Outbreak report of SARS-CoV-2 infection by airborne transmission: Epidemiologic and molecular evidence
Abstract
Introduction: It has been shown that the transmission of SARS-CoV-2 occurs mainly by air, and the risk of infection is greater in closed spaces.
Objective: To describe the epidemiology, virology and molecular characterization of a COVID-19 outbreak at a closed vaccination point during the third wave of SARS-CoV-2 in Colombia.
Materials and methods: Diagnostic tests, interviews, sampling, cell cultures and viral sequencing were carried out, the latter being molecular characterization and lineage identification.
Results: Seven workers were positive for SARS-CoV-2; among these, 3 samples were analyzed, plus an additional sample belonging to the mother of the presumed index
case; all samples were identified with lineage B.1.625, with a maximum of 2 nucleotides difference between them.
Conclusions: Variant B.1.625 was identified as the cause of the COVID-19 outbreak, and a co-worker was also identified as the index case. Unexpectedly, attending a vaccination day became a risk factor for acquiring the infection.
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References
Ministerio de Salud y Protección Social. CORONAVIRUS (COVID-19). Accessed: November 19, 2021. Available at: https://www.minsalud.gov.co/salud/publica/PET/Paginas/Covid.aspx
Johns Hopkins Coronavirus Resource Center. COVID-19 Map. Accessed: November 19, 2021. Available at: https://coronavirus.jhu.edu/map.html
Laiton-Donato K, Franco-Muñoz C, Álvarez-Díaz DA, Ruiz-Moreno HA, Usme-Ciro JA, Prada DA, et al. Characterization of the emerging B.1.621 variant of interest of SARSCoV-2. Infect Genet Evol. 2021;95:105038. https://doi.org/10.1016/j.meegid.2021.105038
Instituto Nacional de Salud. COVID-19 en Colombia. Accessed: November 19, 2021. Available at: https://www.ins.gov.co/Noticias/Paginas/coronavirus-genoma.aspx
Morawska L, Tang JW, Bahnfleth W, Bluyssen PM, Boerstra A, Buonanno G, et al. How can airborne transmission of COVID-19 indoors be minimized? Environ Int. 2020;142:105832. https://doi.org/10.1016/j.envint.2020.105832
Wang CC, Prather KA, Sznitman J, Jiménez JL, Lakdawala SS, Tufekci Z, et al. Airborne transmission of respiratory viruses. Science. 2021;373:eabd9149. https://doi.org/10.1126/science.abd9149.
Centers for Disease Control and Prevention. Real-time RT-PCR primers and probes for COVID-19. Colombia. Accessed: November 19, 2021. Available at: https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html
Díaz FJ, Aguilar-Jiménez W, Flórez-Álvarez L, Valencia G, Laiton-Donato K, Franco-Muñoz C, et al. Isolation and characterization of an early SARS-CoV-2 isolate from the 2020 epidemic in Medellín, Colombia. Biomédica. 2020;40:S148-58. https://doi.org/10.7705/biomedica.5834
Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance. 2020;25:2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.200004510
Farr B, Rajan D, Betteridge E, Shirley L, Quail M. COVID-19 ARTIC v4.1 Illumina library construction and sequencing protocol-tailed method V.2. 2022. Available from: https://www.protocols.io/view/covid-19-artic-v4-1-illumina-library-construction-j8nlk4b36g5r/v2
Bushnell B. BBMap: A fast, accurate, splice-aware aligner. Accessed: November 19, 2021. Available at: https://www.osti.gov/biblio/1241166
Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5:1403-7. https://doi.org/10.1038/s41564-020-0770-5
Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis, version 11. Mol Biol Evol. 2021;38:3022-7. https://doi.org/10.1093/molbev/msab120
Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44:W232-5. https://doi.org/10.1093/nar/gkw256
Letunic I, Bork P. Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293-6. https://doi.org/10.1093/nar/gkab301
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. NextStrain: Realtime tracking of pathogen evolution. Bioinformatics. 2018;34:4121-3. https://doi.org/10.1093/bioinformatics/bty407
Lednicky JA, Lauzardo M, Alam MM, Elbadry MA, Stephenson CJ, Gibson JC, et al. Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness. Int J Infect Dis. 2021;108:212-6. https://doi.org/10.1016/j.ijid.2021.04.063
Liu Y, Ning Z, Chen Y, Guo M, Liu Y, Gali NK, et al. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals. Nature. 2020;582:557-60. https://doi.org/10.1038/s41586-020-2271-3
Guo ZD, Wang ZY, Zhang SF, Li X, Li L, Li C, et al. Aerosol and surface distribution of severe acute respiratory syndrome coronavirus 2 in Hospital Wards, Wuhan, China, 2020. Emerg Infect Dis. 2020;26:1583-91. https://doi.org/10.3201/eid2607.200885
Chia PY, Coleman KK, Tan YK, Ong SW, Gum M, Lau SK, et al. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients. Nat Commun. 2020;11:2800. https://doi.org/10.1038/s41467-020-16670-2
Smither SJ, Eastaugh LS, Findlay JS, Lever MS. Experimental aerosol survival of SARSCoV-2 in artificial saliva and tissue culture media at medium and high humidity. Emerg Microbes Infect. 2020;9:1415-7. https://doi.org/10.1080/22221751.2020.1777906
World Health Organization. Coronavirus disease (COVID-19): How is it transmitted? Accessed: November 19, 2021. Available at: https://www.who.int/news-room/questions-andanswers/item/coronavirus-disease-covid-19-how-is-it-transmitted
Centers for Disease Control and Prevention. SARS-CoV-2 transmission. Accessed: November 19, 2021. Available at: https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/sars-cov-2-transmission.html
Instituto de Hidrología, Meteorología y Estudios Ambientales (IDEAM). Características climatológicas de ciudades principales y municipios turísticos. Accessed: November 19, 2021. Available at: http://www.ideam.gov.co/documents/21021/418894/Caracter%C3%ADsticas+de+Ciudades+Principales+y+Municipios+Tur%C3%ADsticos.pdf/c3ca90c8-1072-434aa235-91baee8c73fc
Oh C, Sashittal P, Zhou A, Wang L, El-Kebir M, Nguyen TH. Design of SARS-CoV-2 variant-specific pcr assays considering regional and temporal characteristics. Appl Environ Microbiol. 2022;88:e0228921. https://doi.org/10.1128/aem.02289-21
Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al. SARSCoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19:409-24. https://doi.org/10.1038/s41579-021-00573-0
Jangra S, Ye C, Rathnasinghe R, Stadlbauer D, Krammer F, Simon V, et al. SARS-CoV-2 spike E484K mutation reduces antibody neutralisation. Lancet Microbe. 2021;2:e283-4. https://doi.org/10.1016/S2666-5247(21)00068-9
Kullappan M, Mary U, Ambrose JM, Veeraraghavan VP, Surapaneni KM. Elucidating the role of N440K mutation in SARS-CoV-2 spike – ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. J Biomol Struct Dyn. 2023;41:912-29. https://doi.org/10.1080/07391102.2021.2014973
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