niman Posted January 10, 2021 Report Share Posted January 10, 2021 (edited) National Institute of Infectious Diseases has released (at GISAID) four 501.v3 (B.1.1.28) SARS-CoV2 COVID Sequences Sans Spike Dels (Japan/IC-0561/2021, Japan/IC-0562/2021, Japan/IC-0563/2021, Japan/IC-0564/2021) collected in Jan. Edited January 12, 2021 by niman Link to comment Share on other sites More sharing options...
niman Posted January 10, 2021 Author Report Share Posted January 10, 2021 (edited) Japan/IC-0561/2021 matched 501.v3 (B.1.1.28) with K417T, E484K, N501Y, and 3 AAs deleted in NSP6 map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=35.52453621809799%2C139.7528242027054&z=11 Edited January 12, 2021 by niman Link to comment Share on other sites More sharing options...
niman Posted January 10, 2021 Author Report Share Posted January 10, 2021 (edited) Japan/IC-0562/2021 matched 501.v3 (B.1.1.28) with K417T, E484K, N501Y, and 3 AAs deleted in NSP6 map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=35.52453621809799%2C139.7528242027054&z=11 Edited January 12, 2021 by niman Link to comment Share on other sites More sharing options...
niman Posted January 10, 2021 Author Report Share Posted January 10, 2021 (edited) Japan/IC-0563/2021 matched 501.v3 (B.1.1.28) with K417T, E484K, N501Y, and 3 AAs deleted in NSP6 map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=35.52453621809799%2C139.7528242027054&z=11 Edited January 12, 2021 by niman Link to comment Share on other sites More sharing options...
niman Posted January 10, 2021 Author Report Share Posted January 10, 2021 (edited) Japan/IC-0564/2021 matched 501.v3 (B.1.1.28) with K417T, E484K, N501Y, and 3 AAs deleted in NSP6 map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=35.52453621809799%2C139.7528242027054&z=11 Edited January 12, 2021 by niman Link to comment Share on other sites More sharing options...
niman Posted January 10, 2021 Author Report Share Posted January 10, 2021 Of the four travellers who arrived at Tokyo’s Haneda airport on Jan. 2, a man in his forties had a problem breathing, a woman in her thirties had a headache and sore throat and a man in his teens had a fever, while a woman in her teens showed no symptoms, the health ministry said. https://www.reuters.com/article/us-health-coronavirus-japan-variant/new-coronavirus-variant-found-in-travellers-from-brazil-japan-government-idUSKBN29F08R Link to comment Share on other sites More sharing options...
niman Posted January 10, 2021 Author Report Share Posted January 10, 2021 New coronavirus variant found in travellers from Brazil: Japan government TOKYO (Reuters) - A new coronavirus variant has been detected in four travellers from Brazil’s Amazonas state, Japan’s Health Ministry said on Sunday, in the latest instance the pandemic virus is evolving. A ministry official said studies were underway into the efficacy of vaccines against the new variant, which differs from highly-infectious variants first found in Britain and South Africa that have driven a surge in cases. “At the moment, there is no proof showing the new variant found in those from Brazil is high in infectiousness,” Takaji Wakita, head of the National Institute of Infectious Diseases, told a health ministry briefing. Of the four travellers who arrived at Tokyo’s Haneda airport on Jan. 2, a man in his forties had a problem breathing, a woman in her thirties had a headache and sore throat and a man in his teens had a fever, while a woman in her teens showed no symptoms, the health ministry said. After seeing a steep rise in coronavirus cases, Japan declared a state of emergency for Tokyo and three prefectures neighbouring the capital on Thursday. Nationwide cases have totalled about 289,000, with 4,061 deaths, public broadcaster NHK said. Reporting by Kiyoshi Takenaka; Editing by Lincoln Feast, William Mallard and Barbara Lewis Link to comment Share on other sites More sharing options...
niman Posted January 12, 2021 Author Report Share Posted January 12, 2021 Here we report a preliminary genomic analysis of SARS-CoV-2 B.1.1.28 lineage circulating in the Brazilian Amazon region and their evolutionary relationship with emerging and potential emerging SARS-CoV-2 Brazilian variants harboring mutations in the RBD of Spike (S) protein. Phylogenetic analysis of 69 B.1.1.28 sequences isolated in the Amazonas state revealed the existence of two major clades that have evolved locally without unusual mutations in the S protein from April to November 2020. The B.1.1.28 viruses harboring mutations S:K417N, S:E484K and S:N501Y, recently detected in Japanese travelers returning from Amazonas, branched within one of the Amazonian B.1.1.28 clades here identified, suggesting that these sequences could be representatives of a novel (unreported) emerging Brazilian clade, here designated B.1.1.28(K417N/E484K/N501Y). Our analysis also confirms that the putative novel clade B.1.1.28(K417N/E484K/N501Y) detected in Japanese travelers did not evolve from the clade B.1.1.28(E484K) recently detected in Rio de Janeiro and other Brazilian states, but both variants arose independently during the evolution of the B.1.1.28 lineage. https://virological.org/t/phylogenetic-relationship-of-sars-cov-2-sequences-from-amazonas-with-emerging-brazilian-variants-harboring-mutations-e484k-and-n501y-in-the-spike-protein/585/1 Link to comment Share on other sites More sharing options...
niman Posted January 12, 2021 Author Report Share Posted January 12, 2021 Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein SARS-CoV-2 coronavirusnCoV-2019 Genomic Epidemiology Jan 11 1 / 1 Jan 12 19h ago paola 1 19h Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein Felipe Naveca 1, Valdinete Nascimento 1, Victor Souza 1, André Corado 1, Fernanda Nascimento 1, George Silva 1, Ágatha Costa 1, Débora Duarte 1, Karina Pessoa 1, Luciana Gonçalves 2, Maria Júlia Brandão 1, Michele Jesus 3, Cristiano Fernandes 2, Rosemary Pinto 2, Marineide Silva 4, Tirza Mattos 4, Gabriel Luz Wallau 5, Marilda Mendonça Siqueira 6, Paola Cristina Resende 6*, Edson Delatorre 7*, Tiago Gräf 8*, Gonzalo Bello 9* *These authors contributed equally to this work 1 Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil.2 Fundação de Vigilância em Saúde do Amazonas, Manaus, Amazonas, Brazil.3 Laboratório de Diversidade Microbiana da Amazônia com Importância para a Saúde, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil.4 Laboratório Central de Saúde Pública do Amazonas, Manaus, Amazonas, Brazil.5 Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil.6 Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil. SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Reference Laboratory for the World Health Organization (WHO).7 Departamento de Biologia. Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil.8 Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.9 Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 40 Brazil. Link to comment Share on other sites More sharing options...
paola 1 19h Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein Felipe Naveca 1, Valdinete Nascimento 1, Victor Souza 1, André Corado 1, Fernanda Nascimento 1, George Silva 1, Ágatha Costa 1, Débora Duarte 1, Karina Pessoa 1, Luciana Gonçalves 2, Maria Júlia Brandão 1, Michele Jesus 3, Cristiano Fernandes 2, Rosemary Pinto 2, Marineide Silva 4, Tirza Mattos 4, Gabriel Luz Wallau 5, Marilda Mendonça Siqueira 6, Paola Cristina Resende 6*, Edson Delatorre 7*, Tiago Gräf 8*, Gonzalo Bello 9* *These authors contributed equally to this work 1 Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil.2 Fundação de Vigilância em Saúde do Amazonas, Manaus, Amazonas, Brazil.3 Laboratório de Diversidade Microbiana da Amazônia com Importância para a Saúde, Instituto Leônidas e Maria Deane, Manaus, Amazonas, Brazil.4 Laboratório Central de Saúde Pública do Amazonas, Manaus, Amazonas, Brazil.5 Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil.6 Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil. SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Reference Laboratory for the World Health Organization (WHO).7 Departamento de Biologia. Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil.8 Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.9 Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 40 Brazil.
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