Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

[1]  O. Pybus,et al.  Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America , 2021, Cell Host & Microbe.

[2]  Julia A. Palacios,et al.  Adaptive Preferential Sampling in Phylodynamics With an Application to SARS-CoV-2 , 2021, J. Comput. Graph. Stat..

[3]  M. Clerici,et al.  The substitution spectra of coronavirus genomes , 2021, Briefings Bioinform..

[4]  M. Kraemer,et al.  Progress and challenges in virus genomic epidemiology. , 2021, Trends in parasitology.

[5]  R. Bouckaert,et al.  Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand , 2021, Emerging infectious diseases.

[6]  Nuno R. Faria,et al.  Global disparities in SARS-CoV-2 genomic surveillance , 2021, medRxiv.

[7]  Rommie E. Amaro,et al.  SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma , 2021, Proceedings of the National Academy of Sciences.

[8]  G. Saberwal,et al.  The lag in SARS-CoV-2 genome submissions to GISAID , 2021, Nature Biotechnology.

[9]  J. Dennehy,et al.  Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater , 2021, Nature Communications.

[10]  Gene W. Yeo,et al.  Emergence of an early SARS-CoV-2 epidemic in the United States , 2021, Cell.

[11]  V. Sintchenko,et al.  Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study , 2021, The Lancet Public Health.

[12]  S. Singh,et al.  SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India , 2021, Microorganisms.

[13]  Mandev S. Gill,et al.  Untangling introductions and persistence in COVID-19 resurgence in Europe , 2021, Nature.

[14]  P. Kaleebu,et al.  Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda , 2021, Nature Microbiology.

[15]  Colin Simpson,et al.  Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations , 2021, Virus evolution.

[16]  G. Wallau,et al.  Identification of SARS-CoV-2 P.1-related lineages in Brazil provides new insights about the mechanisms of emergence of Variants of Concern , 2021 .

[17]  William T. Harvey,et al.  Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7 , 2021, Cell Reports.

[18]  G. Wallau,et al.  COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence , 2021, Nature Medicine.

[19]  G. Barton,et al.  Effects of common mutations in the SARS-CoV-2 Spike RBD domain and its ligand the human ACE2 receptor on binding affinity and kinetics , 2021, bioRxiv.

[20]  M. von Kleist,et al.  Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020 , 2021, Nature Communications.

[21]  Matthew T. Maurano,et al.  Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City , 2021, PLoS pathogens.

[22]  Ravindra K. Gupta.  Will SARS-CoV-2 variants of concern affect the promise of vaccines? , 2021, Nature Reviews Immunology.

[23]  C. Donnelly,et al.  Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions , 2021, Nature Communications.

[24]  Gene W. Yeo,et al.  Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States , 2021, Cell.

[25]  Graham W. Taylor,et al.  Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Nature.

[26]  S. Duchêne,et al.  Development of Phylodynamic Methods for Bacterial Pathogens. , 2021, Trends in microbiology.

[27]  William T. Harvey,et al.  Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies , 2021, Nature.

[28]  Sergei L. Kosakovsky Pond,et al.  Detection of a SARS-CoV-2 variant of concern in South Africa , 2021, Nature.

[29]  D. Ho,et al.  Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 , 2021, Nature.

[30]  R. Lanfear,et al.  Want to track pandemic variants faster? Fix the bioinformatics bottleneck , 2021, Nature.

[31]  D. Stuart,et al.  Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera , 2021, Cell.

[32]  M. Giovanetti,et al.  Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil , 2021, Emerging infectious diseases.

[33]  Richard van Noorden.  Scientists call for fully open sharing of coronavirus genome data , 2021, Nature.

[34]  W. Fischer,et al.  Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-CoV-2 mutations on viral transmissibility , 2021, bioRxiv.

[35]  M. Montecino,et al.  SARS-CoV-2 infection in asymptomatic healthcare workers at a clinic in Chile , 2021, PloS one.

[36]  Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia , 2021, Nature communications.

[37]  D. Ho,et al.  Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 , 2021, bioRxiv.

[38]  Nuno R. Faria,et al.  Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020 , 2021, Emerging infectious diseases.

[39]  Jie-Li Hu,et al.  Emerging SARS-CoV-2 variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies , 2021, Cellular & Molecular Immunology.

[40]  M. N. Kim,et al.  Epidemiologic Linkage of COVID-19 Outbreaks at Two University-affiliated Hospitals in the Seoul Metropolitan Area in March 2020 , 2021, Journal of Korean medical science.

[41]  E. Callaway.  ‘A bloody mess’: Confusion reigns over naming of new COVID variants , 2021, Nature.

[42]  Colin Simpson,et al.  Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing , 2021, Emerging Infectious Diseases.

[43]  A. Tanuri,et al.  Genomic Characterization of a Novel SARS-CoV-2 Lineage from Rio de Janeiro, Brazil , 2020, Journal of Virology.

[44]  Joshua B. Singer,et al.  Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland , 2020, Nature Microbiology.

[45]  Y. Furuse.  Genomic sequencing effort for SARS-CoV-2 by country during the pandemic , 2020, International Journal of Infectious Diseases.

[46]  Melis N. Anahtar,et al.  Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events , 2020, Science.

[47]  K. V. Parag,et al.  Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK , 2020, medRxiv.

[48]  D. A. Jackson,et al.  Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity , 2020, Cell.

[49]  T. Vaughan,et al.  The origin and early spread of SARS-CoV-2 in Europe , 2020, Proceedings of the National Academy of Sciences.

[50]  Eric P. Nawrocki,et al.  Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research , 2020, Briefings Bioinform..

[51]  OUP accepted manuscript , 2021, Virus Evolution.

[52]  Nuno R. Faria,et al.  Genomic characterisation of an emergent SARS- CoV-2 lineage in Manaus: preliminary findings , 2021 .

[53]  A. Godzik,et al.  Detection of a SARS-CoV-2 variant of concern in South Africa , 2021, Nature.

[54]  Genomic sequencing of SARS-CoV-2 , 2021 .

[55]  William L. Hamilton,et al.  Patterns of within-host genetic diversity in SARS-CoV-2 , 2020, bioRxiv.

[56]  B. Cavadas,et al.  Dynamics of a dual SARS-CoV-2 strain co-infection on a prolonged viral shedding COVID-19 case: insights into clinical severity and disease duration , 2020, medRxiv.

[57]  F. Balloux,et al.  No detectable signal for ongoing genetic recombination in SARS-CoV-2 , 2020, bioRxiv.

[58]  Wendy Lu,et al.  Timely intervention and control of a novel coronavirus (COVID-19) outbreak at a large skilled nursing facility—San Francisco, California, 2020 , 2020, Infection Control & Hospital Epidemiology.

[59]  Paolo Calistri,et al.  Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy , 2020, Viruses.

[60]  Santiago Justo Arévalo,et al.  Analysis of the Dynamics and Distribution of SARS-CoV-2 Mutations and its Possible Structural and Functional Implications , 2020, bioRxiv.

[61]  Lisa E. Gralinski,et al.  SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo , 2020, Science.

[62]  M. Schuld,et al.  Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report , 2020, International Journal of Infectious Diseases.

[63]  Mandev S. Gill,et al.  Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework , 2020, Nature Communications.

[64]  A. Pain,et al.  Host-directed editing of the SARS-CoV-2 genome , 2020, Biochemical and Biophysical Research Communications.

[65]  Trent M. Prall,et al.  Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread , 2020, Nature Communications.

[66]  M. Thomson,et al.  A Founder Effect Led Early SARS-CoV-2 Transmission in Spain , 2020, Journal of Virology.

[67]  M. Koopmans,et al.  Unraveling the Modes of Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) During a Nursing Home Outbreak: Looking Beyond the Church Superspreading Event , 2020, Clinical Infectious Diseases.

[68]  Ankit Gupta,et al.  A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences , 2020, bioRxiv.

[69]  A. Tatem,et al.  Uncovering two phases of early intercontinental COVID-19 transmission dynamics , 2020, Journal of travel medicine.

[70]  L. Parida,et al.  A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones , 2020, BMC Genomics.

[71]  J. Sevinsky,et al.  Genomic evidence for reinfection with SARS-CoV-2: a case study , 2020, The Lancet Infectious Diseases.

[72]  M. Suchard,et al.  Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2 , 2020, Nature Communications.

[73]  M. Exner,et al.  SARS‐CoV‐2 outbreak investigation in a German meat processing plant , 2020, EMBO molecular medicine.

[74]  D. Larsen,et al.  Tracking COVID-19 with wastewater , 2020, Nature Biotechnology.

[75]  Lisa A. Jacobson,et al.  Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks — Minnesota, April–June 2020 , 2020, MMWR. Morbidity and mortality weekly report.

[76]  L. Poon,et al.  In-Flight Transmission of SARS-CoV-2 , 2020, Emerging Infectious Diseases.

[77]  H. Sax,et al.  Does respiratory co-infection facilitate dispersal of SARS-CoV-2? investigation of a super-spreading event in an open-space office , 2020, Antimicrobial resistance and infection control.

[78]  T. Vaughan,et al.  Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data , 2020, medRxiv.

[79]  Trevor Bedford,et al.  Cryptic transmission of SARS-CoV-2 in Washington state , 2020, Science.

[80]  Joel O. Wertheim,et al.  The emergence of SARS-CoV-2 in Europe and North America , 2020, Science.

[81]  M. Koopmans,et al.  Unravelling the modes of transmission of SARS-CoV-2 during a nursing home outbreak: looking beyond the church super-spread event , 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[82]  Bethany L. Dearlove,et al.  A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants , 2020, Proceedings of the National Academy of Sciences.

[83]  G. Boland,et al.  The SARS-CoV-2 Spike mutation D614G increases entry fitness across a range of ACE2 levels, directly outcompetes the wild type, and is preferentially incorporated into trimers , 2020, bioRxiv.

[84]  Sarah K. Hilton,et al.  Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding , 2020, Cell.

[85]  B. Lina,et al.  Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France , 2020, bioRxiv.

[86]  Benoit Morel,et al.  Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult , 2020, bioRxiv.

[87]  Colin Simpson,et al.  Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand , 2020, Nature Communications.

[88]  Amogelang R. Raphenya,et al.  A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture , 2020, Viruses.

[89]  Darren L. Smith,et al.  Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 , 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[90]  B. Wiedenheft,et al.  Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater , 2020, Cell Reports Medicine.

[91]  R. Myers,et al.  Increased risk of SARS-CoV-2 infection in staff working across different care homes: enhanced CoVID-19 outbreak investigations in London care Homes , 2020, Journal of Infection.

[92]  D. Flichman,et al.  Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence , 2020, bioRxiv.

[93]  F. Giardina,et al.  Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy , 2020, Nature Communications.

[94]  L. Hurst,et al.  Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design , 2020, Molecular biology and evolution.

[95]  Edward C. Holmes,et al.  A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology , 2020, Nature Microbiology.

[96]  William L. Hamilton,et al.  Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study , 2020, The Lancet Infectious Diseases.

[97]  J. R. Giles,et al.  Sample size calculation for phylogenetic case linkage , 2020, medRxiv.

[98]  M. Zazzi,et al.  Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic , 2020, medRxiv.

[99]  William P. Hanage,et al.  Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear , 2020, Cell.

[100]  A. Rambaut,et al.  COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study , 2020, The Lancet Infectious Diseases.

[101]  T. Wakita,et al.  A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan , 2020, mSphere.

[102]  B. Lina,et al.  Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation , 2020, bioRxiv.

[103]  S. Rowland-Jones,et al.  Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus , 2020, Cell.

[104]  P. Simmonds,et al.  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 , 2020, mSphere.

[105]  Samir Bhatt,et al.  Evolution and epidemic spread of SARS-CoV-2 in Brazil , 2020, Science.

[106]  S. Otto,et al.  On the evolutionary epidemiology of SARS-CoV-2 , 2020, Current Biology.

[107]  Jason D. Fernandes,et al.  Stability of SARS-CoV-2 phylogenies , 2020, bioRxiv.

[108]  Trevor Bedford,et al.  Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California , 2020, Science.

[109]  S. Bhatt,et al.  Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe , 2020, Nature.

[110]  J. Lourenco,et al.  Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report , 2020, International Journal of Infectious Diseases.

[111]  A. Huppert,et al.  Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel , 2020, Nature Communications.

[112]  F. Balloux,et al.  No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2 , 2020, Nature Communications.

[113]  E. Volz,et al.  Emerging phylogenetic structure of the SARS-CoV-2 pandemic , 2020, bioRxiv.

[114]  W. Hanage,et al.  Phylogenetic interpretation during outbreaks requires caution , 2020, Nature Microbiology.

[115]  Mark B. Schultz,et al.  Tracking the COVID-19 pandemic in Australia using genomics , 2020, Nature Communications.

[116]  Victor M Corman,et al.  Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series , 2020, The Lancet Infectious Diseases.

[117]  D. Patrick,et al.  High SARS-CoV-2 Attack Rate Following Exposure at a Choir Practice - Skagit County, Washington, March 2020. , 2020, MMWR. Morbidity and mortality weekly report.

[118]  P. Lemey,et al.  Temporal signal and the phylodynamic threshold of SARS-CoV-2 , 2020, bioRxiv.

[119]  Isaac I. Bogoch,et al.  Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States , 2020, Cell.

[120]  M. Antoniotti,et al.  VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples , 2020, bioRxiv.

[121]  Trevor Bedford,et al.  Cryptic transmission of SARS-CoV-2 in Washington state , 2020, Science.

[122]  Wenjun Ma,et al.  Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China , 2020, Cell.

[123]  Takuri Takahashi,et al.  Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak , 2020, Proceedings of the National Academy of Sciences.

[124]  O. Boyd,et al.  Genomic epidemiology of a densely sampled COVID-19 outbreak in China , 2020, medRxiv.

[125]  Yang Liu,et al.  Secondary attack rate and superspreading events for SARS-CoV-2 , 2020, The Lancet.

[126]  V. Corman,et al.  Severe Acute Respiratory Syndrome Coronavirus 2 Outbreak Related to a Nightclub, Germany, 2020 , 2020, Emerging infectious diseases.

[127]  Kheir M. Al-Kodmany.  Preliminary Findings , 2020, The Urban Book Series.

[128]  Louis du Plessis,et al.  Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences , 2019, bioRxiv.

[129]  E. Holmes,et al.  Infectious disease phylodynamics with occurrence data , 2019, bioRxiv.

[130]  O. Pybus,et al.  Parallel molecular evolution and adaptation in viruses , 2019, Current Opinion in Virology.

[131]  David A. Rasmussen,et al.  Estimating Epidemic Incidence and Prevalence from Genomic Data , 2018, bioRxiv.

[132]  Trevor Bedford,et al.  Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.

[133]  Richard A Neher,et al.  TreeTime: Maximum-likelihood phylodynamic analysis , 2017, bioRxiv.

[134]  Hayden C. Metsky,et al.  Genomic epidemiology reveals multiple introductions of Zika virus into the United States , 2017, Nature.

[135]  Trevor Bedford,et al.  Virus genomes reveal factors that spread and sustained the Ebola epidemic , 2017, Nature.

[136]  Yuelong Shu,et al.  GISAID: Global initiative on sharing all influenza data – from vision to reality , 2017, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[137]  Paul Kellam,et al.  Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases , 2016, Virus evolution.

[138]  Nicola De Maio,et al.  New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation , 2015, PLoS genetics.

[139]  Lucie M. Gattepaille,et al.  Inferring population size changes with sequence and SNP data: lessons from human bottlenecks , 2013, Heredity.

[140]  S. Bonhoeffer,et al.  Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) , 2012, Proceedings of the National Academy of Sciences.

[141]  M. Suchard,et al.  Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A. , 2012, The Journal of general virology.

[142]  B. Preston,et al.  Case Series , 2010, Toxicologic pathology.

[143]  C. Donati,et al.  Phylogeny of the SARS Coronavirus , 2003, Science.

[144]  Alexei J Drummond,et al.  Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. , 2002, Genetics.

[145]  Andrew Rambaut,et al.  Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies , 2000, Bioinform..

[146]  J. Gerring.  A case study , 2011, Technology and Society.