The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Funder

Organizational Unit

Publications

APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016

Publication . O’Toole, Áine; Neher, Richard A.; Ndodo, Nnaemeka; Borges, Vitor; Gannon, Ben; Gomes, João Paulo; Groves, Natalie; King, David J.; Maloney, Daniel; Lemey, Philippe; Lewandowski, Kuiama; Loman, Nicholas; Myers, Richard; Omah, Ifeanyi F.; Suchard, Marc A.; Worobey, Michael; Chand, Meera; Ihekweazu, Chikwe; Ulaeto, David; Adetifa, Ifedayo; Rambaut, Andrew

Historically, mpox has been characterized as an endemic zoonotic disease that transmits through contact with the reservoir rodent host in West and Central Africa. However, in May 2022, human cases of mpox were detected spreading internationally beyond countries with known endemic reservoirs. When the first cases from 2022 were sequenced, they shared 42 nucleotide differences from the closest mpox virus (MPXV) previously sampled. Nearly all these mutations are characteristic of the action of APOBEC3 deaminases, host enzymes with antiviral function. Assuming APOBEC3 editing is characteristic of human MPXV infection, we developed a dual-process phylogenetic molecular clock that-inferring a rate of ~6 APOBEC3 mutations per year-estimates that MPXV has been circulating in humans since 2016. These observations of sustained MPXV transmission present a fundamental shift to the perceived paradigm of MPXV epidemiology as a zoonosis and highlight the need for revising public health messaging around MPXV as well as outbreak management and control.

2023-11-03Journal article

Open access

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Publication . O'Toole, Áine; Hill, Verity; Pybus, Oliver G.; Watts, Alexander; Bogoch, Issac I.; Khan, Kamran; Messina, Jane P.; Tegally, Houriiyah; Lessells, Richard R.; Giandhari, Jennifer; Pillay, Sureshnee; Tumedi, Kefentse Arnold; Nyepetsi, Gape; Kebabonye, Malebogo; Matsheka, Maitshwarelo; Mine, Madisa; Tokajian, Sima; Hassan, Hamad; Salloum, Tamara; Merhi, Georgi; Koweyes, Jad; Geoghegan, Jemma L.; de Ligt, Joep; Ren, Xiaoyun; Storey, Matthew; Freed, Nikki E.; Pattabiraman, Chitra; Prasad, Pramada; Desai, Anita S.; Vasanthapuram, Ravi; Schulz, Thomas F.; Steinbrück, Lars; Stadler, Tanja; Parisi, Antonio; Bianco, Angelica; García de Viedma, Darío; Buenestado-Serrano, Sergio; Borges, Vítor; Isidro, Joana; Duarte, Sílvia; Gomes, João Paulo; Zuckerman, Neta S.; Mandelboim, Michal; Mor, Orna; Seemann, Torsten; Arnott, Alicia; Draper, Jenny; Gall, Mailie; Rawlinson, William; Deveson, Ira; Schlebusch, Sanmarié; McMahon, Jamie; Leong, Lex; Lim, Chuan Kok; Chironna, Maria; Loconsole, Daniela; Bal, Antonin; Josset, Laurence; Holmes, Edward; St. George, Kirsten; Lasek-Nesselquist, Erica; Sikkema, Reina S.; Oude Munnink, Bas; Koopmans, Marion; Brytting, Mia; Sudha rani, V.; Pavani, S.; Smura, Teemu; Heim, Albert; Kurkela, Satu; Umair, Massab; Salman, Muhammad; Bartolini, Barbara; Rueca, Martina; Drosten, Christian; Wolff, Thorsten; Silander, Olin; Eggink, Dirk; Reusken, Chantal; Vennema, Harry; Park, Aekyung; Carrington, Christine; Sahadeo, Nikita; Carr, Michael; Gonzalez, Gabo; de Oliveira, Tulio; Faria, Nuno; Rambaut, Andrew; Kraemer, Moritz U.G.

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

2021-09-17Journal article

Open access