{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T16:02:34Z","timestamp":1776960154727,"version":"3.51.4"},"reference-count":40,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T00:00:00Z","timestamp":1743033600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["Viruses"],"abstract":"<jats:p>In December 2021, an outbreak of the SARS-CoV-2 B.1.640.2 variant, potentially originating from Cameroon, was investigated among schoolchildren in Germany. The index case, an adult who had recently returned from a three-week stay in the Republic of Congo, introduced the variant into a school setting via their children, resulting in subsequent transmission within the school and ultimately to a hospital ward. Whole-genome sequencing of viral samples identified both B.1.640.1 and B.1.640.2 lineages. This outbreak highlights the unpredictable nature of emerging SARS-CoV-2 variants and emphasizes the importance of early detection and containment to mitigate transmission to high-risk populations. Notably, wastewater surveillance detected the variant during the study peri-od, reinforcing the utility of wastewater-based epidemiology as a complementary tool for the early warning and containment of novel variants. These findings underline the critical need for timely research and adherence to quarantine measures to enhance outbreak control efforts.<\/jats:p>","DOI":"10.3390\/v17040477","type":"journal-article","created":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T06:06:35Z","timestamp":1743141995000},"page":"477","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["From Entry to Outbreak in a High School Setting: Clinical and Wastewater Surveillance of a Rare SARS-CoV-2 Variant"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-7742-4743","authenticated-orcid":false,"given":"Sven","family":"Sachse","sequence":"first","affiliation":[{"name":"Institute for Artificial Intelligence (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany"},{"name":"Department of Hygiene and Environmental Medicine, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9677-6094","authenticated-orcid":false,"given":"Ivana","family":"Kraiselburd","sequence":"additional","affiliation":[{"name":"Institute for Artificial Intelligence (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany"},{"name":"Center for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2178-3182","authenticated-orcid":false,"given":"Olympia","family":"Anastasiou","sequence":"additional","affiliation":[{"name":"Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carina","family":"Elsner","sequence":"additional","affiliation":[{"name":"Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Goretzki","sequence":"additional","affiliation":[{"name":"Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Infectiology, Pediatric Neurology, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Goer","sequence":"additional","affiliation":[{"name":"Department of Hygiene and Environmental Medicine, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8738-5884","authenticated-orcid":false,"given":"Michael","family":"Koldehoff","sequence":"additional","affiliation":[{"name":"Department of Hygiene and Environmental Medicine, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Thomas","sequence":"additional","affiliation":[{"name":"Institute for Artificial Intelligence (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-2197-6539","authenticated-orcid":false,"given":"Jens","family":"Schoth","sequence":"additional","affiliation":[{"name":"Emschergenossenschaft Lippeverband (EGLV), 45128 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1544-9903","authenticated-orcid":false,"given":"Sebastian","family":"Voigt","sequence":"additional","affiliation":[{"name":"Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rudolf","family":"Ross","sequence":"additional","affiliation":[{"name":"Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulf","family":"Dittmer","sequence":"additional","affiliation":[{"name":"Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Folker","family":"Meyer","sequence":"additional","affiliation":[{"name":"Institute for Artificial Intelligence (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany"},{"name":"Center for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3736-8672","authenticated-orcid":false,"given":"Ricarda","family":"Schmithausen","sequence":"additional","affiliation":[{"name":"Institute for Artificial Intelligence (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany"},{"name":"Department of Hygiene and Environmental Medicine, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany"},{"name":"Center for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,27]]},"reference":[{"key":"ref_1","unstructured":"Samieefar, N., Rashedi, R., Akhlaghdoust, M., Mashhadi, M., Darzi, P., and Rezaei, N. (2022). Delta Variant: The New Challenge of COVID-19 Pandemic, an Overview of Epidemiological, Clinical, and Immune Characteristics. Acta Biomed., 93."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1001\/jamainternmed.2021.7949","article-title":"Severity of Illness in Persons Infected With the SARS-CoV-2 Delta Variant vs Beta Variant in Qatar","volume":"182","author":"Butt","year":"2022","journal-title":"JAMA Intern. Med."},{"key":"ref_3","first-page":"2251","article-title":"Delta Variant Wasn\u2019t Linked With More Severe Disease","volume":"326","author":"Kuehn","year":"2021","journal-title":"JAMA"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1093\/infdis\/jiae546","article-title":"Lower levels of household transmission of SARS-CoV-2 VOC Omicron compared to Wild-type: An interplay between transmissibility and immune status","volume":"231","author":"Winkel","year":"2024","journal-title":"J. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1016\/S0140-6736(22)00462-7","article-title":"Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: A cohort study","volume":"399","author":"Nyberg","year":"2022","journal-title":"Lancet"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2200077","DOI":"10.2807\/1560-7917.ES.2022.27.4.2200077","article-title":"Reduced risk of hospitalisation among reported COVID-19 cases infected with the SARS-CoV-2 Omicron BA.1 variant compared with the Delta variant, Norway, December 2021 to January 2022","volume":"27","author":"Veneti","year":"2022","journal-title":"Eurosurveillance"},{"key":"ref_7","unstructured":"WHO (2021). Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern, WHO."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e13062","DOI":"10.1111\/irv.13062","article-title":"Comparative hospitalization risk for SARS-CoV-2 Omicron and Delta variant infections, by variant predominance periods and patient-level sequencing results, New York City, August 2021\u2013January 2022","volume":"17","author":"Greene","year":"2023","journal-title":"Influenza Other Respir Viruses"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1007\/s11262-021-01877-2","article-title":"Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France","volume":"58","author":"Colson","year":"2022","journal-title":"Virus Genes"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2200671","DOI":"10.2807\/1560-7917.ES.2023.28.22.2200671","article-title":"Emergence, spread and characterisation of the SARS-CoV-2 variant B.1.640 circulating in France, October 2021 to February 2022","volume":"28","author":"Picard","year":"2023","journal-title":"Eurosurveillance"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Catal\u00e0, M., Coma, E., Alonso, S., Andr\u00e9s, C., Blanco, I., Ant\u00f3n, A., Bordoy, A.E., Cardona, P.J., Fina, F., and Martr\u00f3, E. (2022). Transmissibility, hospitalization, and intensive care admissions due to omicron compared to delta variants of SARS-CoV-2 in Catalonia: A cohort study and ecological analysis. Front. Public Health, 10.","DOI":"10.3389\/fpubh.2022.1060328"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/s41586-021-04245-0","article-title":"The N501Y spike substitution enhances SARS-CoV-2 infection and transmission","volume":"602","author":"Liu","year":"2022","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Liddor Naim, M., Fu, Y., Shagan, M., Bar-Or, I., Marks, R., Sun, Q., Granek, R., and Kushmaro, A. (2023). The Rise and Fall of Omicron BA.1 Variant as Seen in Wastewater Supports Epidemiological Model Predictions. Viruses, 15.","DOI":"10.20944\/preprints202307.1362.v1"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1038\/nprot.2017.066","article-title":"Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples","volume":"12","author":"Quick","year":"2017","journal-title":"Nat. Protoc."},{"key":"ref_15","unstructured":"(2023, December 13). MEGA (Molecular Evolutionary Genetics Analysis). Available online: https:\/\/www.megasoftware.net\/."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Thomas, A., Battenfeld, T., Kraiselburd, I., Anastasiou, O., Dittmer, U., D\u00f6rr, A.K., D\u00f6rr, A., Elsner, C., Gosch, J., and Le-Trilling, V.T.K. (2024). UnCoVar: A reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10539-0"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"veab064","DOI":"10.1093\/ve\/veab064","article-title":"Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool","volume":"7","author":"Scher","year":"2021","journal-title":"Virus Evol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.46234\/ccdcw2021.255","article-title":"GISAID\u2019s Role in Pandemic Response","volume":"3","author":"Khare","year":"2021","journal-title":"China CDC Wkly."},{"key":"ref_20","unstructured":"Garrison, E., and Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: Structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"Rausch","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"K\u00f6ster, J., Dijkstra, L.J., Marschall, T., and Sch\u00f6nhuth, A. (2020). Varlociraptor: Enhancing sensitivity and controlling false discovery rate in somatic indel discovery. Genome Biol., 21.","DOI":"10.1186\/s13059-020-01993-6"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Wilhelm, A., Widera, M., Grikscheit, K., Toptan, T., Schenk, B., Pallas, C., Metzler, M., Kohmer, N., Hoehl, S., and Marschalek, R. (2022). Limited neutralisation of the SARS-CoV-2 Omicron subvariants BA.1 and BA.2 by convalescent and vaccine serum and monoclonal antibodies. EBioMedicine, 82.","DOI":"10.1016\/j.ebiom.2022.104158"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"165458","DOI":"10.1016\/j.scitotenv.2023.165458","article-title":"Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area","volume":"898","author":"Schmiege","year":"2023","journal-title":"Sci. Total. Environ."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e2020048090","DOI":"10.1542\/peds.2020-048090","article-title":"Incidence and Secondary Transmission of SARS-CoV-2 Infections in Schools","volume":"147","author":"Zimmerman","year":"2021","journal-title":"Pediatrics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1016\/S0140-6736(21)01908-5","article-title":"Daily testing for contacts of individuals with SARS-CoV-2 infection and attendance and SARS-CoV-2 transmission in English secondary schools and colleges: An open-label, cluster-randomised trial","volume":"398","author":"Young","year":"2021","journal-title":"Lancet"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1111\/irv.12968","article-title":"Factors affecting the transmission of SARS-CoV-2 in school settings","volume":"16","author":"Yuan","year":"2022","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2112","DOI":"10.1001\/jama.2021.5053","article-title":"Indoor Air Changes and Potential Implications for SARS-CoV-2 Transmission","volume":"325","author":"Allen","year":"2021","journal-title":"JAMA"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"110805","DOI":"10.1016\/j.envres.2021.110805","article-title":"Estimating aerosol transmission risk of SARS-CoV-2 in New York City public schools during reopening","volume":"195","author":"Pavilonis","year":"2021","journal-title":"Environ. Res."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Chen, X., Ran, L., Liu, Q., Hu, Q., Du, X., and Tan, X. (2020). Hand Hygiene, Mask-Wearing Behaviors and Its Associated Factors during the COVID-19 Epidemic: A Cross-Sectional Study among Primary School Students in Wuhan, China. Int. J. Environ. Res. Public Health, 17.","DOI":"10.3390\/ijerph17082893"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e13142","DOI":"10.1111\/ina.13142","article-title":"A multi-layered strategy for COVID-19 infection prophylaxis in schools: A review of the evidence for masks, distancing, and ventilation","volume":"32","author":"McLeod","year":"2022","journal-title":"Indoor Air"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"108139","DOI":"10.1016\/j.buildenv.2021.108139","article-title":"Mitigating aerosol infection risk in school buildings: The role of natural ventilation, volume, occupancy and CO2 monitoring","volume":"204","author":"Zivelonghi","year":"2021","journal-title":"Build. Environ."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"113311","DOI":"10.1063\/5.0067798","article-title":"SARS-CoV-2 transmission in classroom settings: Effects of mitigation, age, and Delta variant","volume":"33","author":"Foster","year":"2021","journal-title":"Phys. Fluids"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"141750","DOI":"10.1016\/j.scitotenv.2020.141750","article-title":"Detection of SARS-CoV-2 in raw and treated wastewater in Germany\u2014Suitability for COVID-19 surveillance and potential transmission risks","volume":"751","author":"Westhaus","year":"2021","journal-title":"Sci. Total. Environ."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"114379","DOI":"10.1016\/j.ijheh.2024.114379","article-title":"Small-scale wastewater-based epidemiology (WBE) for infectious diseases and antibiotic resistance: A scoping review","volume":"259","author":"Schmiege","year":"2024","journal-title":"Int. J. Hyg. Environ. Health"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1007\/s12560-022-09531-2","article-title":"Combining Community Wastewater Genomic Surveillance with State Clinical Surveillance: A Framework for SARS-CoV-2 Public Health Practice","volume":"14","author":"Smith","year":"2022","journal-title":"Food Environ. Virol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"w30178","DOI":"10.4414\/SMW.2022.w30178","article-title":"SARS-CoV-2 aerosol transmission in schools: The effectiveness of different interventions","volume":"152","author":"Villers","year":"2022","journal-title":"Swiss Med Wkly."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1038\/s41591-022-01940-x","article-title":"Wastewater surveillance of pathogens can inform public health responses","volume":"28","author":"Diamond","year":"2022","journal-title":"Nat. Med."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.psep.2021.09.021","article-title":"A critical review of heating, ventilation, and air conditioning (HVAC) systems within the context of a global SARS-CoV-2 epidemic","volume":"155","author":"Elsaid","year":"2021","journal-title":"Process. Saf. Environ. Prot."},{"key":"ref_40","unstructured":"European Centre for Disease Prevention and Control (2020). Heating, Ventilation and Air-Conditioning Systems in the Context of COVID-19, 10 November 2020."}],"updated-by":[{"DOI":"10.3390\/v17121580","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T00:00:00Z","timestamp":1743033600000}}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/4\/477\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,4]],"date-time":"2025-12-04T16:09:22Z","timestamp":1764864562000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/4\/477"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,27]]},"references-count":40,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,4]]}},"alternative-id":["v17040477"],"URL":"https:\/\/doi.org\/10.3390\/v17040477","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,27]]}}}