshiri

SOFTWAREX (2020)

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Article Biochemical Research Methods

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

Niema Moshiri et al.

BIOINFORMATICS (2019)

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Article Biotechnology & Applied Microbiology

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Nathan D. Grubaugh et al.

GENOME BIOLOGY (2019)

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Article Biochemistry & Molecular Biology

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm

Ha Minh Lam et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

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Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

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Article Biochemical Research Methods

Nextstrain: real-time tracking of pathogen evolution

James Hadfield et al.

BIOINFORMATICS (2018)

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Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

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Article Biology

MERS-CoV spillover at the camel-human interface

Gytis Dudas et al.

ELIFE (2018)

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Article Virology

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Marc A. Suchard et al.

VIRUS EVOLUTION (2018)

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Article Virology

TreeTime: Maximum-likelihood phylodynamic analysis

Pavel Sagulenko et al.

VIRUS EVOLUTION (2018)

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Editorial Material Infectious Diseases

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

Yuelong Shu et al.

EUROSURVEILLANCE (2017)

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Article Computer Science, Interdisciplinary Applications

GEMFsim: A stochastic simulator for the generalized epidemic modeling framework

Faryad Darabi Sahneh et al.

JOURNAL OF COMPUTATIONAL SCIENCE (2017)

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Article Virology

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

Andrew Rambaut et al.

VIRUS EVOLUTION (2016)

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Article Medicine, Research & Experimental

Investigating the zoonotic origin of the West African Ebola epidemic

Almudena Mari Saez et al.

EMBO MOLECULAR MEDICINE (2015)

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Article Virology

RDP4: Detection and analysis of recombination patterns in virus genomes

Darren P. Martin et al.

VIRUS EVOLUTION (2015)

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Letter Medicine, General & Internal

Primary and index cases

Johan Giesecke

LANCET (2014)

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Article Biology

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

Sebastian Duchene et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2014)

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Article Ecology

MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

James B. Pease et al.

EVOLUTION (2013)

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Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

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Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

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Article Medicine, General & Internal

Social contacts and mixing patterns relevant to the spread of infectious diseases

Joeel Mossong et al.

PLOS MEDICINE (2008)

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Article Biochemical Research Methods

GARD: a genetic algorithm for recombination detection

Sergei L. Kosakovsky Pond et al.

BIOINFORMATICS (2006)

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Article Virology

Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms

B Kan et al.

JOURNAL OF VIROLOGY (2005)

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Article Multidisciplinary Sciences

Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China

JF He et al.

SCIENCE (2004)

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Article Multidisciplinary Sciences

Modelling disease outbreaks in realistic urban social networks

S Eubank et al.

NATURE (2004)

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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

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