Browsing by Author "Neher, Richard A."
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- APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016Publication . 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, AndrewHistorically, 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.
- Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup LevelPublication . Goya, Stephanie; Ruis, Christopher; Neher, Richard A.; Meijer, Adam; Aziz, Ammar; Hinrichs, Angie S.; von Gottberg, Anne; Roemer, Cornelius; Amoako, Daniel G.; Acuña, Dolores; McBroome, Jakob; Otieno, James R.; Bhiman, Jinal N.; Everatt, Josie; Muñoz-Escalante, Juan C.; Ramaekers, Kaat; Duggan, Kate; Presser, Lance D.; Urbanska, Laura; Venter, Marietjie; Wolter, Nicole; Peret, Teresa C.T.; Salimi, Vahid; Potdar, Varsha; Borges, Vítor; Viegas, MarianaA globally implemented unified phylogenetic classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. We formulated global consensus of HRSV classification on the basis of the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality curated dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to GenBank and GISAID (https://www.gisaid.org) public sequence databases through March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B and provided guidelines for defining prospective lineages. Our classification demonstrated robustness in its applicability to both complete and partial genomes. We envision that this unified HRSV classification proposal will strengthen HRSV molecular epidemiology on a global scale.
- Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virusPublication . Happi, Christian; Adetifa, Ifedayo; Mbala, Placide; Njouom, Richard; Nakoune, Emmanuel; Happi, Anise; Ndodo, Nnaemeka; Ayansola, Oyeronke; Mboowa, Gerald; Bedford, Trevor; Neher, Richard A.; Roemer, Cornelius; Hodcroft, Emma; Tegally, Houriiyah; O’Toole, Áine; Rambaut, Andrew; Pybus, Oliver; Kraemer, Moritz U. G.; Wilkinson, Eduan; Isidro, Joana; Borges, Vítor; Pinto, Miguel; Gomes, João Paulo; Freitas, Lucas; Resende, Paola C.; Lee, Raphael T. C.; Maurer-Stroh, Sebastian; Baxter, Cheryl; Lessells, Richard; Ogwell, Ahmed E.; Kebede, Yenew; Tessema, Sofonias K.; de Oliveira, TulioWe propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause of the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomic surveillance.
- Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in PortugalPublication . Borges, Vítor; Duque, Mariana Perez; Martins, João Vieira; Vasconcelos, Paula; Ferreira, Rita; Sobral, Daniel; Pelerito, Ana; de Carvalho, Isabel Lopes; Núncio, Maria Sofia; Borrego, Maria José; Roemer, Cornelius; Neher, Richard A.; O’Driscoll, Megan; Rocha, Raquel; Lopo, Sílvia; Neves, Raquel; Palminha, Paula; Coelho, Luís; Nunes, Alexandra; Isidro, Joana; Pinto, Miguel; Santos, João Dourado; Mixão, Verónica; Santos, Daniela; Duarte, Silvia; Vieira, Luís; Martins, Fátima; Machado, Jorge; Veríssimo, Vítor Cabral; Grau, Berta; Peralta-Santos, André; Neves, José; Caldeira, Margarida; Pestana, Mafalda; Fernandes, Cândida; Caria, João; Pinto, Raquel; Póvoas, Diana; Maltez, Fernando; Sá, Ana Isabel; Salvador, Mafalda Brito; Teófilo, Eugénio; Rocha, Miguel; Moneti, Virginia; Duque, Luis Miguel; e Silva, Francisco Ferreira; Baptista, Teresa; Vasconcelos, Joana; Casanova, Sara; Mansinho, Kamal; Alves, João Vaz; Alves, João; Silva, António; Alpalhão, Miguel; Brazão, Cláudia; Sousa, Diogo; Filipe, Paulo; Pacheco, Patrícia; Peruzzu, Francesca; de Jesus, Rita Patrocínio; Ferreira, Luís; Mendez, Josefina; Jordão, Sofia; Duarte, Frederico; Gonçalves, Maria João; Pena, Eduarda; Silva, Claúdio Nunes; Guimarães, André Rodrigues; Tavares, Margarida; Freitas, Graça; Cordeiro, Rita; Gomes, João PauloPathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the highest impact on case numbers and fitted them into a global context, finding evidence that several international sublineages probably emerged or spread early in Portugal. We estimated a 62% infection reporting rate and that 1.3% of the population of men who have sex with men in Portugal were infected. We infer the critical role played by sexual networks and superspreader gatherings, such as sauna attendance, in the dissemination of mpox virus. Overall, our findings highlight genomic epidemiology as a tool for the real-time monitoring and control of mpox epidemics, and can guide future vaccine policy in a highly susceptible population.