Dr Thanh Le Viet

Bioinformatician

Contact via email

Informatics and bioinformatics support

Links/websites:

I am a Bioinformatics Scientific Programmer in Dr. Andrew Page’s group.

I obtained a B.E in mapping and an MSc in geographic information system (gis) from the Hanoi University of Mining and Geology. I joined the Oxford University Clinical Research Unit (OUCRU), Hanoi in 2008 for making the Atlas of Human Infectious Diseases (www.infectionatlas.org).

I completed my phd with Prof. Heiman Wertheim and Dr. Marc Choisy, in Ecology, Evolution and Genetic Materials at the University of Montpelier in 2015 on the study of dengue transmission in northern Vietnam.

Afterwards, I worked at OUCRU as a postdoctoral bioinformatician. I was responsible for developing the bioinformatics pipelines for the national reference laboratory and surveillance networks (16 hospitals) for AMR, Vietnam, that was funded by the Fleming fund, UK.

I have experience and interest in: genomics and bioinformatics; machine learning and big data for biology; high-performance computing, open source software, Python and R programming.


Key publications

Ana Bonell, Ryan Azarrafiy, Vu Thi Lan Huong, Thanh Le Viet, Vu Dinh Phu, Vu Quoc Dat, Heiman Wertheim, H. Rogier van Doorn, Sonia Lewycka, Behzad Nadjm, “A systematic review and meta-analysis of ventilator associated pneumonia in adults in Asia; an analysis of national income level on incidence and etiology”, .Clinical Infectious Diseases, (2018) https://doi.org/10.1093/cid/ciy543

Le Viet Thanh, Marc Choisy, Juliet E Bryant, Duoc Vu Trong, Thai Pham Quang, Peter Horby, Hien Nguyen Tran, et al., “A Dengue Outbreak on a Floating Village at Cat Ba Island in Vietnam.”, BMC Public Health 15 (1), (2015) https://doi.org/10.1186/s12889-015-2235-y

Huong V T L, L V Thanh, V D Phu, D T Trinh, K Inui, N Tung, N T K Oanh, et al.,, “Temporal and Spatial Association of Streptococcus Suis Infection in Humans and Porcine Reproductive and Respiratory Syndrome Outbreaks in Pigs in Northern Vietnam.”, Epidemiology and Infection 1-10, . (2015) https://doi.org/10.1017/S0950268815000990

Wertheim, Heiman F. L., Horby, Peter, Woodall, John P, Thanh Le Viet, Thuy Nguyen Thanh. Atlas of Human Infectious Diseases (2012). John Wiley & Sons 2012.

Elek C, Brown T, Le Viet T, Evans R, Baker D, Telatin A, Tiwari S, Al-Khanaq H, Thilliez G, Kingsley R, Hall L, Webber M, Adriaenssens . (2023)

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Microbial Genomics, 9


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Cotton S, McHugh MP, Dewar R, Haas JG, Templeton K, Robson SC, Connor TR, Loman NJ, Golubchik T, Martinez Nunez, Bonsall D, Rambaut A, Snell LB, Livett R, Ludden C, Corden S, Nastouli E, Nebbia G, Johnston I, Prieto JA, Saeed K, Jackson DK, Houlihan C, Frampton D, Hamilton WL, Witney AA, Bucca G, Pope CF, Moore C, Thomson EC, Cutino-Moguel T, Harrison EM, Smith CP, Rogan F, Beckwith SM, Murray A, Singleton D, Eastick K, Sheridan LA, Randell P, Jackson LM, Ariani CV, Gonçalves S, Fairley DJ, Loose MW, Watkins J, Moses S, Nicholls S, Bull M, Amato R, Smith DL, Aanensen DM, Barrett JC, Kele B, Aggarwal D, Shepherd JG, Curran MD, Parmar S, Parker MD, Williams C, Glaysher S, Underwood AP, Bashton M, Pacchiarini N, Loveson KF, Byott M, Carabelli AM, Templeton KE, Peacock SJ, de Silva, Wang D, Langford CF, Sillitoe J, Gunson RN, Cottrell S, O'Grady J, Kwiatkowski D, Lillie PJ, Cortes N, Moore N, Thomas C, Burns PJ, Mahungu TW, Liggett S, Beckett AH, Holden MT, Levett LJ, Osman H, Hassan-Ibrahim MO, Simpson DA, Chand M, Gupta RK, Darby AC, Paterson S, Pybus OG, Volz EM, de Angelis, Robertson DL, Page AJ, Martincorena I, Aigrain L, Bassett AR, Wong N, Taha Y, Erkiert MJ, Spencer Chapman, Dewar R, McHugh MP, Mookerjee S, Aplin S, Harvey M, Sass T, Umpleby H, Wheeler H, McKenna JP, Warne B, Taylor JF, Chaudhry Y, Izuagbe R, Jahun AS, Young GR, McMurray C, McCann CM, Nelson A, Elliott S, Lowe H, Price A, Crown MR, Rey S, Roy S, Temperton B, Shaaban S, Hesketh AR, Laing KG, Monahan IM, Heaney J, Pelosi E, Silviera S, Wilson-Davies E, Fryer H, Adams H, du Plessis, Johnson R, Harvey WT, Hughes J, Orton RJ, Spurgin LG, Bourgeois Y, Ruis C, O'Toole Á, Gourtovaia M, Sanderson T, Fraser C, Edgeworth J, Breuer J, Michell SL, Todd JA, John M, Buck D, Gajee K, Kay GL, Heyburn D, Charalampous T, Alcolea-Medina A, Kitchman K, McNal A, Pritch DT, Dervisevic S, Muir P, Robinson E, Vipond BB, Ramadan NA, Jeanes C, Weldon D, Catalan J, Jones N, da Silva, Williams C, Fuchs M, Miskelly J, Jeffries AR, Oliver K, Park NR, Ash A, Koshy C, Barrow M, Buchan SL, Mantzouratou A, Clark G, Holmes CW, Campbell S, Davis T, Tan NK, Brown JR, Harris KA, Kidd SP, Grant PR, Xu-McCrae L, Cox A, Madona P, Pond M, Randell PA, Withell KT, Williams C, Graham C, Denton-Smith R, Swindells E, Turnbull R, Sloan TJ, Bosworth A, Hutchings S, Pymont HM, Casey A, Ratcliffe L, Jones CR, Knight BA, Haque T, Hart J, Irish-Tavares D, Witele E, Mower C, Watson DipHE, Collins J, Eltringham G, Crudgington D, Macklin B, Iturriza-Gomara M, Lucaci AO, McClure PC, Carlile M, Holmes N, Moore C, Storey N, Rooke S, Yebra G, Craine N, Perry M, Alikhan NF, Bridgett S, Cook KF, Fearn C, Goudarzi S, Lyons RA, Williams T, Haldenby ST, Durham J, Leonard S, Davies RM, Batra R, Blane B, Spyer MJ, Smith P, Yavus M, Williams RJ, Mahanama AI, Samaraweera B, Girgis ST, Hansford SE, Green A, Beaver C, Bellis KL, Dorman MJ, Kay S, Prestwood L, Rajatileka S, Quick J, Poplawski R, Reynolds N, Mack A, Morriss A, Whalley T, Patel B, Georgana I, Hosmillo M, Pinckert ML, Stockton J, Henderson JH, Hollis A, Stanley W, Yew WC, Myers R, Thornton A, Adams A, Annett T, Asad H, Birchley A, Coombes J, Evans JM, Fina L, Gatica-Wilcox B, Gilbert L, Graham L, Hey J, Hilvers E, Jones S, Jones H, Kumziene-Summerhayes S, McKerr C, Powell J, Pugh G, Taylor S, Trotter AJ, Williams CA, Kermack LM, Foulkes BH, Gallis M, Hornsby HR, Louka SF, Pohare M, Wolverson P, Zhang P, MacIntyre-Cockett G, Trebes A, Moll RJ, Ferguson L, Goldstein EJ, Maclean A, Tomb R, Starinskij I, Thomson L, Southgate J, Kraemer MU, Raghwani J, Zarebski AE, Boyd O, Geidelberg L, Illingworth CJ, Jackson C, Pascall D, Vattipally S, Freeman TM, Hsu SN, Lindsey BB, James K, Lewis K, Tonkin-Hill G, Tovar-Corona JM, Cox M, Abudahab K, Menegazzo M, Taylor BE, Yeats CA, Mukaddas A, Wright DW, de Oliveira Martins L, Colquhoun R, Hill V, Jackson B, McCrone JT, Medd N, Scher E, Keatley JP, Curran T, Morgan S, Maxwell P, Smith K, Eldirdiri S, Kenyon A, Holmes AH, Price JR, Wyatt T, Mather AE, Skvortsov T, Hartley JA, Guest M, Kitchen C, Merrick I, Munn R, Bertolusso B, Lynch J, Vernet G, Kirk S, Wastnedge E, Stanley R, Idle G, Bradley DT, Killough NF, Poyner J, Mori M, Jones O, Wright V, Brooks E, Churcher CM, Delgado Callico, Fragakis M, Galai K, Jermy A, Judges S, Markov A, McManus GM, Smith KS, Thomas-McEwen PM, Westwick E, Attwood SW, Bolt F, Davies A, De Lacy, Downing F, Edwards S, Meadows L, Jeremiah S, Smith N, Foulser L, Patel A, Berry L, Boswell T, Fleming VM, Howson-Wells HC, Joseph A, Khakh M, Lister MM, Bird PW, Fallon K, Helmer T, McMurray CL, Odedra M, Shaw J, Tang JW, Willford NJ, Blakey V, Raviprakash V, Sheriff N, Williams LA, Feltwell T, Bedford L, Cargill JS, Hughes W, Moore J, Stonehouse S, Atkinson L, Lee JC, Shah D, Ohemeng-Kumi N, Ramble J, Sehmi J, Williams R, Chatterton W, Pusok M, Everson W, Castigador A, Macnaughton E, El Bouzidi, Lampejo T, Sudhanva M, Breen C, Sluga G, Ahmad SS, George RP, Machin NW, Binns D, James V, Blacow R, Coupland L, Smith L, Barton E, Padgett D, Scott G, Cross A, Mirfenderesky M, Greenaway J, Cole K, Clarke P, Duckworth N, Walsh S, Bicknell K, Impey R, Wyllie S, Hopes R, Bishop C, Chalker V, Harrison I, Gifford L, Molnar Z, Auckland C, Evans C, Johnson K, Partridge DG, Raza M, Baker P, Bonner S, Essex S, Murray LJ, Lawton AI, Burton-Fanning S, Payne BA, Waugh S, Gomes AN, Kimuli M, Murray DR, Ashfield P, Dobie D, Ashford F, Best A, Crawford L, Cumley N, Mayhew M, Megram O, Mirza J, Moles-Garcia E, Percival B, Driscoll M, Ensell L, Lowe HL, Maftei L, Mondani M, Chaloner NJ, Cogger BJ, Easton LJ, Huckson H, Lewis J, Lowdon S, Malone CS, Munemo F, Mutingwende M, Nicodemi R, Podplomyk Fd, Somassa T, Beggs A, Richter A, Cormie C, Dias J, Forrest S, Higginson EE, Maes M, Young J, Davidson RK, Jackson KA, Keeley AJ, Ball J, Byaruhanga T, Chappell JG, Dey J, Hill JD, Park EJ, Fanaie A, Hilson RA, Yaze G, Lo S, Afifi S, Beer R, Maksimovic J, McCluggage K, Spellman K, Bresner C, Fuller W, Marchbank A, Workma T, Shelest E, Debebe J, Sang F, Francois S, Gutierrez B, Vasylyeva TI, Flaviani F, Ragonnet-Cronin M, Smollett KL, Broos A, Mair D, Nichols J, Nomikou K, Tong L, Tsatsani I, O'Brien S, Rushton S, Sanderson R, Perkins J, Cotton S, Gallagher A, Allara E, Pearson C, Bibby D, Dabrer G, Ellaby N, Gallagher E, Hubb J, Lackenby A, Lee D, Manesis N, Mbisa T, Platt S, Twohig KA, Morgan M, Aydin A, Baker DJ, Foster-Nyarko E, Prosolek SJ, Rudder S, Baxter C, Carvalho SF, Lavin D, Mariappan A, Radulescu C, Singh A, Tang M, Morcrette H, Bayzid N, Cotic M, Balcazar CE, Gallagher MD, Maloney D, Stanton TD, Williamson KA, Manley R, Michelsen ML, Sambles CM, Studholme DJ, Warwick-Dugdale J, Eccles R, Gemmell M, Gregory R, Hughes M, Nelson C, Rainbow L, Vamos EE, Webster HJ, Whitehead M, Wierzbicki C, Angyal A, Green LR, Whiteley M, Betteridge E, Bronner IF, Farr BW, Goodwin S, Lensing SV, McCarthy SA, Quail MA, Rajan D, Redshaw NM, Scott C, Shirley L, Thurston SA, Rowe W, Gaskin A, Le Viet T, Bonfield J, Liddle J, Whitwham . (2023)

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.

The Journal of hospital infection


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Merhi G, Trotter AJ, de Oliveira Martins L, Koweyes J, Le Viet T, Abou Naja, Al Buaini, Prosolek SJ, Alikhan NF, Lott M, Tohmeh T, Badran B, Jupp OJ, Gardner S, Felgate MW, Makin KA, Wilkinson JM, Stanley R, Sesay AK, Webber MA, Davidson RK, Ghosn N, Pallen M, Hasan H, Page AJ, Tokajian . (2022)

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.

Microbial genomics


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Eales O, Walters CW, Wang H, Haw D, Ainslie KEC, Atchison CJ, Page AJ, Prosolek S, Trotter AJ, Le Viet, Alikhan N, Jackson LM, Ludden C, Ashby D, Donnelly CA, Cooke G, Barclay W, Ward H, Darzi A, Elliott P, Riley . (2022)

Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2 [version 1; peer review: awaiting peer review]

Wellcome open research


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Trinh TM, Nguyen TT, Le Viet T, Nguyen TT, Ninh DT, Duong BH, Van Nguyen, Kesteman T, Pham LT, Rogier van. (2022)

Neisseria gonorrhoeae FC428 Subclone, Vietnam, 2019-2020.

Emerging infectious diseases


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Vu Thi, Le Viet T, Nguyen Thi, Nguyen Thi, Nguyen Thi, Le Van, Chu Thi, Tran Huy, Penders J, Wertheim H, van Doorn. (2022)

Characterization of Genetic Elements Carrying mcr-1 Gene in Escherichia coli from the Community and Hospital Settings in Vietnam.

Microbiology spectrum


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Aggarwal D, Page A, Schaefer U, Savva GM, Myers R, Volz E, Ellaby N, Platt S, Groves N, Gallagher E, Tumelty NM, Le Viet, Hughes GJ, Chen C, Turner C, Logan S, Harrison A, Peacock SJ, Chand M, Harrison EM, Koshy C, Ash A, Wise E, Moore N, Mori M, Cortes N, Lynch J, Kidd S, Fairley DJ, Curran T, McKenna JP, Adams H, Fraser C, Golubchik T, Bonsall D, Hassan-Ibrahim MO, Malone CS, Cogger BJ, Wantoch M, Reynolds N, Warne B, Maksimovic J, Spellman K, McCluggage K, John M, Beer R, Afifi S, Morgan S, Marchbank A, Price A, Kitchen C, Gulliver H, Merrick I, Southgate J, Guest M, Munn R, Workman T, Connor TR, Fuller W, Bresner C, Snell LB, Patel A, Charalampous T, Nebbia G, Batra R, Edgeworth J, Robson SC, Beckett AH, Aanensen DM, Underwood AP, Yeats CA, Abudahab K, Taylor BEW, Menegazzo M, Clark G, Smith W, Khakh M, Fleming VM, Lister MM, Howson-Wells HC, Berry L, Boswell T, Joseph A, Willingham I, Jones C, Holmes C, Bird P, Helmer T, Fallon K, Tang J, Raviprakash V, Campbell S, Sheriff N, Blakey V, Williams LA, Loose MW, Holmes N, Moore C, Carlile M, Wright V, Sang F, Debebe J, Coll F, Signell AW, Betancor G, Wilson HD, Eldirdiri S, Kenyon A, Davis T, Pybus OG, du Plessis, Zarebski AE, Raghwani J, Kraemer MUG, Francois S, Attwood SW, Vasylyeva TI, Zamudio ME, Gutierrez B, Torok ME, Hamilton WL, Goodfellow IG, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Moses S, Lowe H, Bedford L, Moore J, Stonehouse S, Fisher CL, Awan AR, BoYes J, Breuer J, Harris KA, Brown JR, Shah D, Atkinson L, Lee JCD, Storey N, Flaviani F, Alcolea-Medina A, Williams R, Vernet G, Chapman MR, Levett LJ, Heaney J, Chatterton W, Pusok M, Xu-McCrae L, Smith DL, Bashton M, Young GR, Holmes A, Randell PA, Cox A, Madona P, Bolt F, Price J, Mookerjee S, Ragonnet-Cronin M, Nascimento FF, Jorgensen D, Siveroni I, Johnson R, Boyd O, Geidelberg L, Volz EM, Rowan A, Taylor GP, Smollett KL, Loman NJ, Quick J, McMurray C, Stockton J, Nicholls S, Rowe W, Poplawski R, McNally A, Nunez RTM, Mason J, Robinson TI, O'Toole E, Watts J, Breen C, Cowell A, Sluga G, Machin NW, Ahmad SSY, George RP, Halstead F, Sivaprakasam V, Hogsden W, Illingworth CJ, Jackson C, Thomson EC, Shepherd JG, Asamaphan P, Niebel MO, Li KK, Shah RN, Jesudason NG, Tong L, Broos A, Mair D, Nichols J, Carmichael SN, Nomikou K, Aranday-Cortes E, Johnson N, Starinskij I, da Silva, Robertson DL, Orton RJ, Hughes J, Vattipally S, Singer JB, Nickbakhsh S, Hale AD, Macfarlane-Smith LR, Harper KL, Carden H, Taha Y, Payne BAI, Burton-Fanning S, Waugh S, Collins J, Eltringham G, Rushton S, O'Brien S, Bradley A, Maclean A, Mollett G, Blacow R, Templeton KE, McHugh MP, Dewar R, Wastenge E, Dervisevic S, Stanley R, Meader EJ, Coupland L, Smith L, Graham C, Barton E, Padgett D, Scott G, Swindells E, Greenaway J, Nelson A, McCann CM, Yew WC, Andersson M, Peto T, Justice A, Eyre D, Crook D, Sloan TJ, Duckworth N, Walsh S, Chauhan AJ, Glaysher S, Bicknell K, Wyllie S, Elliott S, Lloyd A, Impey R, Levene N, Monaghan L, Bradley DT, Wyatt T, Allara E, Pearson C, Osman H, Bosworth A, Robinson E, Muir P, Vipond IB, Hopes R, Pymont HM, Hutchings S, Curran MD, Parmar S, Lackenby A, Mbisa T, Miah S, Bibby D, Manso C, Hubb J, Dabrera G, Ramsay M, Bradshaw D, Thornton A, Gallagher E, Lee D, Williams D, Harrison I, Hartman H, Manesis N, Patel V, Bishop C, Chalker V, Ledesma J, Twohig KA, Holden MTG, Shaaban S, Birchley A, Adams A, Davies A, Gaskin A, Plimmer A, Gatica-Wilcox B, McKerr C, Moore C, Williams C, Heyburn D, De Lacy, Hilvers E, Downing F, Shankar G, Jones H, Asad H, Coombes J, Watkins J, Evans JM, Fina L, Gifford L, Gilbert L, Graham L, Perry M, Morgan M, Bull M, Cronin M, Pacchiarini N, Craine N, Jones R, Howe R, Corden S, Rey S, Kumziene-SummerhaYes S, Taylor S, Cottrell S, Jones S, Edwards S, O'Grady J, Mather AE, Baker DJ, Rudder S, Aydin A, Kay GL, Trotter AJ, Alikhan NF, de Oliveira, Le-Viet T, Meadows L, Casey A, Ratcliffe L, Simpson DA, Molnar Z, Thompson T, Acheson E, Masoli JAH, Knight BA, Ellard S, Auckland C, Jones CR, Mahungu TW, Irish-Tavares D, Haque T, Hart J, Witele E, Fenton ML, Dadrah A, Symmonds A, Saluja T, Bourgeois Y, Scarlett GP, Loveson KF, Goudarzi S, Fearn C, Cook K, Dent H, Paul H, Partridge DG, Raza M, Evans C, Johnson K, Liggett S, Baker P, Bonner S, Essex S, Lyons RA, Saeed K, Mahanama AIK, Samaraweera B, Silveira S, Pelosi E, Wilson-Davies E, Williams RJ, Kristiansen M, Roy S, Williams CA, Cotic M, Bayzid N, Westhorpe AP, Hartley JA, Jannoo R, Lowe HL, Karamani A, Ensell L, Prieto JA, Jeremiah S, Grammatopoulos D, Pandey S, Berry L, Jones K, Richter A, Beggs A, Best A, Percival B, Mirza J, Megram O, Mayhew M, Crawford L, Ashcroft F, Moles-Garcia E, Cumley N, Smith CP, Bucca G, Hesketh AR, Blane B, Girgis ST, Leek D, Sridhar S, Forrest S, Cormie C, Gill HK, Dias J, Higginson EE, Maes M, Young J, Kermack LM, Gupta RK, Ludden C, Peacock SJ, Palmer S, Churcher CM, Hadjirin NF, Carabelli AM, Brooks E, Smith KS, Galai K, McManus GM, Ruis C, Davidson RK, Rambaut A, Williams T, Balcazar CE, Gallagher MD, O'Toole Á, Rooke S, Hill V, Williamson KA, Stanton TD, Michell SL, Bewshea CM, Temperton B, Michelsen ML, Warwick-Dugdale J, Manley R, Farbos A, Harrison JW, Sambles CM, Studholme DJ, Jeffries AR, Darby AC, Hiscox JA, Paterson S, Iturriza-Gomara M, Jackson KA, Lucaci AO, Vamos EE, Hughes M, Rainbow L, Eccles R, Nelson C, Whitehead M, Turtle L, Haldenby ST, Gregory R, Gemmell M, Wierzbicki C, Webster HJ, de Silva, Smith N, Angyal A, Lindsey BB, Groves DC, Green LR, Wang D, Freeman TM, Parker MD, Keeley AJ, Parsons PJ, Tucker RM, Brown R, Wyles M, Whiteley M, Zhang P, Gallis M, Louka SF, Constantinidou C, Unnikrishnan M, Ott S, Cheng JKJ, Bridgewater HE, Frost LR, Taylor-Joyce G, Stark R, Baxter L, Alam MT, Brown PE, Aggarwal D, Cerda AC, Merrill TV, Wilson RE, McClure PC, Chappell JG, Tsoleridis T, Ball J, Buck D, Todd JA, Green A, Trebes A, MacIntyre-Cockett G, de Cesare, Alderton A, Amato R, Ariani CV, Beale MA, Beaver C, Bellis KL, Betteridge E, Bonfield J, Danesh J, Dorman MJ, Drury E, Farr BW, Foulser L, Goncalves S, Goodwin S, Gourtovaia M, Harrison EM, Jackson DK, Jamrozy D, Johnston I, Kane L, Kay S, Keatley JP, Kwiatkowski D, Langford CF, Lawniczak M, Letchford L, Livett R, Lo S, Martincorena I, McGuigan S, Nelson R, Palmer S, Park NR, Patel M, Prestwood L, Puethe C, Quail MA, Rajatileka S, Scott C, Shirley L, Sillitoe J, Chapman MHS, Thurston SAJ, Tonkin-Hill G, Weldon D, Rajan D, Bronner IF, Aigrain L, Redshaw NM, Lensing SV, Davies R, Whitwham A, Liddle J, Lewis K, Tovar-Corona JM, Leonard S, Durham J, Bassett AR, McCarthy S, Moll RJ, James K, Oliver K, Makunin A, Barrett J, Gunson R. (2022)

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission.

Nature communications


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The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Science (New York, N.Y.)


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