National Academies of Sciences, Engineering, and Medicine et al. The Built Environment and Microbial Communities. (National Academies Press (US), 2017).
Horve, P. F. et al. Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment. J. Expo. Sci. Environ. Epidemiol. https://doi.org/10.1038/s41370-019-0157-y (2019).
Naming the coronavirus disease (COVID-19) and the virus that causes it. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it. Accessed on 10 August 2021
Lednicky, J. A. et al. Collection of SARS-CoV-2 virus from the air of a clinic within a university student health care center and analyses of the viral genomic sequence. Aerosol. Air Qual. Res. 20, 1167–1171 (2020).
Hamner, L. et al. High SARS-CoV-2 attack rate following exposure at a choir practice—skagit county, washington, March 2020. MMWR Morb. Mortal. Wkly. Rep. 69, 606–610 (2020).
Razzini, K. et al. SARS-CoV-2 RNA detection in the air and on surfaces in the COVID-19 ward of a hospital in Milan, Italy. Sci. Total Environ. 742, 140540 (2020).
Morawska, L. & Cao, J. Airborne transmission of SARS-CoV-2: The world should face the reality. Environ. Int. 139, 105730 (2020).
Liu, J., Huang, J. & Xiang, D. Large SARS-CoV-2 outbreak caused by asymptomatic traveler, China. Emerg. Infect. Dis. 26, 2260–2263 (2020).
Speake, H. et al. Flight-Associated transmission of severe acute respiratory syndrome coronavirus 2 corroborated by Whole-Genome sequencing. Emerg. Infect. Dis. 26, 2872–2880 (2020).
Katelaris, A. L. et al. Epidemiologic evidence for airborne transmission of SARS-CoV-2 during church singing, Australia, 2020. Emerg. Infect. Dis. 27, 1677–1680 (2021).
Nissen, K. et al. Long-distance airborne dispersal of SARS-CoV-2 in COVID-19 wards. Sci. Rep. 10, 19589 (2020).
Somsen, G. A., van Rijn, C., Kooij, S., Bem, R. A. & Bonn, D. Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission. Lancet Respir. Med. 8, 658–659 (2020).
Dumont-Leblond, N. et al. Positive no-touch surfaces and undetectable SARS-CoV-2 aerosols in long-term care facilities: An attempt to understand the contributing factors and the importance of timing in air sampling campaigns. Am. J. Infect. Control https://doi.org/10.1016/j.ajic.2021.02.004 (2021).
Correia, G., Rodrigues, L., Gameiro da Silva, M. & Gonçalves, T. Airborne route and bad use of ventilation systems as non-negligible factors in SARS-CoV-2 transmission. Med. Hypotheses 141, 109781 (2020).
Ye, G. et al. Environmental contamination of SARS-CoV-2 in healthcare premises. J. Infect. https://doi.org/10.1016/j.jinf.2020.04.034 (2020).
Ryu, B.-H. et al. Environmental contamination of SARS-CoV-2 during the COVID-19 outbreak in South Korea. Am. J. Infect. Control 48, 875–879 (2020).
Ahn, J. Y. et al. Environmental contamination in the isolation rooms of COVID-19 patients with severe pneumonia requiring mechanical ventilation or high-flow oxygen therapy. J. Hosp. Infect. 106, 570–576 (2020).
Jin, T. et al. SARS-CoV-2 presented in the air of an intensive care unit (ICU). Sustain. Cities Soc. 65, 102446 (2021).
Cheng, V.C.-C. et al. Air and environmental sampling for SARS-CoV-2 around hospitalized patients with coronavirus disease 2019 (COVID-19). Infect. Control Hosp. Epidemiol. 41, 1258–1265 (2020).
Fernández-de-Mera, I. G. et al. Detection of environmental SARS-CoV-2 RNA in a high prevalence setting in spain. Transbound. Emerg. Dis. 68, 1487–1492 (2021).
Li, Y. H., Fan, Y. Z., Jiang, L. & Wang, H. B. Aerosol and environmental surface monitoring for SARS-CoV-2 RNA in a designated hospital for severe COVID-19 patients. Epidemiol. Infect. 148, e154 (2020).
Escudero, D. et al. SARS-CoV-2 analysis on environmental surfaces collected in an intensive care unit: Keeping ernest shackleton’s spirit. Intensive Care Med. Exp. 8, 68 (2020).
Ong, S. W. X. et al. Air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a symptomatic patient. JAMA https://doi.org/10.1001/jama.2020.3227 (2020).
Coil, D. A. et al. SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC davis. PLoS One 16, e0253578 (2021).
Borges, J. T., Nakada, L. Y. K., Maniero, M. G. & Guimarães, J. R. SARS-CoV-2: A systematic review of indoor air sampling for virus detection. Environ. Sci. Pollut. Res. Int. https://doi.org/10.1007/s11356-021-13001-w (2021).
Lednicky, J. A. et al. Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients. Int. J. Infect. Dis. 100, 476–482 (2020).
Horve, P. F. et al. Identification of SARS-CoV-2 RNA in healthcare heating, ventilation, and air conditioning units. Indoor Air 31, 1826–1832 (2021).
Hermesch, A. C. et al. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination and childbirth. Obstet. Gynecol. 136, 827–829 (2020).
van Doremalen, N. et al. Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. N. Engl. J. Med. https://doi.org/10.1056/NEJMc2004973 (2020).
Joukar, F. et al. Persistence of SARS-CoV-2 RNA in the nasopharyngeal, blood, urine, and stool samples of patients with COVID-19: A hospital-based longitudinal study. Virol. J. 18, 134 (2021).
Aranha, C., Patel, V., Bhor, V. & Gogoi, D. Cycle threshold values in RT-PCR to determine dynamics of SARS-CoV-2 viral load: An approach to reduce the isolation period for COVID-19 patients. J. Med. Virol. 93, 6794–6797 (2021).
Zhou, Y., Zeng, Y. & Chen, C. Presence of SARS-CoV-2 RNA in isolation ward environment 28 days after exposure. Int. J. Infect. Dis. 97, 258–259 (2020).
Lavezzo, E. et al. Suppression of a SARS-CoV-2 outbreak in the italian municipality of vo’. Nature 584, 425–429 (2020).
Finelli, C. & Parisi, S. The clinical impact of COVID-19 epidemic in the hematologic setting. Adv. Biol. Regul. 77, 100742 (2020).
Arons, M. M. et al. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N. Engl. J. Med. 382, 2081–2090 (2020).
Zhou, R. et al. Viral dynamics in asymptomatic patients with COVID-19. Int. J. Infect. Dis. 96, 288–290 (2020).
Wei, W. E. et al. Presymptomatic transmission of SARS-CoV-2—singapore, january 23-march 16, 2020. MMWR Morb. Mortal. Wkly. Rep. 69, 411–415 (2020).
Bernal, J. L. et al. Transmission dynamics of COVID-19 in household and community settings in the united kingdom. bioRxiv https://doi.org/10.1101/2020.08.19.20177188 (2020).
Decker, A. et al. Prolonged SARS-CoV-2 shedding and mild course of COVID-19 in a patient after recent heart transplantation. Am. J. Transplant 20, 3239–3245 (2020).
Folgueira, M. D., Luczkowiak, J., Lasala, F., Pérez-Rivilla, A. & Delgado, R. Persistent SARS-CoV-2 replication in severe COVID-19. bioRxiv https://doi.org/10.1101/2020.06.10.20127837 (2020).
van Kampen, J. J. A. et al. Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19). Nat. Commun. 12, 267 (2021).
Santarpia, J. L. et al. Aerosol and surface contamination of SARS-CoV-2 observed in quarantine and isolation care. Sci. Rep. 10, 12732 (2020).
Riediker, M. & Tsai, D.-H. Estimation of viral aerosol emissions from simulated individuals with asymptomatic to moderate coronavirus disease 2019. JAMA Netw. Open 3, e2013807–e2013807 (2020).
Wang, Y., Xu, G. & Huang, Y.-W. Modeling the load of SARS-CoV-2 virus in human expelled particles during coughing and speaking. PLoS One 15, e0241539 (2020).
Peccia, J. et al. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nat. Biotechnol. 38, 1164–1167 (2020).
Parasa, S. et al. Prevalence of gastrointestinal symptoms and fecal viral shedding in patients with coronavirus disease 2019: A systematic review and meta-analysis. JAMA Netw. Open 3, e2011335–e2011335 (2020).
Schulze, J. et al. Analysis of severe acute respiratory syndrome 2 replication in explant cultures of the human upper respiratory RTract reveals broad tissue tropism of wild-type and B.1.1.7 variant viruses. J. Infect. Dis. 224, 2020–2024 (2021).
AlJishi, J. M. & Al-Tawfiq, J. A. Intermittent viral shedding in respiratory samples of patients with SARS-CoV-2: Observational analysis with infection control implications. J. Hosp. Infect. 107, 98–100 (2021).
Li, N., Wang, X. & Lv, T. Prolonged SARS-CoV-2 RNA shedding: Not a rare phenomenon. J. Med. Virol. 92, 2286–2287 (2020).
Liu, W.-D. et al. Prolonged virus shedding even after seroconversion in a patient with COVID-19. J. Infect. 81, 318–356 (2020).
Lau, M. S. Y. et al. Characterizing superspreading events and age-specific infectiousness of SARS-CoV-2 transmission in georgia, USA. Proc. Natl. Acad. Sci. U. S. A. 117, 22430–22435 (2020).
Parhizkar, H., Van Den Wymelenberg, K. G., Haas, C. N. & Corsi, R. L. A quantitative risk estimation platform for indoor aerosol transmission of COVID-19. Risk Anal. https://doi.org/10.1111/risa.13844 (2021).
Majra, D., Benson, J., Pitts, J. & Stebbing, J. SARS-CoV-2 (COVID-19) superspreader events. J. Infect. 82, 36–40 (2021).
Jianyun, L. et al. COVID-19 outbreak associated with air conditioning in restaurant, Guangzhou, China, 2020. Emerg. Infect. Dis. J. 26, 2789–2791 (2020).
Thanh, H. N. et al. Outbreak investigation for COVID-19 in Northern Vietnam. Lancet Infect. Dis. 20, 535–536 (2020).
Escandón, K. et al. COVID-19 false dichotomies and a comprehensive review of the evidence regarding public health, COVID-19 symptomatology, SARS-CoV-2 transmission, mask wearing, and reinfection. BMC Infect. Dis. 21, 710 (2021).
The American Society of Heating, Refrigerating and Air Condition Engineers, Inc. (ASHRAE). Ventilation of health care facilities (ANSI/ASHRAE/ASHE standard 170-2017). https://www.academia.edu/40918042/ASHRAE_Standard_170-2017 (2017). Accessed on 10 August 2021
Allen, J. G. & Ibrahim, A. M. Indoor air changes and potential implications for SARS-CoV-2 transmission. JAMA 325, 2112–2113 (2021).
Chia, P. Y. et al. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients. Nat. Commun. 11, 2800 (2020).
Dietz, L. et al. 2019 novel coronavirus (COVID-19) pandemic: Built environment considerations to reduce transmission. mSystems 5, e00245-20 (2020).
Klompas, M., Baker, M. A. & Rhee, C. Airborne transmission of SARS-CoV-2: Theoretical considerations and available evidence. JAMA 324, 441–442 (2020).
Howard-Reed, C., Wallace, L. A. & Ott, W. R. The effect of opening windows on air change rates in two homes. J. Air Waste Manag. Assoc. 52, 147–159 (2002).
Qian, H. et al. Natural ventilation for reducing airborne infection in hospitals. Build. Environ. 45, 559–565 (2010).
Escombe, A. R. et al. Natural ventilation for the prevention of airborne contagion. PLoS Med. 4, e68 (2007).
Morawska, L. et al. How can airborne transmission of COVID-19 indoors be minimised?. Environ. Int. 142, 105832 (2020).
Nembhard, M. D., Burton, D. J. & Cohen, J. M. Ventilation use in nonmedical settings during COVID-19: Cleaning protocol, maintenance, and recommendations. Toxicol. Ind. Health 36, 644–653 (2020).
Mathai, V., Das, A., Bailey, J. A. & Breuer, K. Airflows inside passenger cars and implications for airborne disease transmission. Sci. Adv. 7, eabe0166 (2021).
Bhagat, R. K., Davies Wykes, M. S., Dalziel, S. B. & Linden, P. F. Effects of ventilation on the indoor spread of COVID-19. J. Fluid Mech. 903, F1 (2020).
Jarvis, M. C. Aerosol transmission of SARS-CoV-2: Physical principles and implications. Front. Public Health 8, 590041 (2020).
Zhou, C. et al. Impact of age on duration of viral RNA shedding in patients with COVID-19. Aging 12, 22399–22404 (2020).
Daniali, H. & Flaten, M. A. What psychological factors make individuals believe they are infected by coronavirus 2019?. Front. Psychol. 12, 667722 (2021).
den Bergh, M. F. Q. K. et al. Prevalence and clinical presentation of health care workers with symptoms of coronavirus disease 2019 in 2 Dutch hospitals during an early phase of the pandemic. JAMA Netw. Open 3, e209673–e209673 (2020).
Nomura, S. et al. An assessment of self-reported COVID-19 related symptoms of 227,898 users of a social networking service in japan: Has the regional risk changed after the declaration of the state of emergency?. Lancet Reg. Health Western Pac. 1, 100011 (2020).
Merckelbach, H., Dandachi-FitzGerald, B., van Helvoort, D., Jelicic, M. & Otgaar, H. When patients overreport symptoms: More than just malingering. Curr. Dir. Psychol. Sci. 28, 321–326 (2019).
Zhang, Y. et al. Prevalence and persistent shedding of fecal SARS-CoV-2 RNA in patients with COVID-19 infection: A systematic review and meta-analysis. Clin. Transl. Gastroenterol. 12, e00343 (2021).
Rawlings, S. A. et al. No evidence of SARS-CoV-2 seminal shedding despite SARS-CoV-2 persistence in the upper respiratory tract. Open Forum Infect. Dis. 7, ofaa325 (2020).
Yang, J.-R. et al. Persistent viral RNA positivity during the recovery period of a patient with SARS-CoV-2 infection. J. Med. Virol. 92, 1681–1683 (2020).
Kang, H., Wang, Y., Tong, Z. & Liu, X. Retest positive for SARS-CoV-2 RNA of ‘recovered’ patients with COVID-19: Persistence, sampling issues, or re-infection?. J. Med. Virol. 92, 2263–2265 (2020).
University of Oregon. Monitoring and assessment program (MAP). https://coronavirus.uoregon.edu/map. Accessed on 10 August 2021
R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2021).
Laird, N. M. & Ware, J. H. Random-effects models for longitudinal data. Biometrics 38, 963–974 (1982).
Raudenbush, S. W. & Bryk, A. S. Hierarchical Linear Models: Applications and Data Analysis Methods. (SAGE, 2002).
David, R., Alex, H. & Simon, C. broom: Convert Statistical Objects into Tidy Tibbles. R package version 0.7.8. (2021). https://CRAN.R-project.org/package=broom. Accessed on 10 August 2021
Hadley, W., Romain, F., Lionel, H. & Kirill, M. dplyr: A grammar of data manipulation. R package version 1.0.7. (2021). https://CRAN.R-project.org/package=dplyr. Accessed on 10 August 2021
David, G. flextable: Functions for Tabular Reporting. R package version 0.6.6. (2021). https://CRAN.R-project.org/package=flextable. Accessed on 10 August 2021
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Alboukadel, K. ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.4.0. (2020). https://CRAN.R-project.org/package=ggpubr. Accessed on 10 August 2021
Ahlmann-Eltze, C. & Patil, I. ggsignif: R Package for displaying significance brackets for “ggplot2”. PsyArxiv https://doi.org/10.31234/osf.io/7awm6 (2021).
Kuznetsova, A., Brockhoff, P. B. & Christensen, R. H. B. lmerTest Package: Tests in linear mixed effects models. J. Stat. Softw. 82(13), 1–26. https://doi.org/10.18637/jss.v082.i13 (2017).
Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67(1), 1–48. https://doi.org/10.18637/jss.v067.i01 (2015).
Garrett, G. & Hadley, W. Dates and times made easy with lubridate. J. Stat. Softw. 40(3), 1–25 (2011).
Hadley, W. The split-apply-combine strategy for data analysis. J. Stat. Softw. 40(1), 1–29 (2011).
Hadley, W. & Dana, S. scales: Scale Functions for Visualization. R package version 1.1.1. (2020). https://CRAN.R-project.org/package=scales. Accessed on 10 August 2021
Wickham, et al. Welcome to the tidyverse. J. Open Source Softw. 4(43), 1686. https://doi.org/10.21105/joss.01686 (2019).
Simon, G., Noam, R., Robert, R., Antônio, P. C., Marco, S., & Cédric, S. Rvision—Colorblind-Friendly Color Maps for R. R package version 0.6.1. (2021).
Karthik, R. & Hadley, W. wesanderson: A Wes Anderson Palette Generator. R package version 0.3.6. (2018). https://CRAN.R-project.org/package=wesanderson.