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ABSTRACT Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases. 

The complexity of transmission of COVID-19 in the human population cannot be overstated. Although major transmission routes of COVID-19 remain as human-to-human interactions, understanding the possible role of climatic and weather processes in accelerating such interactions is still a challenge. The majority of studies on the transmission of this disease have suggested a positive association between a decrease in ambient air temperature and an increase in human cases. Using data from 19 early epicenters, we show that the relationship between the incidence of COVID-19 and temperature is a complex function of prevailing climatic conditions influencing human behavior that govern virus transmission dynamics. We note that under a dry (low-moisture) environment, notably at dew point temperatures below 0°C, the incidence of the disease was highest. Prevalence of the virus in the human population, when ambient air temperatures were higher than 24°C or lower than 17°C, was hypothesized to be a function of the interaction between humans and the built or ambient environment. An ambient air temperature range of 17 to 24°C was identified, within which virus transmission appears to decrease, leading to a reduction in COVID-19 human cases. 

Intensification of smog episodes, following harvesting of paddy crops in agricultural plains of the Indus basin in the Indian subcontinent, are often attributed to farming practice of burning standing stubble during late autumn (October, November) months. Biomass burning (paddy stubble residual) is a preferred technique to clear farmlands for centuries by farmers in that basin. However, despite stable agricultural landholding and yield, smog is being increasingly associated with burning agricultural biomass, thus creating a paradox. Here, we show that the concentration of smog (NOx, PM2.5, SO2) in the ambient air exceeds the safe threshold limits throughout the entire year in the region. This study argues that agricultural biomass burning is an ephemeral event in the basin that may act as a catalyst to a deteriorated air quality in the entire region. Results further demonstrate that simultaneous saturation of air pollutants along with high ambient moisture content and low wind speeds following the monsoon season are strongly related to aggravated smog events. Findings from this study should help make holistic mitigation and intervention policies to monitor air quality for sustainability of public health in agricultural regions where farming activities are a dominant economic driver for society.