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1. A genomics network established to respond rapidly to public health threats in South Africa

Author

Nokukhanya Msomi, Koleka Mlisana, Tulio de Oliveira, Carolyn Willianson, Jinal N. Bhiman, Dominique Goedhals, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Diana Hardie, Marvin Hsiao, Nicola Mulder, Darren Martin, Alan Christoffels, Denis York, Jennifer Giandhari, Eduan Wilkinson, Sureshnee Pillay, Houriiyah Tegally, San Emmanuel James, Aquilah Kanzi, and Richard John Lessells

Subjects
Medicine (General), R5-920, Microbiology, QR1-502
Published
2020
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2. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Author

Giovanetti, Marta, Slavov, Svetoslav Nanev, Fonseca, Vagner, Wilkinson, Eduan, Tegally, Houriiyah, Patané, José Salvatore Leister, Viala, Vincent Louis, San, Emmanuel James, Rodrigues, Evandra Strazza, Santos, Elaine Vieira, Aburjaile, Flavia, Xavier, Joilson, Fritsch, Hegger, Adelino, Talita Emile Ribeiro, Pereira, Felicidade, Leal, Arabela, Iani, Felipe Campos de Melo, de Carvalho Pereira, Glauco, Vazquez, Cynthia, Sanabria, Gladys Mercedes Estigarribia, Oliveira, Elaine Cristina de, Demarchi, Luiz, Croda, Julio, dos Santos Bezerra, Rafael, Paola Oliveira de Lima, Loyze, Martins, Antonio Jorge, Renata dos Santos Barros, Claudia, Marqueze, Elaine Cristina, de Souza Todao Bernardino, Jardelina, Moretti, Debora Botequio, Brassaloti, Ricardo Augusto, de Lello Rocha Campos Cassano, Raquel, Mariani, Pilar Drummond Sampaio Corrêa, Kitajima, João Paulo, Santos, Bibiana, Proto-Siqueira, Rodrigo, Cantarelli, Vlademir Vicente, Tosta, Stephane, Nardy, Vanessa Brandão, Reboredo de Oliveira da Silva, Luciana, Gómez, Marcela Kelly Astete, Lima, Jaqueline Gomes, Ribeiro, Adriana Aparecida, Guimarães, Natália Rocha, Watanabe, Luiz Takao, Barbosa Da Silva, Luana, da Silva Ferreira, Raquel, da Penha, Mara Patricia F., Ortega, María José, de la Fuente, Andrea Gómez, Villalba, Shirley, Torales, Juan, Gamarra, María Liz, Aquino, Carolina, Figueredo, Gloria Patricia Martínez, Fava, Wellington Santos, Motta-Castro, Ana Rita C., Venturini, James, do Vale Leone de Oliveira, Sandra Maria, Gonçalves, Crhistinne Cavalheiro Maymone, do Carmo Debur Rossa, Maria, Becker, Guilherme Nardi, Giacomini, Mayra Presibella, Marques, Nelson Quallio, Riediger, Irina Nastassja, Raboni, Sonia, Mattoso, Gabriela, Cataneo, Allan D., Zanluca, Camila, Duarte dos Santos, Claudia N., Assato, Patricia Akemi, Allan da Silva da Costa, Felipe, Poleti, Mirele Daiana, Lesbon, Jessika Cristina Chagas, Mattos, Elisangela Chicaroni, Banho, Cecilia Artico, Sacchetto, Lívia, Moraes, Marília Mazzi, Grotto, Rejane Maria Tommasini, Souza-Neto, Jayme A., Nogueira, Maurício Lacerda, Fukumasu, Heidge, Coutinho, Luiz Lehmann, Calado, Rodrigo Tocantins, Neto, Raul Machado, Bispo de Filippis, Ana Maria, Venancio da Cunha, Rivaldo, Freitas, Carla, Peterka, Cassio Roberto Leonel, de Fátima Rangel Fernandes, Cássia, Navegantes, Wildo, do Carmo Said, Rodrigo Fabiano, Campelo de A e Melo, Carlos F., Almiron, Maria, Lourenço, José, de Oliveira, Tulio, Holmes, Edward C., Haddad, Ricardo, Sampaio, Sandra Coccuzzo, Elias, Maria Carolina, Kashima, Simone, Junior de Alcantara, Luiz Carlos, and Covas, Dimas Tadeu

Published
2022
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4. Detection of a SARS-CoV-2 variant of concern in South Africa

Author

Tegally, Houriiyah, Wilkinson, Eduan, Giovanetti, Marta, Iranzadeh, Arash, Fonseca, Vagner, Giandhari, Jennifer, Doolabh, Deelan, Pillay, Sureshnee, San, Emmanuel James, Msomi, Nokukhanya, Mlisana, Koleka, von Gottberg, Anne, Walaza, Sibongile, Allam, Mushal, Ismail, Arshad, and Mohale, Thabo

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus.sup.1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance.sup.3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data--which show rapid expansion and displacement of other lineages in several regions--suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape.sup.6-8. The 501Y.V2 variant of SARS-CoV-2 in South Africa became dominant over other variants within weeks of its emergence, suggesting that this variant is linked to increased transmissibility or immune escape., Author(s): Houriiyah Tegally [sup.1] , Eduan Wilkinson [sup.1] , Marta Giovanetti [sup.2] [sup.3] , Arash Iranzadeh [sup.4] , Vagner Fonseca [sup.1] [sup.3] , Jennifer Giandhari [sup.1] , Deelan Doolabh [sup.5] [...]

Published
2021
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5. Sixteen novel lineages of SARS-CoV-2 in South Africa

Author

Tegally, Houriiyah, Wilkinson, Eduan, Lessells, Richard J., Giandhari, Jennifer, Pillay, Sureshnee, Msomi, Nokukhanya, Mlisana, Koleka, Bhiman, Jinal N., von Gottberg, Anne, Walaza, Sibongile, Fonseca, Vagner, Allam, Mushal, Ismail, Arshad, Glass, Allison J., Engelbrecht, Susan, Van Zyl, Gert, Preiser, Wolfgang, Williamson, Carolyn, Petruccione, Francesco, Sigal, Alex, Gazy, Inbal, Hardie, Diana, Hsiao, Nei-yuan, Martin, Darren, York, Denis, Goedhals, Dominique, San, Emmanuel James, Giovanetti, Marta, Lourenço, José, Alcantara, Luiz Carlos Junior, and de Oliveira, Tulio

Published
2021
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7. SeqPanther: Sequence manipulation and mutation statistics toolset

Author

San, Emmanuel James, Van Wyk, Stephanie, Tegally, Houriiyah, Eche, Simeon, Wilkinson, Eduan, Kanzi, Aquillah, de Oliveira, Tulio, and Kiran, Anmol

Subjects
SARS-CoV-2, BAM
Abstract

Pathogen genomes harbor critical information necessary to support genomic investigations that inform public health interventions such as treatment, control, and eradication. To extract this information, their sequences are analysed to identify structural variations such as single nucleotide polymorphisms (SNPs) and insertions and deletions (indels) that may be associated with phenotypes of interest. Typically, this involves generating a consensus sequence from raw reads, aligning it to a reference and identifying positions where variations occur. Several pipelines exist to map raw reads and assemble whole genomes for downstream analysis. However, there is no easy to use, freely available bioinformatics quality control (QC) tool to explore mappings for both positional codons and nucleotide distributions in mapped short reads of microbial genomes. To address this problem, we have developed a fast and accurate tool to summarise read counts associated with codons, nucleotides, and indels in mapped next-generation sequencing (NGS) short reads. The tool, developed in Python, also provides a visualization of the genome sequencing depth and coverage. Furthermore, the tool can be run in single or batch mode, where several genomes need to be analysed. Our tool produces a text-based report that enables quick review or can be imported into any analytical tool for upstream analysis. Additionally, the tool also provides functionality to modify the consensus sequences by adding, masking, or restoring to wild type mutations specified by the user.AvailabilitySeqPanther is available athttps://github.com/codemeleon/seqPanther, along with the necessary documentation for installation and usage.

Published
2023
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9. Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq

Author

Tshiabuila, Derek, primary, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Ramphal, Upasana, additional, Ramphal, Yajna, additional, Maharaj, Arisha, additional, Anyaneji, Ugochukwu Jacob, additional, Naidoo, Yeshnee, additional, Tegally, Houriiyah, additional, San, Emmanuel James, additional, Wilkinson, Eduan, additional, Lessells, Richard J., additional, and de Oliveira, Tulio, additional

Published
2022
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10. Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic

Author

Giovanetti, Marta, primary, Fonseca, Vagner, additional, Wilkinson, Eduan, additional, Tegally, Houriiyah, additional, San, Emmanuel James, additional, Althaus, Christian L, additional, Xavier, Joilson, additional, Nanev Slavov, Svetoslav, additional, Viala, Vincent Louis, additional, Ranieri Jerônimo Lima, Alex, additional, Ribeiro, Gabriela, additional, Souza-Neto, Jayme A, additional, Fukumasu, Heidge, additional, Lehmann Coutinho, Luiz, additional, Venancio da Cunha, Rivaldo, additional, Freitas, Carla, additional, Campelo de A e Melo, Carlos F, additional, Navegantes de Araújo, Wildo, additional, Do Carmo Said, Rodrigo Fabiano, additional, Almiron, Maria, additional, de Oliveira, Tulio, additional, Coccuzzo Sampaio, Sandra, additional, Elias, Maria Carolina, additional, Covas, Dimas Tadeu, additional, Holmes, Edward C, additional, Lourenço, José, additional, Kashima, Simone, additional, and de Alcantara, Luiz Carlos Junior, additional

Published
2022
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11. SARS-CoV-2 evolved during advanced HIV disease immunosuppression has Beta-like escape of vaccine and Delta infection elicited immunity

Author

Shi-Hsia Hwa, Khadija Khan, Tandile Hermanus, Alex Sigal, Farina Karim, Yashica Ganga, Willem A. Hanekom, Ntombifuthi Mthabela, Bernadett I Gosnell, Wesley C. Van Voorhis, Penny L. Moore, Houriiyah Tegally, Eduan Wilkinson, Salim S. Abdool Karim, San Emmanuel James, Tulio de Oliveira, Jumari Snyman, Sasha W Tilles, Jennifer Giandhari, Sandile Cele, Thumbi Ndung'u, Mahomed-Yunus S. Moosa, Mallory Bernstein, Gila Lustig, Matilda Mazibuko, and Richard J Lessells

Subjects
Adult, Delta variant, COVID-19 Vaccines, Evolution, Vaccine Efficacy, HIV Infections, Antibodies, Viral, Article, Neutralization, Virus, Cell Line, Serology, Immunocompromised Host, South Africa, Immunogenicity, Vaccine, Neutralization Tests, Immunity, Chlorocebus aethiops, Animals, Humans, Beta (finance), Vero Cells, BNT162 Vaccine, Immune Evasion, Variants of concern, biology, SARS-CoV-2, Immune escape, Transmission (medicine), Vaccination, HIV, COVID-19, Antibodies, Neutralizing, Phenotype, Virology, Beta variant, Advanced HIV disease, HIV-1, biology.protein, Female, Antibody
Abstract

Summary Characterizing SARS-CoV-2 evolution in specific geographies may help predict the properties of variants coming from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from the ancestral virus in a person with advanced HIV disease. Infection was before the emergence of the Beta variant first identified in South Africa, and the Delta variant. We compared early and late evolved virus to the ancestral, Beta, Alpha, and Delta viruses and tested against convalescent plasma from ancestral, Beta, and Delta infections. Early virus was similar to ancestral, whereas late virus was similar to Beta, exhibiting vaccine escape and, despite pre-dating Delta, strong escape of Delta-elicited neutralization. This example is consistent with the notion that variants arising in immune-compromised hosts, including those with advanced HIV disease, may evolve immune escape of vaccines and enhanced escape of Delta immunity, with implications for vaccine breakthrough and reinfections., Graphical Abstract

Published
2021
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12. Replacement of the Gamma by the Delta variant in Brazil: impact of lineage displacement on the ongoing pandemic

Author

Giovanetti, Marta, primary, Fonseca, Vagner, additional, Wilkinson, Eduan, additional, Tegally, Houriiyah, additional, San, Emmanuel James, additional, Althaus, Christian L., additional, Xavier, Joilson, additional, Nanev Slavov, Svetoslav, additional, Viala, Vincent Louis, additional, Ranieri Jeronimo Lima, Alex, additional, Ribeiro, Gabriela, additional, Souza-Neto, Jayme A., additional, Fukumasu, Heidge, additional, Lehmann Coutinho, Luiz, additional, Venancio da Cunha, Rivaldo, additional, Freitas, Carla, additional, Campelo de A e Melo, Carlos F, additional, Navegantes, Wildo, additional, do Carmo Said, Rodrigo Fabiano, additional, Almiron, Maria, additional, de Oliveira, Tulio, additional, Sampaio, Sandra Coccuzzo, additional, Elias, Maria Carolina, additional, Tadeu Covas, Dimas, additional, Holmes, Edward C, additional, Lourenco, Jose, additional, Kashima, Simone, additional, and Alcantara, Luiz Carlos Junior, additional

Published
2021
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13. Management and containment of a SARS-CoV-2 Beta variant outbreak at the Malawi University of Science and Technology

Author

Bandawe, Gama Petulo, primary, Chigwechokha, Petros, additional, Kunyenje, Precious, additional, Kazembe, Yohane, additional, Mwale, Jeverson, additional, Kamaliza, Maladalitso, additional, Mpakati, Mtisunge, additional, Nyakanyaka, Yanjanani, additional, Makamo, Charles, additional, Kimu, Saizi, additional, Madanitsa, Mwayiwawo, additional, Bitilinyu-Bangoh, Joseph, additional, Nyirenda, Tonney, additional, Luhanga, Richard, additional, Sambani, Martha, additional, Mvula, Bernard, additional, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Naidoo, Yashnee, additional, Ramphal, Upasana, additional, San, Emmanuel James, additional, Tegally, Houriiyah, additional, Wilkinson, Eduan, additional, de Oliveira, Tulio, additional, and Malata, Address, additional

Published
2021
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14. Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil

Author

Giovanetti, Marta, primary, Nanev Slavov, Svetoslav, additional, Fonseca, Vagner, additional, Wilkinson, Eduan, additional, Tegally, Houriiyah, additional, Patane, Jose, additional, Viala, Vincent Louis, additional, San, Emmanuel James, additional, Strazza Rodrigues, Evandra, additional, Vieira Santos, Elaine, additional, Aburjaile, Flavia, additional, Xavier, Joilson, additional, Fritsch, Hegger, additional, Ribeiro Adelino, Talita Emile, additional, Pereira, Felicidade, additional, Leal, Arabela, additional, Campos de Melo Iani, Felipe, additional, de Carvalho Pereira, Glauco, additional, Vazquez, Cynthia, additional, Mercedes Estigarribia Sanabria, Gladys, additional, Cristina de Oliveira, Elaine, additional, Demarchi, Luiz, additional, Croda, Julio, additional, Bezerra, Rafael Dos Santos, additional, Oliveira de Lima, Loyze Paola, additional, Martins, Antonio Jorge, additional, dos Santos Barros, Claudia Renata, additional, Marqueze, Elaine Cristina, additional, de Souza Todao Bernardino, Jardelina, additional, Botequio Moretti, Debora, additional, Brassaloti, Ricardo Augusto, additional, de Lello Rocha Campos Cassano, Raquel, additional, Drummond Sampaio Correa Mariani, Pilar, additional, Paulo Kitajima, Joao, additional, Santos, Bibiana, additional, Proto Siqueira, Rodrigo, additional, Cantarelli, Vlademir Vicente, additional, Tosta, Stephane, additional, Brandao Nardy, Vanessa, additional, Reboredo de Oliveira da Silva, Luciana, additional, Astete Gomez, Marcela Kelly, additional, Gomes Lima, Jaqueline, additional, Ribeiro, Adriana Aparecida, additional, Rocha Guimaraes, Natalia, additional, Takao Watanabe, Luiz, additional, Barbosa Da Silva, Luana, additional, da Silva Ferreira, Raquel, additional, F. da Penha, Mara Patricia, additional, Ortega, Maria Jose, additional, Gomez de la Fuente, Andrea, additional, Villalba, Shirley, additional, Torales, Juan, additional, Gamarra, Maria Liz, additional, Aquino, Carolina, additional, Martinez Figueredo, Gloria Patricia, additional, Santos Fava, Wellington, additional, Motta Castro, Ana Rita C., additional, Venturini, James, additional, do Vale Leone de Oliveira, Sandra Maria, additional, Cavalheiro Maymone Goncalves, Crhistinne, additional, do Carmo Debur Rossa, Maria, additional, Nardi Becker, Guilherme, additional, Marinho Presibella, Mayra, additional, Quallio Marques, Nelson, additional, Nastassja Riediger, Irina, additional, Raboni, Sonia, additional, Mattoso, Gabriela, additional, Cataneo, Allan D., additional, Zanluca, Camila, additional, Duarte dos Santos, Claudia N, additional, Akemi Assato, Patricia, additional, da Silva da Costa, Felipe Allan, additional, Poleti, Mirele Daiana, additional, Chagas Lesbon, Jessika Cristina, additional, Chicaroni Mattos, Elisangela, additional, Artico Banho, Cecilia, additional, Sacchetto, Livia S, additional, Mazzi Moraes, Marilia, additional, Tommasini Grotto, Rejane Maria, additional, Souza-Neto, Jayme A., additional, Nogueira, Mauricio L, additional, Fukumasu, Heidge, additional, Lehmann Coutinho, Luiz, additional, Tocantins Calado, Rodrigo, additional, Machado Neto, Raul, additional, Bispo de Filippis, Ana Maria, additional, Venancio da Cunha, Rivaldo, additional, Freitas, Carla, additional, Leonel Peterka, Cassio Roberto, additional, Rangel Fernandes, Cassia de Fatima, additional, Navegantes, Wildo, additional, do Carmo Said, Rodrigo Fabiano, additional, Almiron, Maria, additional, Campelo de A e Melo, Carlos F, additional, Lourenco, Jose, additional, de Oliveira, Tulio, additional, Holmes, Edward C, additional, Haddad, Ricardo, additional, Sampaio, Sandra Coccuzzo, additional, Elias, Maria Carolina, additional, Kashima, Simone, additional, Alcantara, Luiz Carlos Junior, additional, and Covas, Dimas Tadeu, additional

Published
2021
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15. Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil

Author

Giovanetti, Marta, Slavov, Svetoslav Nanev, Fonseca, Vagner, Wilkinson, Eduan, Tegally, Houriiyah, Patané, José Salvatore Leister, Viala, Vincent Louis, San, Emmanuel James, Rodrigues, Evandra Strazza, Santos, Elaine Vieira, Aburjaile, Flavia, Xavier, Joilson, Fritsch, Hegger, Adelino, Talita Emile Ribeiro, Pereira, Felicidade, Leal, Arabela, de Melo Iani, Felipe Campos, de Carvalho Pereira, Glauco, Vazquez, Cynthia, Sanabria, Gladys Mercedes Estigarribia, de Oliveira, Elaine Cristina, Demarchi, Luiz, Croda, Julio, dos Santos Bezerra, Rafael, de Lima, Loyze Paola Oliveira, Martins, Antonio Jorge, dos Santos Barros, Claudia Renata, Marqueze, Elaine Cristina, de Souza Todao Bernardino, Jardelina, Moretti, Debora Botequio, Brassaloti, Ricardo Augusto, de Lello Rocha Campos Cassano, Raquel, Mariani, Pilar Drummond Sampaio Corrêa, Kitajima, João Paulo, Santos, Bibiana, Proto-Siqueira, Rodrigo, Cantarelli, Vlademir Vicente, Tosta, Stephane, Nardy, Vanessa Brandão, da Silva, Luciana Reboredo de Oliveira, Gómez, Marcela Kelly Astete, Lima, Jaqueline Gomes, Ribeiro, Adriana Aparecida, Guimarães, Natália Rocha, Watanabe, Luiz Takao, Da Silva, Luana Barbosa, da Silva Ferreira, Raquel, da Penha, Mara Patricia F., Ortega, María José, de la Fuente, Andrea Gómez, Villalba, Shirley, Torales, Juan, Gamarra, María Liz, Aquino, Carolina, Figueredo, Gloria Patricia Martínez, Fava, Wellington Santos, Motta-Castro, Ana Rita C., Venturini, James, de Oliveira, Sandra Maria do Vale Leone, Gonçalves, Crhistinne Cavalheiro Maymone, do Carmo Debur Rossa, Maria, Becker, Guilherme Nardi, Presibella, Mayra Marinho, Marques, Nelson Quallio, Riediger, Irina Nastassja, Raboni, Sonia, Coelho, Gabriela Mattoso, Cataneo, Allan Henrique Depieri, Zanluca, Camila, dos Santos, Claudia N Duarte, Assato, Patricia Akemi, Allan Costa, Felipe da Silva da, Poleti, Mirele Daiana, Lesbon, Jessika Cristina Chagas, Mattos, Elisangela Chicaroni, Banho, Cecilia Artico, Sacchetto, Lívia, Moraes, Marília Mazzi, Grotto, Rejane Maria Tommasini, Souza-Neto, Jayme A., Nogueira, Maurício Lacerda, Fukumasu, Heidge, Coutinho, Luiz Lehmann, Calado, Rodrigo Tocantins, Neto, Raul Machado, de Filippis, Ana Maria Bispo, da Cunha, Rivaldo Venancio, Freitas, Carla, Peterka, Cassio Roberto Leonel, de Fátima Rangel Fernandes, Cássia, de Araújo, Wildo Navegantes, do Carmo Said, Rodrigo Fabiano, Almiron, Maria, de Albuquerque e Melo, Carlos Frederico Campelo, Lourenço, José, de Oliveira, Tulio, Holmes, Edward C., Haddad, Ricardo, Sampaio, Sandra Coccuzzo, Elias, Maria Carolina, Kashima, Simone, de Alcantara, Luiz Carlos Junior, and Covas, Dimas Tadeu

Subjects
Coronavirus, COVID-19
Abstract

Brazil has experienced some of the highest numbers of COVID-19 infections and deaths globally and made Latin America a pandemic epicenter from May 2021. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of local virus transmission dynamics. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and an adjacent country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed, the absence of effective restriction measures led to the local emergence and international spread of Variants of Concern (VOC) and under monitoring (VUM), including the Gamma (P.1) and Zeta (P.2) variants. In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring and providing a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

Published
2021

16. Genomic epidemiology of SARS-CoV-2 in Mauritius reveals a new wave of infections dominated by the B.1.1.318, a variant under investigation

Author

Tegally, Houriiyah, primary, Ramuth, Magalutcheemee, additional, Amoaka, Daniel, additional, Scheepers, Cathrine, additional, Wilkinson, Eduan, additional, Giovanetti, Marta, additional, Lessells, Richard J, additional, Giandhari, Jennifer, additional, Ismail, Arshad, additional, Martin, Darren, additional, San, Emmanuel James, additional, Crawford, Margaret, additional, Daniels, Rodney S, additional, Harvey, Ruth, additional, Bahadoor, Somduthsingh, additional, Sonoo, Janaki, additional, Timol, Myriam, additional, Veerapa-Mangroo, Lovena, additional, Gottberg, Anne von, additional, Bhiman, Jinal N., additional, de Oliveira, Tulio, additional, and Manraj, Shyam, additional

Published
2021
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17. High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity

Author

Sureshnee Pillay, Houriiyah Tegally, Inbal Gazy, de Oliveira T, Benjamin Chimukangara, Sinaye Ngcapu, Richard J Lessells, Jennifer Giandhari, Eduan Wilkinson, Lavanya Singh, San Emmanuel James, Maryam Fish, Khulekani Sedwell Khanyile, Aquillah M. Kanzi, and Fonseca

Subjects
bottleneck, Phylogenetic tree, SARS-CoV-2, Mechanism (biology), nonsynonymous, AcademicSubjects/SCI01130, AcademicSubjects/SCI02285, within-host variants, selection, Respiratory infection, Outbreak, NGS whole-genome sequencing, Biology, Genome, Bottleneck, law.invention, South Africa, Negative selection, Transmission (mechanics), transmission dynamics, law, Evolutionary biology, AcademicSubjects/MED00860, Research Article
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in both humans and wide range of animal species. Its rapid spread globally and devasting effects have resulted into a major public health emergency prompting the need for methodological interventions to understand and control its spread. In particular, The ability to effectively retrace its transmission pathways in outbreaks remains a major challenge. This is further exacerbated by our limited understanding of its underlying evolutionary mechanism. Using NGS whole-genome data, we determined whether inter- and intra-host diversity coupled with bottleneck analysis can retrace the pathway of viral transmission in two epidemiologically well characterised nosocomial outbreaks in healthcare settings supported by phylogenetic analysis. Additionally, we assessed the mutational landscape, selection pressure and diversity of the identified variants. Our findings showed evidence of intrahost variant transmission and evolution of SARS-CoV-2 after infection These observations were consistent with the results from the bottleneck analysis suggesting that certain intrahost variants in this study could have been transmitted to recipients. In both outbreaks, we observed iSNVs and SNVs shared by putative source-recipients pairs. Majority of the observed iSNVs were positioned in the S and ORF1ab region. AG, CT and TC nucleotide changes were enriched across SARS-COV-2 genome. Moreover, SARS-COV-2 genome had limited diversity in some loci while being highly conserved in others. Overall, Our findings show that the synergistic effect of combining withinhost diversity and bottleneck estimations greatly enhances resolution of transmission events in Sars-Cov-2 outbreaks. They also provide insight into the genome diversity suggesting purifying selection may be involved in the transmission. Together these results will help in developing strategies to elucidate transmission events and curtail the spread of Sars-Cov-2

Published
2020
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18. A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa

Author

de Oliveira, Tulio, primary, Lutucuta, Silvia, additional, Nkengasong, John, additional, Morais, Joana, additional, Paixão, Joana Paula, additional, Neto, Zoraima, additional, Afonso, Pedro, additional, Miranda, Julio, additional, David, Kumbelembe, additional, Inglês, Luzia, additional, Raisa Rivas Carralero, Amilton Pereira Agostinho Paulo, additional, Freitas, Helga Reis, additional, Mufinda, Franco, additional, Tessema, Sofonias Kifle, additional, Tegally, Houriiyah, additional, San, Emmanuel James, additional, Wilkinson, Eduan, additional, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Giovanetti, Marta, additional, Naidoo, Yeshnee, additional, Katzourakis, Aris, additional, Ghafari, Mahan, additional, Singh, Lavanya, additional, Tshiabuila, Derek, additional, Martin, Darren, additional, and Lessells, Richard J, additional

Published
2021
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19. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

Author

Tegally, Houriiyah, primary, Wilkinson, Eduan, additional, Giovanetti, Marta, additional, Iranzadeh, Arash, additional, Fonseca, Vagner, additional, Giandhari, Jennifer, additional, Doolabh, Deelan, additional, Pillay, Sureshnee, additional, San, Emmanuel James, additional, Msomi, Nokukhanya, additional, Mlisana, Koleka, additional, von Gottberg, Anne, additional, Walaza, Sibongile, additional, Allam, Mushal, additional, Ismail, Arshad, additional, Mohale, Thabo, additional, Glass, Allison J, additional, Engelbrecht, Susan, additional, Van Zyl, Gert, additional, Preiser, Wolfgang, additional, Petruccione, Francesco, additional, Sigal, Alex, additional, Hardie, Diana, additional, Marais, Gert, additional, Hsiao, Marvin, additional, Korsman, Stephen, additional, Davies, Mary-Ann, additional, Tyers, Lynn, additional, Mudau, Innocent, additional, York, Denis, additional, Maslo, Caroline, additional, Goedhals, Dominique, additional, Abrahams, Shareef, additional, Laguda-Akingba, Oluwakemi, additional, Alisoltani-Dehkordi, Arghavan, additional, Godzik, Adam, additional, Wibmer, Constantinos Kurt, additional, Sewell, Bryan Trevor, additional, Lourenço, José, additional, Alcantara, Luiz Carlos Junior, additional, Pond, Sergei L Kosakovsky, additional, Weaver, Steven, additional, Martin, Darren, additional, Lessells, Richard J, additional, Bhiman, Jinal N, additional, Williamson, Carolyn, additional, and de Oliveira, Tulio, additional

Published
2020
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20. Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown

Author

Tegally, Houriiyah, primary, Wilkinson, Eduan, additional, Lessells, Richard R, additional, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Msomi, Nokukhanya, additional, Mlisana, Koleka, additional, Bhiman, Jinal, additional, Allam, Mushal, additional, Ismail, Arshad, additional, Engelbrecht, Susan, additional, Van Zyl, Gert, additional, Preiser, Wolfgang, additional, Williamson, Carolyn, additional, Pettruccione, Francesco, additional, Sigal, Alex, additional, Gazy, Inbal, additional, Hardie, Diana, additional, Hsiao, Marvin, additional, Martin, Darren, additional, York, Denis, additional, Goedhals, Dominique, additional, San, Emmanuel James, additional, Giovanetti, Marta, additional, Lourenco, Jose, additional, Alcantara, Luiz Carlos Junior, additional, and de Oliveira, Tulio, additional

Published
2020
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22. ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies

Author

Ruhamyankaka, Emmanuel, primary, Brunk, Brian P., additional, Dorsey, Grant, additional, Harb, Omar S., additional, Helb, Danica A., additional, Judkins, John, additional, Kissinger, Jessica C., additional, Lindsay, Brianna, additional, Roos, David S., additional, San, Emmanuel James, additional, Stoeckert, Christian J., additional, Zheng, Jie, additional, and Tomko, Sheena Shah, additional

Published
2020
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23. Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression

Author

Morais-Rodrigues, Francielly, primary, Silv́erio-Machado, Rita, additional, Kato, Rodrigo Bentes, additional, Rodrigues, Diego Lucas Neres, additional, Valdez-Baez, Juan, additional, Fonseca, Vagner, additional, San, Emmanuel James, additional, Gomes, Lucas Gabriel Rodrigues, additional, dos Santos, Roselane Gonçalves, additional, Vinicius Canário Viana, Marcus, additional, da Cruz Ferraz Dutra, Joyce, additional, Teixeira Dornelles Parise, Mariana, additional, Parise, Doglas, additional, Campos, Frederico F., additional, de Souza, Sandro J., additional, Ortega, José Miguel, additional, Barh, Debmalya, additional, Ghosh, Preetam, additional, Azevedo, Vasco A.C., additional, and dos Santos, Marcos A., additional

Published
2020
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24. Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era

Author

San Emmanuel James, Marta Giovanetti, Joilson Xavier, Tulio de Oliveira, Vagner Fonseca, Ana Maria Bispo de Filippis, and Luiz Carlos Junior Alcantara

Subjects
InformationSystems_INFORMATIONSTORAGEANDRETRIEVAL, Genomics, Biology, Virology, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
Published
2019

25. ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies

Author

Ruhamyankaka, Emmanuel, primary, Brunk, Brian P., additional, Dorsey, Grant, additional, Harb, Omar S., additional, Helb, Danica A., additional, Judkins, John, additional, Kissinger, Jessica C., additional, Lindsay, Brianna, additional, Roos, David S., additional, San, Emmanuel James, additional, Stoeckert, Christian J., additional, Zheng, Jie, additional, and Tomko, Sheena Shah, additional

Published
2019
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26. The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.

Author

Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, and Kosakovsky Pond SL

Abstract

The emergence and rapid rise in prevalence of three independent SARS-CoV-2 "501Y lineages", B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary capacity of SARS-CoV-2 to adapt to both rising population immunity, and public health interventions such as vaccines and social distancing. Viruses giving rise to the different 501Y lineages have, presumably under intense natural selection following a shift in host environment, independently acquired multiple unique and convergent mutations. As a consequence, all have gained epidemiological and immunological properties that will likely complicate the control of COVID-19. Here, by examining patterns of mutations that arose in SARSCoV-2 genomes during the pandemic we find evidence of a major change in the selective forces acting on various SARS-CoV-2 genes and gene segments (such as S, nsp2 and nsp6), that likely coincided with the emergence of the 501Y lineages. In addition to involving continuing sequence diversification, we find evidence that a significant portion of the ongoing adaptive evolution of the 501Y lineages also involves further convergence between the lineages. Our findings highlight the importance of monitoring how members of these known 501Y lineages, and others still undiscovered, are convergently evolving similar strategies to ensure their persistence in the face of mounting infection and vaccine induced host immune recognition.

Published
2021
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