This paper is in the following e-collection/theme issue:

Theme Issue: Novel Coronavirus (COVID-19) Outbreak Rapid Reports (1517) Data Science (270) Digital Science, Open Science (79) JMIR Theme Issue: COVID-19 Special Issue (2452) Infectious Diseases (non-STD/STI) (1575) Outbreak and Pandemic Preparedness and Management (1727)

Published on in Vol 6, No 2 (2020): Apr-Jun

Preprints (earlier versions) of this paper are available at https://preprints.jmir.org/preprint/19170, first published .
A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis

A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis

A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis

Authors of this article:

Carla Mavian1, 2 Author Orcid Image ;   Simone Marini1, 3 Author Orcid Image ;   Mattia Prosperi3 Author Orcid Image ;   Marco Salemi1, 2 Author Orcid Image
Article Authors Cited by (25) Tweetations (2) Metrics

Journals

  1. Delatorre E, Mir D, Gräf T, Bello G. Tracking the onset date of the community spread of SARS-CoV-2 in western countries. Memórias do Instituto Oswaldo Cruz 2020;115 View
  2. Funk C, Laferrière C, Ardakani A. A Snapshot of the Global Race for Vaccines Targeting SARS-CoV-2 and the COVID-19 Pandemic. Frontiers in Pharmacology 2020;11 View
  3. Forster P, Forster L. Errors in Tracing Coronavirus SARS-CoV-2 Transmission Using a Maximum Likelihood Tree. Comment on “A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis”. JMIR Public Health and Surveillance 2020;6(4):e23542 View
  4. Armero A, Berthet N, Avarre J. Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia. Viruses 2021;13(1):133 View
  5. Viedma E, Dahdouh E, González-Alba J, González-Bodi S, Martínez-García L, Lázaro-Perona F, Recio R, Rodríguez-Tejedor M, Folgueira M, Cantón R, Delgado R, García-Rodríguez J, Galán J, Mingorance J. Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. Microorganisms 2021;9(2):454 View
  6. Pereson M, Mojsiejczuk L, Martínez A, Flichman D, Garcia G, Di Lello F. Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence. Journal of Medical Virology 2021;93(3):1722 View
  7. Zhang W, Govindavari J, Davis B, Chen S, Kim J, Song J, Lopategui J, Plummer J, Vail E. Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic. JAMA Network Open 2020;3(10):e2024191 View
  8. Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki E, Mamais I, Kozlov A, Pavlidis P, Paraskevis D, Stamatakis A, Malik H. Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult. Molecular Biology and Evolution 2021;38(5):1777 View
  9. Resende P, Delatorre E, Gräf T, Mir D, Motta F, Appolinario L, Paixão A, Mendonça A, Ogrzewalska M, Caetano B, Wallau G, Docena C, Santos M, de Almeida Ferreira J, Sousa Junior E, Silva S, Fernandes S, Vianna L, Souza L, Ferro J, Nardy V, Santos C, Riediger I, do Carmo Debur M, Croda J, Oliveira W, Abreu A, Bello G, Siqueira M. Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil. Frontiers in Microbiology 2021;11 View
  10. Didelot X, Kendall M, Xu Y, White P, McCarthy N. Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo. Current Protocols 2021;1(2) View
  11. Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O’Toole Á, McCrone J, Andersen K, Worobey M, Nelson M, Rambaut A, Suchard M. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature Communications 2020;11(1) View
  12. Mavian C, Marini S, Prosperi M, Salemi M. Authors' Reply to: Errors in Tracing Coronavirus SARS-CoV-2 Transmission Using a Maximum Likelihood Tree. Comment on “A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis”. JMIR Public Health and Surveillance 2020;6(4):e24661 View
  13. Hryhorowicz S, Ustaszewski A, Kaczmarek-Ryś M, Lis E, Witt M, Pławski A, Ziętkiewicz E. European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients. Journal of Applied Genetics 2021;62(2):327 View
  14. Bandoy D, Weimer B. Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation. Scientific Reports 2021;11(1) View
  15. Lythgoe K, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, Andersson M, Otecko N, Wise E, Moore N, Lynch J, Kidd S, Cortes N, Mori M, Williams R, Vernet G, Justice A, Green A, Nicholls S, Ansari M, Abeler-Dörner L, Moore C, Peto T, Eyre D, Shaw R, Simmonds P, Buck D, Todd J, Connor T, Ashraf S, da Silva Filipe A, Shepherd J, Thomson E, Bonsall D, Fraser C, Golubchik T. SARS-CoV-2 within-host diversity and transmission. Science 2021;372(6539) View
  16. Rocheleau L, Laroche G, Fu K, Stewart C, Mohamud A, Côté M, Giguère P, Langlois M, Pelchat M, Paraskevis D. Identification of a High-Frequency Intrahost SARS-CoV-2 Spike Variant with Enhanced Cytopathic and Fusogenic Effects. mBio 2021;12(3) View
  17. Porter A, Sherry N, Andersson P, Johnson S, Duchene S, Howden B, Crawford D. New rules for genomics-informed COVID-19 responses–Lessons learned from the first waves of the Omicron variant in Australia. PLOS Genetics 2022;18(10):e1010415 View
  18. Marini S, Mavian C, Riva A, Prosperi M, Salemi M, Rife Magalis B, Luigi Martelli P. Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. Bioinformatics 2022;38(3):856 View
  19. Rana V, Chien E, Peng J, Milenkovic O. Small-Sample Estimation of the Mutational Support and Distribution of SARS-CoV-2. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2023;20(1):668 View
  20. Wang Y, Zhao Y, Pan Q. Advances, challenges and opportunities of phylogenetic and social network analysis using COVID-19 data. Briefings in Bioinformatics 2022;23(1) View
  21. Lu Z, Wang Z, Song Z, Chen C, Ma H, Gong P, Xu Y. Single-cell sequencing of brain tissues reveal the central nervous system’s susceptibility to SARS-CoV-2 and the drug. Frontiers in Pharmacology 2022;13 View
  22. Porter A, Featherstone L, Lane C, Sherry N, Nolan M, Lister D, Seemann T, Duchene S, Howden B. The importance of utilizing travel history metadata for informative phylogeographical inferences: a case study of early SARS-CoV-2 introductions into Australia. Microbial Genomics 2023;9(8) View
  23. Louge Uriarte E, Badaracco A, Spetter M, Miño S, Armendano J, Zeller M, Heylen E, Späth E, Leunda M, Moreira A, Matthijnssens J, Parreño V, Odeón A. Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas. Viruses 2023;15(10):2115 View

Books/Policy Documents

  1. Mishra A, Shukla D, Aich S, Singh R, Mishra S, Roy B, Singh P, Mishra A, Saxena S. Applications of Artificial Intelligence in COVID-19. View
  2. Patil S, Srinivasa C, Ramu R, Kollur S, Ramesh S, Shivamallu C. Coronavirus Drug Discovery. View