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Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study

BACKGROUND: From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level...

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Autores principales: Martínez-Martínez, Francisco José, Massinga, Arsenia J, De Jesus, Áuria, Ernesto, Rita M, Cano-Jiménez, Pablo, Chiner-Oms, Álvaro, Gómez-Navarro, Inmaculada, Guillot-Fernández, Marina, Guinovart, Caterina, Sitoe, António, Vubil, Delfino, Bila, Rubão, Gujamo, Rufino, Enosse, Sónia, Jiménez-Serrano, Santiago, Torres-Puente, Manuela, Comas, Iñaki, Mandomando, Inácio, López, Mariana G, Mayor, Alfredo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Ltd 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10187989/
https://www.ncbi.nlm.nih.gov/pubmed/37202028
http://dx.doi.org/10.1016/S2214-109X(23)00169-9
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author Martínez-Martínez, Francisco José
Massinga, Arsenia J
De Jesus, Áuria
Ernesto, Rita M
Cano-Jiménez, Pablo
Chiner-Oms, Álvaro
Gómez-Navarro, Inmaculada
Guillot-Fernández, Marina
Guinovart, Caterina
Sitoe, António
Vubil, Delfino
Bila, Rubão
Gujamo, Rufino
Enosse, Sónia
Jiménez-Serrano, Santiago
Torres-Puente, Manuela
Comas, Iñaki
Mandomando, Inácio
López, Mariana G
Mayor, Alfredo
author_facet Martínez-Martínez, Francisco José
Massinga, Arsenia J
De Jesus, Áuria
Ernesto, Rita M
Cano-Jiménez, Pablo
Chiner-Oms, Álvaro
Gómez-Navarro, Inmaculada
Guillot-Fernández, Marina
Guinovart, Caterina
Sitoe, António
Vubil, Delfino
Bila, Rubão
Gujamo, Rufino
Enosse, Sónia
Jiménez-Serrano, Santiago
Torres-Puente, Manuela
Comas, Iñaki
Mandomando, Inácio
López, Mariana G
Mayor, Alfredo
author_sort Martínez-Martínez, Francisco José
collection PubMed
description BACKGROUND: From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling the knowledge gaps of genomic information and understanding pandemic dynamics in low-income countries is essential for public health decision making and to prepare for future pandemics. In this context, we aimed to discover the timing and origin of SARS-CoV-2 variant introductions in Mozambique, taking advantage of pandemic-scale phylogenies. METHODS: We did a retrospective, observational study in southern Mozambique. Patients from Manhiça presenting with respiratory symptoms were recruited, and those enrolled in clinical trials were excluded. Data were included from three sources: (1) a prospective hospital-based surveillance study (MozCOVID), recruiting patients living in Manhiça, attending the Manhiça district hospital, and fulfilling the criteria of suspected COVID-19 case according to WHO; (2) symptomatic and asymptomatic individuals with SARS-CoV-2 infection recruited by the National Surveillance system; and (3) sequences from SARS-CoV-2-infected Mozambican cases deposited on the Global Initiative on Sharing Avian Influenza Data database. Positive samples amenable for sequencing were analysed. We used Ultrafast Sample placement on Existing tRees to understand the dynamics of beta and delta waves, using available genomic data. This tool can reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We reconstructed a phylogeny (~7·6 million sequences) adding new and publicly available beta and delta sequences. FINDINGS: A total of 5793 patients were recruited between Nov 1, 2020, and Aug 31, 2021. During this time, 133 328 COVID-19 cases were reported in Mozambique. 280 good quality new SARS-CoV-2 sequences were obtained after the inclusion criteria were applied and an additional 652 beta (B.1.351) and delta (B.1.617.2) public sequences were included from Mozambique. We evaluated 373 beta and 559 delta sequences. We identified 187 beta introductions (including 295 sequences), divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August, 2020 and July, 2021. For delta, we identified 220 introductions (including 494 sequences), with 49 transmission groups and 171 unique introductions, mostly from the UK, India, and South Africa, between April and November, 2021. INTERPRETATION: The timing and origin of introductions suggests that movement restrictions effectively avoided introductions from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between the consequences of restrictions and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants. FUNDING: European and Developing Countries Clinical Trials, European Research Council, Bill & Melinda Gates Foundation, and Agència de Gestió d’Ajuts Universitaris i de Recerca.
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spelling pubmed-101879892023-05-17 Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study Martínez-Martínez, Francisco José Massinga, Arsenia J De Jesus, Áuria Ernesto, Rita M Cano-Jiménez, Pablo Chiner-Oms, Álvaro Gómez-Navarro, Inmaculada Guillot-Fernández, Marina Guinovart, Caterina Sitoe, António Vubil, Delfino Bila, Rubão Gujamo, Rufino Enosse, Sónia Jiménez-Serrano, Santiago Torres-Puente, Manuela Comas, Iñaki Mandomando, Inácio López, Mariana G Mayor, Alfredo Lancet Glob Health Articles BACKGROUND: From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling the knowledge gaps of genomic information and understanding pandemic dynamics in low-income countries is essential for public health decision making and to prepare for future pandemics. In this context, we aimed to discover the timing and origin of SARS-CoV-2 variant introductions in Mozambique, taking advantage of pandemic-scale phylogenies. METHODS: We did a retrospective, observational study in southern Mozambique. Patients from Manhiça presenting with respiratory symptoms were recruited, and those enrolled in clinical trials were excluded. Data were included from three sources: (1) a prospective hospital-based surveillance study (MozCOVID), recruiting patients living in Manhiça, attending the Manhiça district hospital, and fulfilling the criteria of suspected COVID-19 case according to WHO; (2) symptomatic and asymptomatic individuals with SARS-CoV-2 infection recruited by the National Surveillance system; and (3) sequences from SARS-CoV-2-infected Mozambican cases deposited on the Global Initiative on Sharing Avian Influenza Data database. Positive samples amenable for sequencing were analysed. We used Ultrafast Sample placement on Existing tRees to understand the dynamics of beta and delta waves, using available genomic data. This tool can reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We reconstructed a phylogeny (~7·6 million sequences) adding new and publicly available beta and delta sequences. FINDINGS: A total of 5793 patients were recruited between Nov 1, 2020, and Aug 31, 2021. During this time, 133 328 COVID-19 cases were reported in Mozambique. 280 good quality new SARS-CoV-2 sequences were obtained after the inclusion criteria were applied and an additional 652 beta (B.1.351) and delta (B.1.617.2) public sequences were included from Mozambique. We evaluated 373 beta and 559 delta sequences. We identified 187 beta introductions (including 295 sequences), divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August, 2020 and July, 2021. For delta, we identified 220 introductions (including 494 sequences), with 49 transmission groups and 171 unique introductions, mostly from the UK, India, and South Africa, between April and November, 2021. INTERPRETATION: The timing and origin of introductions suggests that movement restrictions effectively avoided introductions from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between the consequences of restrictions and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants. FUNDING: European and Developing Countries Clinical Trials, European Research Council, Bill & Melinda Gates Foundation, and Agència de Gestió d’Ajuts Universitaris i de Recerca. Elsevier Ltd 2023-05-16 /pmc/articles/PMC10187989/ /pubmed/37202028 http://dx.doi.org/10.1016/S2214-109X(23)00169-9 Text en © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Articles
Martínez-Martínez, Francisco José
Massinga, Arsenia J
De Jesus, Áuria
Ernesto, Rita M
Cano-Jiménez, Pablo
Chiner-Oms, Álvaro
Gómez-Navarro, Inmaculada
Guillot-Fernández, Marina
Guinovart, Caterina
Sitoe, António
Vubil, Delfino
Bila, Rubão
Gujamo, Rufino
Enosse, Sónia
Jiménez-Serrano, Santiago
Torres-Puente, Manuela
Comas, Iñaki
Mandomando, Inácio
López, Mariana G
Mayor, Alfredo
Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study
title Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study
title_full Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study
title_fullStr Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study
title_full_unstemmed Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study
title_short Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study
title_sort tracking sars-cov-2 introductions in mozambique using pandemic-scale phylogenies: a retrospective observational study
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10187989/
https://www.ncbi.nlm.nih.gov/pubmed/37202028
http://dx.doi.org/10.1016/S2214-109X(23)00169-9
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