Viral-Bacterial Interactions That Impact Viral Thermostability and Transmission.

Enteric viruses are significant human pathogens that commonly cause foodborne illnesses worldwide. These viruses initiate infection in the gastrointestinal tract, home to a diverse population of intestinal bacteria. In a novel paradigm, data indicate that enteric viruses utilize intestinal bacteria to promote viral replication and pathogenesis. While mechanisms underlying these observations are not fully understood, data suggest that some enteric viruses bind directly to bacteria, stabilizing the virion to retain infectivity. Here, we discuss the current knowledge of these viral-bacterial interactions and examine the impact of these interactions on viral transmission.

Application of digital PCR for public health-related water quality monitoring.

Digital polymerase chain reaction (dPCR) is emerging as a reliable platform for quantifying microorganisms in the field of water microbiology. This paper reviews the fundamental principles of dPCR and its application for health-related water microbiology. The relevant literature indicates increasing adoption of dPCR for measuring fecal indicator bacteria, microbial source tracking marker genes, and pathogens in various aquatic environments. The adoption of dPCR has accelerated recently due to increasing use for wastewater surveillance of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) - the virus that causes Coronavirus Disease 2019 (COVID-19). The collective experience in the scientific literature indicates that well-optimized dPCR assays can quantify genetic material from microorganisms without the need for a calibration curve and often with superior analytical performance (i.e., greater sensitivity, precision, and reproducibility) than quantitative polymerase chain reaction (qPCR). Nonetheless, dPCR should not be viewed as a panacea for the fundamental uncertainties and limitations associated with measuring microorganisms in water microbiology. With dPCR platforms, the sample analysis cost and processing time are typically greater than qPCR. However, if improved analytical performance (i.e., sensitivity and accuracy) is critical, dPCR can be an alternative option for quantifying microorganisms, including pathogens, in aquatic environments.

Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19.

Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have been collected from wastewater via passive sampling with Moore swabs. In response to the COVID-19 pandemic, passive sampling is re-emerging as a promising technique to monitor SARS-CoV-2 RNA in wastewater. Method comparisons and disease surveillance using composite, grab, and passive sampling for SARS-CoV-2 RNA detection have found passive sampling with a variety of materials routinely produced qualitative results superior to grab samples and useful for sub-sewershed surveillance of COVID-19. Among individual studies, SARS-CoV-2 RNA concentrations derived from passive samplers demonstrated heterogeneous correlation with concentrations from paired composite samples ranging from weak (R2 = 0.27, 0.31) to moderate (R2 = 0.59) to strong (R2 = 0.76). Among passive sampler materials, electronegative membranes have shown great promise with linear uptake of SARS-CoV-2 RNA observed for exposure durations of 24 to 48 h and in several cases RNA positivity on par with composite samples. Continuing development of passive sampling methods for the surveillance of infectious diseases via diverse forms of fecal waste should focus on optimizing sampler materials for the efficient uptake and recovery of biological analytes, kit-free extraction, and resource-efficient testing methods capable of rapidly producing qualitative or quantitative data. With such refinements passive sampling could prove to be a fundamental tool for scaling wastewater surveillance of infectious disease, especially among the 1.8 billion persons living in low-resource settings served by non-traditional wastewater collection infrastructure.

Persistence of viable MS2 and Phi6 bacteriophages on carpet and dust.

Resuspension of dust from flooring is a major source of human exposure to microbial contaminants, but the persistence of viruses on dust and carpet and the contribution to human exposure are often unknown. The goal of this work is to determine viability of MS2 and Phi6 bacteriophages on cut carpet, looped carpet, and house dust both over time and after cleaning. Bacteriophages were nebulized onto carpet or dust in artificial saliva. Viability was measured at 0, 1, 2, 3, 4, 24, and 48 h and after cleaning by vacuum, steam, hot water extraction, and disinfection. MS2 bacteriophages showed slower viability decay rates in dust (-0.11 hr-1 ), cut carpet (-0.20 hr-1 ), and looped carpet (-0.09 hr-1 ) compared to Phi6 (-3.36 hr-1 , -1.57 hr-1 , and -0.20 hr-1 , respectively). Viable viral concentrations were reduced to below the detection limit for steam and disinfection for both MS2 and Phi6 (p < 0.05), while vacuuming and hot water extraction showed no significant changes in concentration from uncleaned carpet (p > 0.05). These results demonstrate that MS2 and Phi6 bacteriophages can remain viable in carpet and dust for several hours to days, and cleaning with heat and disinfectants may be more effective than standard vacuuming.

Sodium hypochlorite disinfection of SARS-CoV-2 spiked in water and municipal wastewater.

Infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has the potential to be collected in wastewater from mucus, sputum, and feces of infected individuals, raising questions about the appropriate handling and treatment of the resulting wastewater. Current evidence indicates the likelihood of waterborne SARS-CoV-2 transmission is low; nonetheless, confirming the efficacy of disinfection against SARS-CoV-2 is prudent to ensure multiple barriers of protection for infectious SARS-CoV-2 that could be present in municipal and hospital wastewater. Sodium hypochlorite (free chlorine) is widely used for pathogen control in water disinfection applications. In the current study, we investigated the inactivation of SARS-CoV-2 in DI water and municipal wastewater primary influent by sodium hypochlorite (free chlorine) addition. Our results showed rapid disinfection of SARS-CoV-2, with less than 1 mg-min/L required for >3 log10 TCID50 reduction in DI water. More than 5 mg-min/L was required for 3 log10 TCID50 reduction in primary influent, suggesting potential shielding of the virus by suspended solids. These results are consistent with expected virus inactivation by free chlorine and suggest the adequacy of free chlorine disinfection for inactivation of infectious SARS-CoV-2 in water matrices.

Persistence of emerging viral fecal indicators in large-scale freshwater mesocosms.

Fecal indicator bacteria (FIB) are typically used to monitor microbial water quality but are poor representatives of viruses due to different environmental fate. Viral fecal indicators have been proposed as alternatives to FIB; however, data evaluating the persistence of emerging viral fecal indicators under realistic environmental conditions is necessary to evaluate their potential application. In this study, we examined the persistence of five viral fecal indicators, including crAssphage and pepper mild mottle virus (PMMoV), and three bacterial fecal indicators (E. coli, enterococci and HF183/BacR287) in large-scale experimental ponds and freshwater mesocosms. Observed inactivation rate constants were highly variable and ranged from a minimum of -0.09 d-1 for PMMoV to a maximum of -3.5 d-1 for HF183/BacR287 in uncovered mesocosms. Overall, viral fecal indicators had slower inactivation than bacterial fecal indicators and PMMoV was inactivated more slowly than all other targets. These results demonstrate that bacterial fecal indicators inadequately represent viral fate following aging of sewage contaminated water due to differential persistence, and that currently used fecal indicator monitoring targets demonstrate highly variable persistence that should be considered during water quality monitoring and risk assessment.

Comparative fate of CrAssphage with culturable and molecular fecal pollution indicators during activated sludge wastewater treatment.

Wastewater treatment plants are typically monitored using fecal indicator bacteria to ensure adequate microbial water quality of the treated effluent. Fecal indicator bacteria exhibit poor correlation with virus fate in the environment, including during wastewater treatment. Viral-based microbial source tracking methods have the potential to overcome this limitation. The recently discovered human gut bacteriophage crAssphage is a promising viral human fecal indicator. In this current study, primary influent, primary effluent, secondary effluent, and final effluent of a conventional activated sludge wastewater treatment plant were analyzed for a suite of fecal indicators to evaluate the suitability of crAssphage as a wastewater process indicator for virus removal. CrAssphage was the most abundant fecal indicator measured through the wastewater treatment process. Culturable and molecular bacterial fecal pollution indicators showed higher removal than viral fecal pollution indicators, including crAssphage, confirming the necessity of a viral-specific fecal monitoring target. CrAssphage was strongly correlated with adenovirus and polyomavirus molecular indicators through the wastewater treatment process. Literature comparison demonstrated site-specific removal of molecular fecal indicators during wastewater treatment highlighting the need for local performance validation. The high abundance of crAssphage and correlation with pathogenic viruses suggests the potential suitability of crAssphage as a viral fecal pollution process indicator during wastewater treatment.

Persistence of SARS-CoV-2 in Water and Wastewater.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is frequently detected in the feces of infected individuals. While infectious SARS-CoV-2 has not previously been identified in wastewater, infectious SARS-CoV-2 has been isolated from the feces of at least one patient, raising concerns about the presence of infectious SARS-CoV-2 in wastewater. The fate and inactivation characteristics of SARS-CoV-2 in water and wastewater are unknown, with current inactivation estimates based on surrogate models. In this study, the persistence of SARS-CoV-2 infectivity and RNA signal was determined in water and wastewater. The times for 90% reduction (T90) of viable SARS-CoV-2 in wastewater and tap water at room temperature were 1.5 and 1.7 days, respectively. In high-starting titer (105 TCID50 mL-1) experiments, infectious virus persisted for the entire 7-day sampling time course. In wastewater at 50 and 70 °C, the observed T90 values for infectious SARS-CoV-2 were decreased to 15 and 2 min, respectively. SARS-CoV-2 RNA was found to be significantly more persistent than infectious SARS-CoV-2, indicating that the environmental detection of RNA alone does not substantiate risk of infection.

Endemic cattle diseases: comparative epidemiology and governance.

Cattle are infected by a community of endemic pathogens with different epidemiological properties that invoke different managerial and governmental responses. We present characteristics of pathogens that influence their ability to persist in the UK, and describe a qualitative framework of factors that influence the political response to a livestock disease. We develop simple transmission models for three pathogens (bovine viral diarrhoea virus, bovine herpesvirus and Mycobacterium avium spp. paratuberculosis) using observed cattle movements, and compare the outcomes to an extensive dataset. The results demonstrate that the epidemiology of the three pathogens is determined by different aspects of within- and between-farm processes, which has economic, legal and political implications for control. We consider how these pathogens, and Mycobacterium bovis (the agent of bovine tuberculosis), may be classified by the process by which they persist and by their political profile. We further consider the dynamic interaction of these classifications with pathogen prevalence and with the action taken by the government.

The development, regulation and use of biopesticides for integrated pest management.

Over the past 50 years, crop protection has relied heavily on synthetic chemical pesticides, but their availability is now declining as a result of new legislation and the evolution of resistance in pest populations. Therefore, alternative pest management tactics are needed. Biopesticides are pest management agents based on living micro-organisms or natural products. They have proven potential for pest management and they are being used across the world. However, they are regulated by systems designed originally for chemical pesticides that have created market entry barriers by imposing burdensome costs on the biopesticide industry. There are also significant technical barriers to making biopesticides more effective. In the European Union, a greater emphasis on Integrated Pest Management (IPM) as part of agricultural policy may lead to innovations in the way that biopesticides are regulated. There are also new opportunities for developing biopesticides in IPM by combining ecological science with post-genomics technologies. The new biopesticide products that will result from this research will bring with them new regulatory and economic challenges that must be addressed through joint working between social and natural scientists, policy makers and industry.