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Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
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Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Anelizze Castro-Martinez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
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Ramadan M, Kheirallah KA, Cegolon L, Bellizzi S. Maintaining Cross-Border Cargo Movements Between Jordan and Saudi Arabia During the COVID-19 Pandemic. Health Secur 2023; 21:319-322. [PMID: 37466656 DOI: 10.1089/hs.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
One of Jordan's essential border crossings, the Al-Omari border crossing, is 1 of 3 land crossings between Jordan and Saudi Arabia and is located 160 km west of the capital city of Amman. Given its economic importance and essential role in the functioning of food supply networks across the region, Jordan undertook evidence-driven actions to keep the border crossing safely open during the initial phase of the COVID-19 pandemic. Cross-border coordination and collaboration, specifically with international contact tracing and case management, have been critical elements of Jordan's response. While several bottlenecks and delays led to documented clusters of infections among truck drivers, this case study illustrates the use of evidence to mitigate disease exposure and spread. Plans to manage public health threats need to consider sustainable strengthened surveillance and laboratory capacities coupled with efficient cross-border communication and coordination plans implemented across multiple sectors engaged in cross-country health.
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Affiliation(s)
- Mohannad Ramadan
- Mohannad Ramadan, MD, MSc, is a Research Assistant, Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Khalid A Kheirallah
- Khalid A. Kheirallah, PhD, is an Associate Professor, Department of Public Health, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Luca Cegolon
- Luca Cegolon, MD, MSc, DTM&H, PhD, is a Clinical Lecturer in Public Health Medicine, University of Trieste, Department of Medical, Surgical & Health Science, and a Consultant Medical Epidemiologist, Unit of Occupational Medicine, University Health Agency Giuliano-Isontina; both in Trieste, Italy
| | - Saverio Bellizzi
- Saverio Bellizzi, MD, MSc, PhD, is a Consulting Medical Epidemiologist, Sassari, Italy
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Martínez-Martínez FJ, Massinga AJ, De Jesus Á, Ernesto RM, Cano-Jiménez P, Chiner-Oms Á, Gómez-Navarro I, Guillot-Fernández M, Guinovart C, Sitoe A, Vubil D, Bila R, Gujamo R, Enosse S, Jiménez-Serrano S, Torres-Puente M, Comas I, Mandomando I, López MG, Mayor A. Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study. Lancet Glob Health 2023; 11:e933-e941. [PMID: 37202028 DOI: 10.1016/s2214-109x(23)00169-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/09/2023] [Accepted: 03/23/2023] [Indexed: 05/20/2023]
Abstract
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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Affiliation(s)
- Francisco José Martínez-Martínez
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Áuria De Jesus
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Rita M Ernesto
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Pablo Cano-Jiménez
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Álvaro Chiner-Oms
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Inmaculada Gómez-Navarro
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Marina Guillot-Fernández
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - António Sitoe
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Rubão Bila
- Hospital Distrital da Manhiça, Marracuene, Mozambique
| | | | - Sónia Enosse
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Santiago Jiménez-Serrano
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Mariana G López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain.
| | - Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique
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Olawoye IB, Oluniyi PE, Oguzie JU, Uwanibe JN, Kayode TA, Olumade TJ, Ajogbasile FV, Parker E, Eromon PE, Abechi P, Sobajo TA, Ugwu CA, George UE, Ayoade F, Akano K, Oyejide NE, Nosamiefan I, Fred-Akintunwa I, Adedotun-Sulaiman K, Brimmo FB, Adegboyega BB, Philip C, Adeleke RA, Chukwu GC, Ahmed MI, Ope-Ewe OO, Otitoola SG, Ogunsanya OA, Saibu MF, Sijuwola AE, Ezekiel GO, John OG, Akin-John JO, Akinlo OO, Fayemi OO, Ipaye TO, Nwodo DC, Omoniyi AE, Omwanghe IB, Terkuma CA, Okolie J, Ayo-Ale O, Ikponmwosa O, Benevolence E, Naregose GO, Patience AE, Blessing O, Micheal A, Jacqueline A, Aiyepada JO, Ebhodaghe P, Racheal O, Rita E, Rosemary GE, Solomon E, Anieno E, Edna Y, Chris AO, Donatus AI, Ogbaini-Emovon E, Tatfeng MY, Omunakwe HE, Bob-Manuel M, Ahmed RA, Onwuamah CK, Shaibu JO, Okwuraiwe A, Ataga AE, Bock-Oruma A, Daramola F, Yusuf IF, Fajola A, Ntia NA, Ekpo JJ, Moses AE, Moore-Igwe BW, Fakayode OE, Akinola M, Kida IM, Oderinde BS, Wudiri ZW, Adeyemi OO, Akanbi OA, Ahumibe A, Akinpelu A, Ayansola O, Babatunde O, Omoare AA, Chukwu C, Mba NG, Omoruyi EC, Olisa O, Akande OK, Nwafor IE, Ekeh MA, Ndoma E, Ewah RL, Duruihuoma RO, Abu A, Odeh E, Onyia V, Ojide CK, Okoro S, Igwe D, Ogah EO, Khan K, Ajayi NA, Ugwu CN, Ukwaja KN, Ugwu NI, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Isamotu RO, Gadzama G, Petros BA, Siddle KJ, Schaffner SF, Akpede G, Erameh CO, Baba MM, Oladiji F, Audu R, Ndodo N, Fowotade A, Okogbenin S, Okokhere PO, Park DJ, Mcannis BL, Adetifa IM, Ihekweazu C, Salako BL, Tomori O, Happi AN, Folarin OA, Andersen KG, Sabeti PC, Happi CT. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria. Nat Commun 2023; 14:811. [PMID: 36781860 PMCID: PMC9924892 DOI: 10.1038/s41467-023-36449-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates.
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Affiliation(s)
- Idowu B Olawoye
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Jessica N Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tolulope A Kayode
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony J Olumade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Priscilla Abechi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tope A Sobajo
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Chinedu A Ugwu
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Uwem E George
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Femi Ayoade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kazeem Akano
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Nicholas E Oyejide
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iguosadolo Nosamiefan
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kemi Adedotun-Sulaiman
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Farida B Brimmo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde B Adegboyega
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Courage Philip
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Richard A Adeleke
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Grace C Chukwu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Muhammad I Ahmed
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oludayo O Ope-Ewe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shobi G Otitoola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olusola A Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Mudasiru F Saibu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Ayotunde E Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Grace O Ezekiel
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Julie O Akin-John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwasemilogo O Akinlo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olanrewaju O Fayemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony O Ipaye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Deborah C Nwodo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Abolade E Omoniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyobosa B Omwanghe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christabel A Terkuma
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Johnson Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olubukola Ayo-Ale
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Odia Ikponmwosa
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ebo Benevolence
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Osiemi Blessing
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Airende Micheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - John O Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Omiunu Racheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Esumeh Rita
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Giwa E Rosemary
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Ekanem Anieno
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Yerumoh Edna
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Aire O Chris
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Mirabeau Y Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Amassoma, Bayelsa State, Nigeria
| | - Hannah E Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Mienye Bob-Manuel
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Rahaman A Ahmed
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Chika K Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Joseph O Shaibu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Azuka Okwuraiwe
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Anthony E Ataga
- Molecular Laboratory, Regional Centre for Biotechnology and Bioresources Research, University of Port Harcourt, Port Harcourt, Rivers State, Nigeria
| | | | - Funmi Daramola
- Clinical Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Akinwumi Fajola
- Regional Community Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Julie J Ekpo
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | - Anietie E Moses
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | | | | | - Monilade Akinola
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Ibrahim M Kida
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Bamidele S Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Zara W Wudiri
- Department of Community Medicine, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Oluwapelumi O Adeyemi
- Department of Medical Microbiology and Parasitology. Faculty of Basic Clinical Sciences. College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | | | | | | | | | | | | | - Nwando G Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Ewean C Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olasunkanmi Olisa
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Olatunji K Akande
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Ifeanyi E Nwafor
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Matthew A Ekeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Erim Ndoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Richard L Ewah
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Rosemary O Duruihuoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Augustine Abu
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Elizabeth Odeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Venatius Onyia
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Chiedozie K Ojide
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Sylvanus Okoro
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Daniel Igwe
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Emeka O Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Nnennaya A Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Collins N Ugwu
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kingsley N Ukwaja
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ngozi I Ugwu
- Haematology Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | | | | | | | - Galadima Gadzama
- Department of Medical Microbiology, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | | | | | | | - George Akpede
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Marycelin M Baba
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Femi Oladiji
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Rosemary Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | | | - Adeola Fowotade
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | | | | | - Danny J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | | | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Anise N Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe A Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
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Douglas J, Winter D, McNeill A, Carr S, Bunce M, French N, Hadfield J, de Ligt J, Welch D, Geoghegan JL. Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border. Nat Commun 2022; 13:6484. [PMID: 36309507 PMCID: PMC9617600 DOI: 10.1038/s41467-022-34186-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/18/2022] [Indexed: 12/25/2022] Open
Abstract
In the second quarter of 2022, there was a global surge of emergent SARS-CoV-2 lineages that had a distinct growth advantage over then-dominant Omicron BA.1 and BA.2 lineages. By generating 10,403 Omicron genomes, we show that Aotearoa New Zealand observed an influx of these immune-evasive variants (BA.2.12.1, BA.4, and BA.5) through the border. This is explained by the return to significant levels of international travel following the border's reopening in March 2022. We estimate one Omicron transmission event from the border to the community for every ~5,000 passenger arrivals at the current levels of travel and restriction. Although most of these introductions did not instigate any detected onward transmission, a small minority triggered large outbreaks. Genomic surveillance at the border provides a lens on the rate at which new variants might gain a foothold and trigger new waves of infection.
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Affiliation(s)
- Jordan Douglas
- grid.9654.e0000 0004 0372 3343Centre for Computational Evolution,School of Computer Science, University of Auckland, Auckland, New Zealand
| | - David Winter
- grid.419706.d0000 0001 2234 622XInstitute of Environmental Science and Research, Wellington, New Zealand
| | - Andrea McNeill
- grid.419706.d0000 0001 2234 622XInstitute of Environmental Science and Research, Wellington, New Zealand
| | - Sam Carr
- grid.419706.d0000 0001 2234 622XInstitute of Environmental Science and Research, Wellington, New Zealand
| | - Michael Bunce
- grid.419706.d0000 0001 2234 622XInstitute of Environmental Science and Research, Wellington, New Zealand
| | - Nigel French
- grid.148374.d0000 0001 0696 9806Tāwharau Ora/School of Veterinary Science, Massey University, Palmerston North, New Zealand ,grid.419706.d0000 0001 2234 622XTe Niwha, Infectious Diseases Research Platform, Institute of Environmental Science and Research, Palmerston North, New Zealand
| | - James Hadfield
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Centre, Seattle, WA USA
| | - Joep de Ligt
- grid.419706.d0000 0001 2234 622XInstitute of Environmental Science and Research, Wellington, New Zealand
| | - David Welch
- grid.9654.e0000 0004 0372 3343Centre for Computational Evolution,School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Jemma L. Geoghegan
- grid.419706.d0000 0001 2234 622XInstitute of Environmental Science and Research, Wellington, New Zealand ,grid.29980.3a0000 0004 1936 7830Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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