{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T06:11:22Z","timestamp":1790921482048,"version":"4.1.0"},"reference-count":27,"publisher":"JMIR Publications Inc.","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JMIR Public Health Surveill"],"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n Traditional infectious disease surveillance systems face significant limitations, including delayed detection, underreporting of asymptomatic cases, and inequitable health care access. Wastewater-based epidemiology (WBE), enhanced with genomic analysis, offers a noninvasive and cost-effective alternative for early pathogen detection and variant characterization, particularly valuable for monitoring international disease transmission.<\/jats:p>\n <\/jats:sec>\n \n Objective<\/jats:title>\n This study aimed to implement and evaluate a genomics-enhanced WBE surveillance system for detecting and characterizing SARS-CoV-2 variants among international travelers at the Kigali International Airport, Rwanda, and to assess its potential as an early warning system for pandemic preparedness.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n Between May and December 2023, we collected wastewater samples from international flights arriving at the Kigali International Airport under Rwanda\u2019s National One Health strategy. Molecular detection was performed using polymerase chain reaction (PCR) assays, followed by whole-genome sequencing of positive samples. Bioinformatics analysis included quality assessment with Nanoplot (version 1.41.6), genome mapping using minimap2 (version 2.26), and lineage identification using the Freyja tool (version 1.4.5). Spatial and temporal analyses were used to identify transmission patterns and variant origins.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Of 630 wastewater samples collected from flights originating from 9 countries, 603 were successfully processed, with 21% (132\/617) testing positive for SARS-CoV-2. Whole-genome sequencing was conducted on 33 samples, yielding an average viral sequence depth of 1250 reads with 92% genome coverage (range 78%\u201097%). Genomic analysis identified 7 SARS-CoV-2 variants, including Omicron subvariants XBB.1.5, XBB.1.16.6 (eg, 5.1), GE.1, and FE.1.1.1. Notably, 70% (23\/33) of sequenced samples could not be assigned to existing lineages, suggesting potential novel variants. Most samples came from Qatar (21.4%, 135\/1630), the United Arab Emirates (19.5%, 123\/1630), and the United Kingdom (19.4%, 122\/1630). Positive samples were detected from 11 countries, with variants frequently found in flights from the United Kingdom, France, Belgium, Kenya, Tanzania, and South Africa. Sample collection capacity increased from 6 in week 1 to 33 by week 27. SARS-CoV-2 positivity rates showed seasonal variation, with a marked decline in June-July 2023.<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n Genomics-enhanced WBE demonstrated a high sensitivity for the early detection of SARS-CoV-2 variants among international travelers, including potential novel variants undetectable through traditional surveillance. Its noninvasive and cost-effective nature, combined with the ability to generate population-level epidemiological insights, makes it particularly suitable for resource-limited settings. This approach supports Rwanda\u2019s National One Health strategy and offers a scalable model for advancing global health security in Sub-Saharan Africa through innovative surveillance tools.<\/jats:p>\n <\/jats:sec>","DOI":"10.2196\/71104","type":"journal-article","created":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T13:46:31Z","timestamp":1764337591000},"page":"e71104-e71104","source":"Crossref","is-referenced-by-count":5,"title":["SARS-CoV-2 Detection in International Travelers Through Wastewater-Based Epidemiology at the Kigali International Airport: Genomic Surveillance Study"],"prefix":"10.2196","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-5002-0829","authenticated-orcid":false,"given":"Rwagasore","family":"Edson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4818-1552","authenticated-orcid":false,"given":"Robert","family":"Rutayisire","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0756-7280","authenticated-orcid":false,"given":"Ziad","family":"El-Khatib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9238-4691","authenticated-orcid":false,"given":"Olivier","family":"Nsekuye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4054-3417","authenticated-orcid":false,"given":"Hugues Valois","family":"Mucunguzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2324-3254","authenticated-orcid":false,"given":"Raissa","family":"Muvunyi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3941-9939","authenticated-orcid":false,"given":"Esperance","family":"Umumararungu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6084-8877","authenticated-orcid":false,"given":"Eric","family":"Remera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1010","published-online":{"date-parts":[[2025,11,27]]},"reference":[{"issue":"3","key":"R1","doi-asserted-by":"publisher","DOI":"10.1001\/jamanetworkopen.2022.1760","article-title":"The COVID-19 pandemic strikes again and again and again","volume":"5","author":"Myers","journal-title":"JAMA Netw Open"},{"issue":"4","key":"R2","doi-asserted-by":"publisher","first-page":"382","DOI":"10.34172\/hpp.2021.49","article-title":"COVID-19 surveillance systems in African countries","volume":"11","author":"Adebisi","journal-title":"Health Promot Perspect"},{"issue":"11","key":"R3","doi-asserted-by":"publisher","first-page":"1630","DOI":"10.1016\/j.jiph.2020.07.019","article-title":"Epidemiologic surveillance for controlling Covid-19 pandemic: types, challenges and implications","volume":"13","author":"Ibrahim","journal-title":"J Infect Public Health"},{"issue":"3","key":"R4","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1093\/trstmh\/trab119","article-title":"The role of integrated programs in the prevention of COVID-19 in a humanitarian setting","volume":"116","author":"Ali","journal-title":"Trans R Soc Trop Med Hyg"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1016\/j.envint.2020.105689","article-title":"Future perspectives of wastewater-based epidemiology: monitoring infectious disease spread and resistance to the community level","volume":"139","author":"Sims","journal-title":"Environ Int"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1016\/j.trac.2018.06.004","article-title":"Wastewater-based epidemiology biomarkers: past, present and future","volume":"105","author":"Choi","journal-title":"TrAC Trends in Analytical Chemistry"},{"issue":"9","key":"R7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0162493","article-title":"Detection of invasive mosquito vectors using environmental DNA (eDNA) from water samples","volume":"11","author":"Schneider","journal-title":"PLoS ONE"},{"issue":"18","key":"R8","doi-asserted-by":"publisher","first-page":"8931","DOI":"10.1073\/pnas.1815046116","article-title":"Environmental DNA for improved detection and environmental surveillance of schistosomiasis","volume":"116","author":"Sengupta","journal-title":"Proc Natl Acad Sci U S A"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2021.148810","article-title":"Pathogens and disease vectors\/hosts monitoring in aquatic environments: potential of using eDNA\/eRNA based approach","volume":"796","author":"Amarasiri","journal-title":"Sci Total Environ"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1016\/j.envres.2020.110265","article-title":"SARS-CoV-2 coronavirus in water and wastewater: a critical review about presence and concern","volume":"193","author":"Tran","journal-title":"Environ Res"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1016\/j.watres.2020.115942","article-title":"SARS-CoV-2 RNA in wastewater anticipated COVID-19 occurrence in a low prevalence area","volume":"181","author":"Randazzo","journal-title":"Water Res"},{"key":"R12","unstructured":"WHO COVID19 dashboard. World Health Organization. Jun 4, 2023. URL: https:\/\/covid19.who.int\/region\/afro\/country\/rw [Accessed 03-10-2023]"},{"issue":"2","key":"R13","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1038\/s41576-023-00649-y","article-title":"Genomic surveillance for antimicrobial resistance - a One Health perspective","volume":"25","author":"Djordjevic","journal-title":"Nat Rev Genet"},{"issue":"1","key":"R14","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/nrg.2017.88","article-title":"Towards a genomics-informed, real-time, global pathogen surveillance system","volume":"19","author":"Gardy","journal-title":"Nat Rev Genet"},{"key":"R15","unstructured":"Global report on neglected tropical diseases 2023. World Health Organization; 2023. URL: https:\/\/www.who.int\/teams\/control-of-neglected-tropical-diseases\/global-report-on-neglected-tropical-diseases-2023 [Accessed 18-11-2025]"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2019.00109","article-title":"One health surveillance: a matrix to evaluate multisectoral collaboration","volume":"6","author":"Bordier","journal-title":"Front Vet Sci"},{"key":"R17","unstructured":"World Health Organization. One Health Joint Plan of Action (2022\u20122026): Working Together for The Health of Humans, Animals, Plants and the Environment. 2022. URL: https:\/\/www.who.int\/publications\/i\/item\/9789240059139 [Accessed 18-11-2025] ISBN: 978-92-4-005913-9"},{"issue":"9","key":"R18","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens12091153","article-title":"Monitoring monkeypox: safeguarding global health through rapid response and global surveillance","volume":"12","author":"Giovanetti","journal-title":"Pathogens"},{"key":"R19","unstructured":"EWARS- improving early detection and prompt response to acute public health events. World Health Organization. Nov 1, 2019. URL: https:\/\/www.afro.who.int\/news\/ewars-improving-early-detection-and-prompt-response-acute-public-health-events [Accessed 18-11-2025]"},{"key":"R20","unstructured":"International Health Regulations (2005) \u2013 Third Edition. World Health Organization; 2005. URL: https:\/\/www.who.int\/publications\/i\/item\/9789241580496 [Accessed 20-11-2025] ISBN: 978-92-4-158049-6"},{"issue":"4","key":"R21","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1093\/inthealth\/ihz122","article-title":"Urgent call for a global enforcement of the public sharing of health emergencies data: lesson learned from serious arboviral disease epidemics in Sudan","volume":"12","author":"Ahmed","journal-title":"Int Health"},{"key":"R22","unstructured":"GAVI TGAfVaI. The next pandemic: rift valley fever? May 27, 2021. URL: https:\/\/www.gavi.org\/vaccineswork\/next-pandemic\/rift-valley-fever [Accessed 18-11-2025]"},{"key":"R23","unstructured":"Preventing the next pandemic - zoonotic diseases and how to break the chain of transmission. UNEP. 2020. URL: https:\/\/www.unep.org\/resources\/report\/preventing-future-zoonotic-disease-outbreaks-protecting-environment-animals-and [Accessed 18-11-2025]"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2020.10.091","article-title":"The prevalence of asymptomatic and symptomatic COVID-19 in a cohort of quarantined subjects","volume":"102","author":"Al-Qahtani","journal-title":"Int J Infect Dis"},{"issue":"14","key":"R25","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1001\/jama.2020.2565","article-title":"Presumed asymptomatic carrier transmission of COVID-19","volume":"323","author":"Bai","journal-title":"JAMA"},{"issue":"45","key":"R26","doi-asserted-by":"publisher","first-page":"1681","DOI":"10.15585\/mmwr.mm6945a4","article-title":"Risk assessment and management of COVID-19 among travelers arriving at designated U.S. airports, January 17-September 13, 2020","volume":"69","author":"Dollard","journal-title":"MMWR Morb Mortal Wkly Rep"},{"issue":"7925","key":"R27","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/s41586-022-05049-6","article-title":"Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission","volume":"609","author":"Karthikeyan","journal-title":"Nature New Biol"}],"container-title":["JMIR Public Health and Surveillance"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/publichealth.jmir.org\/2025\/1\/e71104","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T18:00:13Z","timestamp":1782842413000},"score":1,"resource":{"primary":{"URL":"https:\/\/publichealth.jmir.org\/2025\/1\/e71104"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,27]]},"references-count":27,"URL":"https:\/\/doi.org\/10.2196\/71104","relation":{},"ISSN":["2369-2960"],"issn-type":[{"value":"2369-2960","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,27]]},"article-number":"v11i3e71104"}}