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The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.

The Lancet. Microbe

Baker DJ,Aydin A,Le Viet T,Kay GL,Rudder S,de Oliveira Martins L,Tedim AP,Kolyva A,Diaz M,Alikhan NF,Meadows L,Bell A,Gutierrez AV,Trotter AJ,Thomson NM,Gilroy R,Griffith L,Adriaenssens EM,Stanley R,Charles IG,Elumogo N,Wain J,Prakash R,Meader E,Mather AE,Webber M,Dervisevic S,Page AJ,O J. (2021)

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.

Genome medicine

Foster-Nyarko E,Alikhan NF,Ikumapayi UN,Sarwar G,Okoi C,Tientcheu PM,Defernez M,O J,Antonio M,Pallen MJ. (2021)

Genomic diversity of Escherichia coli from healthy children in rural Gambia.

PeerJ

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Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Cell

Charalampous T, Alcolea-Medina A, Snell LB, Williams TGS, Batra R, Alder C, Telatin A, Camporota L, Meadows CIS, Wyncoll D, Barrett NA, Hemsley CJ, Bryan L, Newsholme W, Boyd SE, Green A, Mahadeva U, Patel A, Cliff PR, Page A, O'Grady J, Edgeworth J. (2021)

Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units.

Genome medicine

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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

Science (New York, N.Y.)

Mashe T, Takawira FT, de Oliveira Martins L, Gudza-Mugabe M, Chirenda J, Munyanyi M, Chaibva BV, Tarupiwa A, Gumbo H, Juru A, Nyagupe C, Ruhanya V, Phiri I, Manangazira P, Goredema A, Danda S, Chabata I, Jonga J, Munharira R, Masunda K, Mukeredzi I, Mangwanya D, Trotter A, Le Viet T, Rudder S, Kay G, Baker D, Thilliez G, Gutierrez AV, O'Grady J, Hove M, Mutapuri-Zinyowera S, Page AJ, Kingsley RA, Mhlanga G. (2021)

Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.

The Lancet. Global health

Li T, Garcia-Gutierrez E, Yara D, Scadden J, Davies J, Hutchins C, Aydin A, O'Grady J, Narbad A, Romano S, Sayavedra L. (2021)

An optimised protocol for detection of SARS-CoV-2 in stool.

BMC microbiology