Environmental Epidemiology

Ahmed, W., Angel, N., Edson, J., et al., 2020. First Confirmed Detection of SARS-CoV- 2 in Untreated Wastewater in Australia: A Proof of Concept for the Wastewater Surveillance of COVID-19 in the Community. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2020.138764. 2019 Feb 20. 
Alexyuk, M.S., Turmagambetova, A.S., Alexyuk, P.G., et al., 2017. Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis. VirusDis 28, 18e25. https://doi.org/ 10.1007/s13337-016-0353-5.
Amirian, E. S. Potential fecal transmission of SARS-CoV-2: Current evidence and implications for public health. Int. J. Infect. Dis. 95, 363–370 (2020).  doi:10.1016/j.ijid.2020.04.057  
Bibby, K., Peccia, J., 2013. Identification of viral pathogen diversity in sewage sludge by metagenome analysis. Environmental Science & Technology 47, 1945e1951.
Bibby, K., Viau, E., Peccia, J., 2011. Viral metagenome analysis to guide human pathogen monitoring in environmental samples. Lett. Appl. Microbiol. 52, 386e392. 
Blanco, A., Abid, I., Al-Otaibi, N., Perez-Rodriguez, F.J., Fuentes, C., Guix, S., Pinto, R.M., Bosch, A., 2019. Glass wool concentration optimization for the detection of enveloped and non-enveloped waterborne viruses. Food and Environmental Virology 11, 184e192.
Carrea, L. & Merchant, C. J. GloboLakes: Lake Surface Water Temperature (LSWT) v4.0 (1995-2016). Cent. Environ. Data Anal. (2019).  doi:10.5285/76a29c5b55204b66a40308fc2ba9cdb3
Casanova, L., Rutala, W.A., Weber, D.J., Sobsey, M.D., 2009. Survival of surrogate coronaviruses in water. Water Res. 43, 1893e1898.
Chin, A. et al. Stability of SARS-CoV-2 in different environmental conditions. 341 medRxiv 2020.03.15.20036673 (2020). doi:10.1101/2020.03.15.20036673
Collomb, J., Laporte, J., Vautherot, J.F., Schwartzbrod, L., 1986. Recherche des coronavirus dans l’eau. Note I. Adsorption et elution des coronavirus sur poudre de verre [Research on coronaviruses in water. I. Adsorption and elution of the coronavirus on glass powder]. Virologie, 37 (2), 95e105.
Damas, J. et al. Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates. bioRxiv 2020.04.16.045302 (2020).  doi:10.1101/2020.04.16.045302  
Derraik, J. G. B., Anderson, W. A., Connelly, E. A. & Anderson, Y. C. Rapid evidence summary on SARS-CoV-2 survivorship and disinfection, and a reusable  PPE protocol using a double-hit process. medRxiv (2020).  doi:10.1101/2020.04.02.20051409  
Esper, F., Ou, Z., Huang, Y.T., 2010. Human coronaviruses are uncommon in patients with gastrointestinal illness. J. Clin. Virol. 48 (2), 131e133. https://doi.org/ 10.1016/j.jcv.2010.03.007. 
Giuseppina La Rosa, Lucia Bonadonna, Luca Lucentini, Sebastien Kenmoe, Elisabetta Suffredini. Coronavirus in water environments: Occurrence, persistence and concentration methods - A scoping review. Water Research Volume 179, 15 July 2020, 115899. https://doi.org/10.1016/j.watres.2020.115899
Gundy, P. M., Gerba, C. P. & Pepper, I. L. Survival of Coronaviruses in Water and 355 Wastewater. Food Environ. Virol. 1, 10–14 (2009). doi:10.1007/s12560-008-9001-6
Gundy, P., Gerba, C., Pepper, I.L., 2019. Survival of coronaviruses in water and wastewater. Food Environ Virol 1 (1), 10, 2009. 
Huyvaert, K. P. et al. Freshwater Clams As Bioconcentrators of Avian Influenza Virus in Water. Vector-Borne Zoonotic Dis. 12, 904–906 (2012).  doi:10.1089/vbz.2012.0993  
Jevsnik, M., Steyer, A., Zrim, T., et al., 2013. Detection of human coronaviruses in simultaneously collected stool samples and nasopharyngeal swabs from hospitalized children with acute gastroenteritis. Virol. J. 10, 46. https://doi.org/10.1186/1743-422X-10-46. Published 2013 Feb 5.
Jones, T. C. et al. An analysis of SARS-CoV-2 viral load by patient age. Report, 363 (2020).
Keller, V. D. J., Williams, R. J., Lofthouse, C. & Johnson, A. C. Worldwide estimation of river concentrations of any chemical originating from sewage-treatment plants using dilution factors. Environ. Toxicol. Chem. 33, 447–452 (2014). doi:10.1002/etc.2441  
La Rosa G., M. Iaconelli, P. Mancini, G. Bonanno Ferraro, C. Veneri, L. Bonadonna, L. Lucentini, E. Suffredini. First detection of SARS-CoV-2 in untreated wastewaters in Italy. https://doi.org/10.1101/2020.04.25.20079830.
La Rosa, G. et al. First detection of SARS-CoV-2 in untreated wastewaters in Italy. 349 Sci. Total Environ. 736, 139652 (2020). doi:10.1016/j.scitotenv.2020.139652
La Rosa, G., Bonadonna, L., Lucentini, L., Kenmoe, S. & Suffredini, E. Coronavirus in water environments: Occurrence, persistence and concentration methods - A scoping review. Water Res. 179, 115899 (2020) doi:10.1016/j.watres.2020.115899  
Lai, C. C., Shih, T. P., Ko, W. C., Tang, H. J. & Hsueh, P. R. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. International Journal of Antimicrobial  Agents 55, 105924 (2020). doi:10.1016/j.ijantimicag.2020.105924  
Lavezzo, E. et al. Suppression of COVID-19 outbreak in the municipality of Vo, Italy. 347 medRxiv 2020.04.17.20053157 (2020). doi:10.1101/2020.04.17.20053157
Lee, P.-I. & Hsueh, P.-R. Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV. J. Microbiol. Immunol. Infect. 53, 365–367 (2020). doi:10.1016/j.jmii.2020.02.001  
McBride, G. B., Stott, R., Miller, W., Bambic, D. & Wuertz, S. Discharge-based QMRA for estimation of public health risks from exposure to stormwater-borne pathogens in recreational waters in the United States. Water Res. 47, 5282–5297 (2013). doi:10.1016/j.watres.2013.06.001  
Medema, G., Heijnen, L., Elsinga, G., Italiaander, R., Brouwer, A., 2020. Presence of SARS-Coronavirus-2 in sewage. https://doi.org/10.1101/2020.03.29.20045880.
Nikitin, N., Petrova, E., Trifonova, E. & Karpova, O. Influenza Virus Aerosols in the 418 Air and Their Infectiousness. Adv. Virol. (2014). doi:10.1155/2014/859090
Nikolaenko Dmitry (2020). Crisis as a new opportunity: COVID-19 and the old hidden problems of infectious disease research. Environmental Epidemiology. Preprint (in Russian). DOI: 10.13140/RG.2.2.26872.19209
Nikolaenko Dmitry. Adaptation hypothesis of the manifestation of spring viral infectious diseases: case of COVID-19. Environmental Epidemiology. 2020, Preprint (in Russian). DOI: 10.13140/RG.2.2.20688.87043
Nikolaenko Dmitry. Adaptation hypothesis of the origin COVID-19: clarification of terminology. Environmental Epidemiology. 2020, Preprint (in Russian). DOI: 10.13140/RG.2.2.35257.52322
Nikolaenko Dmitry. Advanced geographical algorithm of the site detection of activation pathogenic properties of microorganisms and adaptation hypothesis of origin COVID-19. Conference: 18.06.2020. Kiev, Ukraine
Nikolaenko Dmitry. Advanced geographical algorithm of the site detection of activation pathogenic properties of microorganisms (version 3.1). June 2020. DOI: 10.13140/RG.2.2.20693.86246
Nikolaenko Dmitry. COVID-19: pandemic research methodology and terminology of Infectious ecology. June 2020. DOI: 10.13140/RG.2.2.29245.49128
Nikolaenko Dmitry. Data on COVID-19: scientific and homely reflection, associated with a pandemic. Environmental Epidemiology. 2020. Preprint. DOI: 10.13140/RG.2.2.31641.65127
Nikolaenko Dmitry. Investigation of Legionella freshwater bodies in connection with the adaptation hypothesis origin of COVID-19: Theory and Methodology. DOI: 10.13140/RG.2.2.23585.63842
Nikolaenko Dmitry. Medical geography and infectious ecology of COVID-19 in the United States: approaches to a systematic GIS description. Environmental Epidemiology. 2020. Preprint. DOI: 10.13140/RG.2.2.28685.97768
Nikolaenko Dmitry. Fresh water and COVID-19: a fundamental gap in scientific knowledge regarding manifestation of the pathogenic properties of microorganism. June 2020. DOI: 10.13140/RG.2.2.17611.21287
Nikolaenko, Dmitry & Fiedler, Beth Ann. Dynamic and selective geography of COVID-19: Impact groups and their place in the infection process, Part 1. Environmental Epidemiology. 2020, Preprint (in Russian).
Nikolaenko Dmitry and Beth Ann Fiedler. Dynamic and selective geography of COVID-19: impact groups and their place in the infection process. Part 2. Environmental Epidemiology. 2020, Preprint (in Russian). DOI: 10.13140/RG.2.2.24750.46404
Nikolaenko Dmitry and Beth Ann Fiedler. Experimental Infectious Ecology: hypothesis of origin COVID-19 and its verification. Environmental Epidemiology. 2020, Preprint (in Russian). DOI: 10.13140/RG.2.2.16171.80165
Nikolaenko Dmitry and Fiedler Beth Ann. Experimental Infectious Ecology: hypothesis of origin COVID-19 and its verification. Environmental Epidemiology. 2020, Preprint (in English). DOI: 10.13140/RG.2.2.17744.66560
Nikolaenko Dmitry and Fiedler Beth Ann. S-Theory about COVID-19: protozoa – microorganisms hydrobionts - human infectious diseases. Environmental Epidemiology. 2020, Preprint (in Russian). DOI: 10.13140/RG.2.2.32691.78884
Olds, H. T. et al. High levels of sewage contamination released from urban areas after storm events: A quantitative survey with sewage specific bacterial indicators. PLOS Med. 15, e1002614 (2018). doi:10.1371/journal.pmed.1002614  
Penn, R., Ward, B. J., Strande, L. & Maurer, M. Review of synthetic human faeces and faecal sludge for sanitation and wastewater research. Water Res. 132, 222–240  (2018). doi:10.1016/j.watres.2017.12.063  
Rodino, K. G. et al. Evaluation of saline, phosphate buffered saline and minimum essential medium as potential alternatives to viral transport media for SARS-CoV-2 testing. Journal of clinical microbiology (2020). doi:10.1128/JCM.00590-20  
Rodríguez, R. A., Polston, P. M., Wu, M. J., Wu, J. & Sobsey, M. D. An improved infectivity assay combining cell culture with real-time PCR for rapid quantification of human adenoviruses 41 and semi-quantification of human adenovirus in sewage.  Water Res. 47, 3183–3191 (2013). doi:10.1016/j.watres.2013.03.022  
Rose, C., Parker, A., Jefferson, B. & Cartmell, E. The Characterization of Feces and Urine: A Review of the Literature to Inform Advanced Treatment Technology. Crit.  Rev. Environ. Sci. Technol. 45, 1827–1879 (2015).  doi:10.1080/10643389.2014.1000761  
Rusiñol, M. et al. Evidence of viral dissemination and seasonality in a Mediterranean river catchment: Implications for water pollution management. J. Environ. Manage.  159, 58–67 (2015). doi:10.1016/j.jenvman.2015.05.019  
Sedji, M. I. et al. Quantification of human adenovirus and norovirus in river water in the north-east of France. Environ. Sci. Pollut. Res. 25, 30497–30507 (2018). doi:10.1007/s11356-018-3045-4  
Shutler, Jamie & Zaraska, Krzysztof & Holding, Thomas & Machnik, Monika & Uppuluri, Kiranmai & Ashton, Ian & Migdal, Lukasz & Dahiya, Ravinder. (2020). Risk of SARS-CoV-2 infection from contaminated water systems. 10.1101/2020.06.17.20133504.
Vabret, A., Dina, J., Gouarin, S., Petitjean, J., Corbet, S., Freymuth, F., 2006. Detection of the new human coronavirus HKU1: a report of 6 cases. Clin. Infect. Dis. 42 (5), 634e639. https://doi.org/10.1086/500136.
Wang, Q., Vlasova, A.N., Kenney, S.P., Saif, L.J., 2019. Emerging and re-emerging coronaviruses in pigs. Curr Opin Virol 34, 39e49. https://doi.org/10.1016/ j.coviro.2018.12.001.
Wang, X.-W. et al. Study on the resistance of severe acute respiratory syndrome- associated coronavirus. J. Virol. Methods 126, 171–177 (2005).  doi:10.1016/j.jviromet.2005.02.005  
Wang, X.W., Li, J.S., Guo, T.K., et al., 2005c. Concentration and detection of SARS coronavirus in sewage from Xiao tang Shan hospital and the 309th hospital [published correction appears in J virol methods. 2005 dec;130(1-2):210]. J Virol Methods 128 (1e2), 156e161.
Wang, X.W., Li, J.S., Jin, M., Zhen, B., Kong, Q.X., Song, N., Xiao, W.J., Yin, J., Wei, W., Wang, G.J., By, Si, Guo, B.Z., Liu, C., Ou, G.R., Wang, M.N., Fang, T.Y., Chao, F.H., Li, J.W., 2005a Jun. Study on the resistance of severe acute respiratory syndrome-associated coronavirus. J Virol Methods 126 (1e2), 171e177.
Wang, X.W.1, Li, J.S., Guo, T.K., Zhen, B., Kong, Q.X., Yi, B., Li, Z., Song, N., Jin, M., Wu, X.M., Xiao, W.J., Zhu, X.M., Gu, C.Q., Yin, J., Wei, W., Yao, W., Liu, C., Li, J.F., Ou, G.R., Wang, M.N., Fang, T.Y., Wang, G.J., Qiu, Y.H., Wu, H.H., Chao, F.H., Li, J.W., 2005b Jul 28. Excretion and detection of SARS coronavirus and its nucleic acid from digestive system. World J. Gastroenterol. 11 (28), 4390e4395.
Werth, A. J. Models of hydrodynamic flow in the bowhead whale filter feeding 423 apparatus. J. Exp. Biol. 207, 3569–3580 (2004). doi:10.1242/jeb.01202 424
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WHO. Water, sanitation, hygiene, and waste water management for the COVID-19 394 virus: interim guidance. (2020).
Wölfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. 345 Nature 581, 465–469 (2020). doi:10.1038/s41586-020-2196-x
Wu, F., Xiao, A., Zhang, J., Gu, X., Lee, W.L., Kauffman, K., Hanage, W., Matus, M., Ghaeli, N., Endo, N., Duvallet, C., Moniz, K., Erickson, T., Chai, P., Thompson, J., Alm, E., 2020. SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases. medRxiv preprint. https://doi.org/10.1101/2020.04. 05.20051540.
Wurtzer, S. et al. Evaluation of lockdown impact on SARS-CoV-2 dynamics through viral genome quantification in Paris wastewaters. medRxiv 2020.04.12.20062679  (2020). doi:10.1101/2020.04.12.20062679  
Wurtzer, S., Marechal, V., Mouchel, J.M., 2020. Time course quantitative detection of SARS-CoV-2 in Parisian wastewaters correlates with COVID-19 confirmed cases. medRxiv preprint. https://doi.org/10.1101/2020.04.12.20062679. 
Xiao, F. et al. Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19. 343 Emerg. Infect. Dis. 26, (2020). doi:10.3201/eid2608.200681
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