Longitudinal and Long-Term Wastewater Surveillance for COVID-19: Infection Dynamics and Zoning of Urban Community.

Wastewater-based epidemiology (WBE) is emerging as a potential approach to study the infection dynamics of SARS-CoV-2 at a community level. Periodic sewage surveillance can act as an indicative tool to predict the early surge of pandemic within the community and understand the dynamics of infection and, thereby, facilitates for proper healthcare management. In this study, we performed a long-term epidemiological surveillance to assess the SARS-CoV-2 spread in domestic sewage over one year (July 2020 to August 2021) by adopting longitudinal sampling to represent a selected community (~2.5 lakhs population). Results indicated temporal dynamics in the viral load. A consistent amount of viral load was observed during the months from July 2020 to November 2020, suggesting a higher spread of the viral infection among the community, followed by a decrease in the subsequent two months (December 2020 and January 2021). A marginal increase was observed during February 2021, hinting at the onset of the second wave (from March 2021) that reached it speak in April 2021. Dynamics of the community infection rates were calculated based on the viral gene copies to assess the severity of COVID-19 spread. With the ability to predict the infection spread, longitudinal WBE studies also offer the prospect of zoning specific areas based on the infection rates. Zoning of the selected community based on the infection rates assists health management to plan and manage the infection in an effective way. WBE promotes clinical inspection with simultaneous disease detection and management, in addition to an advance warning signal to anticipate outbreaks, with respect to the slated community/zones, to tackle, prepare for and manage the pandemic.

Mutation resource of Samba Mahsuri revealed the presence of high extent of variations among key traits for rice improvement.

To create novel variants for morphological, physiological, and biotic stress tolerance traits, induced mutations were created using Ethyl Methane Sulphonate (EMS) in the background of Samba Mahsuri (BPT 5204), a popular and mega rice variety of India. A population derived from 10, 500 M1 plants and their descendants were phenotyped for a wide range of traits leading to the identification of 124 mutants having variations in key agro-morphological traits, and 106 mutants exhibiting variation for physiological traits. Higher yield is the ultimate goal of crop improvement and we identified 574 mutants having higher yield compared to wild type by having better yield attributing traits. Further, a total of 50 mutants showed better panicle exertion phenotypes as compared to Samba Mahsuri leading to enhancement of yield. Upon rigorous screening for three major biotic stresses, 8 mutants showed enhanced tolerance for yellow stem borer (YSB), and 13 different mutants each showed enhanced tolerance for sheath blight (ShB) and bacterial leaf blight (BLB), respectively. In addition, screening at multiple locations that have diverse field isolates identified 3, 3, and 5 lines for tolerance to ShB, YSB and BLB, respectively. On the whole, 1231 desired mutant lines identified at M2 were forwarded to an advanced generation (M5). PCR based allele mining indicated that the BLB tolerant mutants have a different allele than the reported alleles for well-known genes affecting bacterial blight resistance. Whole genome re-sequencing revealed substantial variation in comparison to Samba Mahsuri. The lines showing enhanced tolerance to important biotic stresses (YSB, ShB and BLB) as well as several economically important traits are unique genetic resources which can be utilized for the identification of novel genes/alleles for different traits. The lines which have better agronomic features can be used as pre-breeding lines. The entire mutant population is maintained as a national resource for genetic improvement of the rice crop.

Comprehensive and Temporal Surveillance of SARS-CoV-2 in Urban Water Bodies: Early Signal of Second Wave Onset

The possible faecal-oral transmission of SARS-CoV-2 through domestic discharges has emerged as a serious public health concern. Based on persistence of the virus in environment, the wastewater-based epidemiology (WBE) enabled the surveillance of infection in a community. The water bodies connected to the anthropogenic activities have strong possibility of presence of the SARS-CoV-2 genetic material. In this work, we monitored urban, peri-urban and rural lakes in and around Hyderabad as a long-term surveillance study for presence of enteric virus SARS-CoV-2 gene fragments. The study time of seven months coincided with the first and second wave of COVID-19 infection. The study depicted differential viral RNA copies in the urban lake with high viral load observed during the peaks of wave I and wave II. Distinct variability in viral genes detection was observed amongst all five lakes which were in concordance with the human activity of the catchment area. The SARS-CoV-2 genes were not detected in peri-urban and rural lakes, whereas the urban lakes having direct functional attributes from domestic activity, in the community showed presence of viral load. The outcome of the study clearly shows that the urban water streams linked with domestic discharge will function as a proxy for wastewater epidemiological studies. The surge in viral gene load from February 2021 sample suggests the on shoot of the second wave of infection, which correlated well with the prevailing pandemic situation. Implementation of regular WBE based monitoring system for the water bodies/wastewater in the urban and semi-urban areas will help to understand the outbreak and spread of virus in the community.

Understanding SARS-CoV-2 Infection and Dynamics with Long Term Wastewater based Epidemiological Surveillance

Wastewater-based epidemiology (WBE) of SARS-CoV-2 emerged as an advantageous method to study the infection dynamics at substantial population level. A temporal glimpse at sewage viral genome helps as diagnostic tool to understand the viral spread at community level. In this study, for the long-term epidemiological surveillance, we monitored the SARS-CoV-2 genetic material in domestic sewage by adopting the longitudinal sampling to represent a selected community ([~]1.8 lakhs population which occupies 1.79% of the total population of Hyderabad city) to understand the dynamics of infection. Dynamics and spread of COVID-19 outbreak within the selected community were achieved by studying the longitudinal sampling for a specific period of time. WBE also promotes clinical scrutiny along with disease detection and management, in contrast to an advance warning signal to anticipate outbreaks.

Methodological Approach for Wastewater Based Epidemiological Studies for SARS-CoV-2

Post COVID-19 outbreak, wastewater-based epidemiology (WBE) studies as surveillance system is becoming an emerging interest due to its functional advantage as tool for early warning signal and to catalyze effective disease management strategies based on the community diagnosis. A comprehensive attempt was made in this study to define a methodological approach for conducting WBE studies in the framework of identifying/selection of surveillance sites, standardizing sampling policy, designing sampling protocols to improve sensitivity, adopting safety protocol, and interpreting the data. The methodology was applied to a community and studied its epidemiological status with reference to occurrence, persistence, and variation of SARS-CoV-2 genome load in wastewater system to understand the prevalence of infection. Hourly and daily grab samples were analyzed and compared with the composite samples over a surveillance window of 7 days. Based on the SARS-CoV-2 RNA copies/L, faeces shedding, and volume of sewage generated the infected individuals and the population who are in active phase in the studied community was estimated.

Improved and Simplified Diagnosis of Covid-19 using TE Extraction from Dry Swabs

Rigorous testing is the way forward to fight the Covid-19 pandemic. Here we show that the currently used and most reliable RT-PCR based SARS-CoV-2 procedure can be further simplified to make it faster, safer and economical by bypassing the RNA isolation step. The modified method is not only fast and convenient but also at par with the traditional method in terms of accuracy, and therefore, can be used for mass screening. Our method takes about half the time and is cheaper by about 40% compared to current most widely used method. We also provide a variant of the new method that increases the efficiency of detection by about 20% compared to the currently used method. Taken together, we demonstrate a more effective and reliable method of SARS-CoV-2 detection.