Modeling the persistence of viruses in untreated groundwater

Development and evaluation of an intensive short course: the Quantitative Microbial Risk Assessment Interdisciplinary Instructional Institute (QMRA III)

Quantitative microbial risk assessment (QMRA) is a growing interdisciplinary field addressing exposures to microbial pathogens and infectious disease processes. Risk science is inherently interdisciplinary, but few of the contributing disciplinary programs offer courses and training specifically in QMRA. To develop multidisciplinary training in QMRA, an annual 10-day long intensive workshop was conducted from 2015 to 2019-the Quantitative Microbial Risk Assessment Interdisciplinary Instructional Institute (QMRA III). National leaders in the fields of public health, engineering, microbiology, epidemiology, communications, public policy, and QMRA served as instructors and mentors over the course of the program. To provide cross-training, multidisciplinary teams of 5-6 trainees were created from the approximately 30 trainees each year. A formal assessment of the program was performed based on observations and surveys containing Likert-type scales and open-ended prompts. In addition, a longitudinal alumni survey was also disseminated to facilitate the future redevelopment of QMRA institutes and determine the impact of the program. Across all years, trainees experienced statistically significant increases (P < 0.05) in their perceptions of their QMRA abilities (e.g., use of specific computer programs) and knowledge of QMRA constructs (e.g., risk management). In addition, 12 publications, three conference presentations, and two research grants were derived from the QMRA III institute projects or tangential research. The success of QMRA III indicates that a short course format can effectively address many multidisciplinary training needs. Key features of QMRA III, including the inter-disciplinary training approach, hands-on exercises, real-world institute projects, and interaction through a mentoring process, were vital for training multidisciplinary teams housing multiple forms of expertise. Future QMRA institutes are being redeveloped to leverage hybrid learning formats that can further the multidisciplinary training and mentoring objectives.

Viability of Moniliophthora roreri on Cocoa Beans Under Microfermentation and Long-Term Survival on Carrier Materials

The viability of Moniliophthora roreri inoculum was evaluated during the microfermentation process of diseased and healthy pulp-seed masses and on a range of carrier materials: aluminum, cloth, glass, paper, plastic, raffia, and rubber tire. Fungal survival was assessed before the microfermentation (0 h) and every 24 to 96 h by the growth of colonies in potato-dextrose-agar (PDA) and sporulation in seed shells. Colonies of M. roreri and sporulation on seed shells were observed from seeds not submitted to microfermentation. No growth was recovered from diseased cocoa beans after 48 h under the microfermentation. The viability of M. roreri spores recovered from carrier materials was evaluated at 7, 15, 30, 45, and 100 days after inoculation (DAI) by collecting spores and plating them on Sabouraud dextrose yeast extract agar amended with chloramphenicol (50 mg l1). The viability was determined by counting germinated and ungerminated spores under a light microscope (40×) after incubating in a moist chamber at 26 ± 2°C for 72 h. Spores maintained long-term viability on all tested carrier materials toward the end of the experiment (overall 26%) with significant differences (<0.05) among them. Maximum spore viability occurred at 7 and 15 DAI, with cloth and plastic carrier materials considered at high risk of acting as vehicles for the fungal spread. Mathematical models of spore viability over time were fit to the data using the Bayesian information criterion. Findings confirmed the importance of the fermentation process to hamper M. roreri growth and the potential of carrier materials for fungal dispersal.

Meta-Analysis Addressing the Implications of Model Uncertainty in Understanding the Persistence of Indicators and Pathogens in Natural Surface Waters

This study evaluates the impact persistence model selection has on the prediction of persistence values of interest and the identification of influential water quality and environmental factors for microorganisms in natural surface waters. Five persistence models representing first-order decay and nonlinear decay profiles were fit to a comprehensive database of 629 data sets for fecal indicator bacteria (FIB), bacteriophages, bacteria, viruses, and protozoa mined from the literature. Initial periods of minimal decay and decay rates tapering off over time were often observed, and a two-parameter model, based on the logistic probability distribution, provided the best fit to the data most frequently. First-order decay kinetics provided the best fit to less than 20% of the analyzed data. Using the best fitting models in this analysis, T90 and T99 metrics were calculated for each data set and used as the dependent variable in a variety of exploratory factor analyses. Random forest methods identified temperature and predation as some of the most important water quality factors influencing persistence, and the protozoa target type differed the most from FIB. This analysis further confirmed the interactions between temperature and predation and suggests that pH and turbidity be more frequently documented in persistence studies to further elucidate their impact on target persistence. The findings from this analysis and the calculated persistence metrics can be used to better inform quantitative microbial risk assessments and may lead to improved predictions of human health risks and water management decisions.

Persistence of poliovirus types 2 and 3 in waste-impacted water and sediment

Eradication of poliovirus (PV) is a global public health priority, and as clinical cases decrease, the role of environmental surveillance becomes more important. Persistence of PV and the environmental factors that influence it (such as temperature and sample type) are an important part of understanding and interpreting positive environmental surveillance samples. The objective of this study was to evaluate the persistence of poliovirus type 2 (PV2) and type 3 (PV3) in wastewater and sediment. Microcosms containing either 1) influent wastewater or 2) influent wastewater with a sediment matrix were seeded with either PV2 or PV3, and stored for up to 126 days at three temperatures (4°C, room temperature [RT], and 30°C). Active PV in the liquid of (1), and the sediment and liquid portions of (2) were sampled and quantified at up to 10 time points via plaque assay and RT-qPCR. A suite of 17 models were tested for best fit to characterize decay of PV2 and PV3 over time and determine the time points at which >90% (T90) and >99% (T99) reduction was reached. Linear models assessed the influence of experimental factors (matrix, temperature, virus type and method of detection) on the predicted T90 and T99 values. Results showed that when T90 was the dependent variable, virus type, matrix, and temperature significantly affected decay, and there was a clear interaction between the sediment matrix and temperature. When T99 was the dependent variable, only temperature and matrix type significantly influenced the decay metric. This study characterizes the persistence of both active and molecular PV2 and PV3 in relevant environmental conditions, and demonstrates that temperature and sediment both play important roles in PV viability. As eradication nears and clinical cases decrease, environmental surveillance and knowledge of PV persistence will play a key role in understanding the silent circulation in endemic countries.

Viability of SARS-CoV-2 in river water and wastewater at different temperatures and solids content

COVID-19 patients can excrete viable SARS-CoV-2 virus via urine and faeces, which has raised concerns over the possibility of COVID-19 transmission via aerosolized contaminated water or via the faecal-oral route. These concerns are especially exacerbated in many low- and middle-income countries, where untreated sewage is frequently discharged to surface waters. SARS-CoV-2 RNA has been detected in river water (RW) and raw wastewater (WW) samples. However, little is known about SARS-CoV-2 viability in these environmental matrices. Determining the persistence of SARS-CoV-2 in water under different environmental conditions is of great importance for basic assumptions in quantitative microbial risk assessment (QMRA). In this study, the persistence of SARS-CoV-2 was assessed using plaque assays following spiking of RW and WW samples with infectious SARS-CoV-2 that was previously isolated from a COVID-19 patient. These assays were carried out on autoclaved RW and WW samples, filtered (0.22 µm) and unfiltered, at 4 °C and 24 °C. Linear and nonlinear regression models were adjusted to the data. The Weibull regression model achieved the lowest root mean square error (RMSE) and was hence chosen to estimate T₉₀ and T₉₉ (time required for 1 log and 2 log reductions, respectively). SARS-CoV-2 remained viable longer in filtered compared with unfiltered samples. RW and WW showed T₉₀ values of 1.9 and 1.2 day and T₉₉ values of 6.4 and 4.0 days, respectively. When samples were filtered through 0.22 µm pore size membranes, T₉₀ values increased to 3.3 and 1.5 days, and T₉₉ increased to 8.5 and 4.5 days, for RW and WW samples, respectively. Remarkable increases in SARS-CoV-2 persistence were observed in assays at 4 °C, which showed T₉₀ values of 7.7 and 5.5 days, and T₉₉ values of 18.7 and 17.5 days for RW and WW, respectively. These results highlight the variability of SARS-CoV-2 persistence in water and wastewater matrices and can be highly relevant to efforts aimed at quantifying water-related risks, which could be valuable for understanding and controlling the pandemic.

Energy Requirements for Loss of Viral Infectivity

Outside the host, viruses will eventually lose their ability to infect cells due to conformational changes that occur to proteins on the viral capsid. In order to undergo a conformational change, these proteins require energy to activate the chemical reaction that leads to the conformational change. In this study, data from the literature is used to calculate the energy required for viral inactivation for a variety of different viruses by means of the Arrhenius equation. We find that some viruses (rhinovirus, poliovirus, human immunodeficiency virus, Alkhumra hemorrhagic fever virus, and hepatitis A virus) have high inactivation energies, indicative of breaking of a chemical double bond. We also find that several viruses (respiratory syncytial virus, poliovirus, and norovirus) have nonlinear Arrhenius plots, suggesting that there is more than a single pathway for inactivation of these viruses.