Multiple pathogen contamination of water, hands, and fomites in rural Nepal and the effect of WaSH interventions.

Water, Sanitation, and Hygiene (WaSH) interventions are the most effective in reducing diarrheal disease severity and prevalence. However, very few studies have investigated the effectiveness of WaSH intervention in reducing pathogen presence and concentration. In this study, we employed a microfluidic PCR approach to quantify twenty bacterial pathogens in water (n = 360), hands (n = 180), and fomite (n = 540) samples collected in rural households of Nepal to assess the pathogen exposures and the effect of WaSH intervention on contamination and exposure rates. The pathogen load and the exposure pathways for each pathogen in intervention and control villages were compared to understand the effects of WaSH intervention. Pathogens were detected in higher frequency and concentration from fomites samples, toilet handle (21.42%; 5.4,0 95%CI: mean log10 of 4.69, 5.96), utensils (23.5%; 5.47, 95%CI: mean log10 of 4.77, 6.77), and water vessels (22.42%; 5.53, 95%CI: mean log10 of 4.79, 6.60) as compared to cleaning water (14.36%; 5.05, 95%CI: mean log10 of 4.36, 5.89), drinking water (14.26%; 4.37, 85%CI: mean log10 of 4.37, 5.87), and hand rinse samples (16.92%; 5.49, 95%CI: mean log10 of 4.77, 6.39). There was no clear evidence that WaSH intervention reduced overall pathogen contamination in any tested pathway. However, we observed a significant reduction (p < 0.05) in the prevalence, but not concentration, of some target pathogens, including Enterococcus spp. in the intervention village compared to the control village for water and hands rinse samples. Conversely, no significant reduction in target pathogen concentration was observed for water and hand rinse samples. In swab samples, there was a reduction mostly in pathogen concentration rather than pathogen prevalence, highlighting that a reduction in pathogen prevalence was not always accompanied by a reduction in pathogen concentration. This study provides an understanding of WaSH intervention on microbe concentrations. Such data could help with better planning of intervention activities in the future.

Application of wastewater-based epidemiology for monitoring COVID-19 in hospital and housing wastewaters.

An alternative and complementary diagnostic method of surveillance is provided by wastewater-based surveillance (WBS), particularly in low-income nations like Nepal with scant wastewater treatment facilities and clinical testing infrastructure. In this study, a total of 146 water samples collected from two hospitals (n = 63) and three housing wastewaters (n = 83) from the Kathmandu Valley over the period of March 2021-Febraury 2022 were investigated for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using quantitative reverse transcription TaqMan PCR assays targeting the N and E genes. Of the total, 67 % (98/146) samples were positive for SARS-CoV-2 RNA either by using N- or E-gene assay, with concentrations ranging from 3.6 to 9.1 log10 copies/L. There was a significant difference found between positive ratio (Chi-square test, p < 0.05) and concentration (t-test, p = 0.009) of SARS-CoV-2 RNA detected from hospital wastewater and housing waters. Wastewater data are correlated with COVID-19 active cases, indicating significance in specific areas like the Hospital (APFH) (p < 0.05). According to the application of a bivariate linear regression model (p < 0.05), the concentrations of N gene may be used to predict the COVID-19 cases in the APFH. Remarkably, SARS-CoV-2 RNA was detected prior to, during, and following clinical case surges, implying that wastewater surveillance could serve as an early warning system for public health decisions. The significance of WBS in tracking and managing pandemics is emphasized by this study, especially in resource-constrained settings.

Surveillance of Naegleria fowleri in Louisiana's public water systems.

The free-living amoeba Naegleria fowleri (Nf) inhabits soil and natural waters worldwide: it is thermophilic and thrives at temperatures up to 45 °C and in a multitude of environments. Three deaths in Louisiana were attributed to primary amoebic meningoencephalitis (PAM) caused by Nf infection in 2011 and 2013. Following these incidents, public water systems are now monitored for the presence of Nf in Louisiana. From 2014 to 2018, 29% (27/93) of samples collected showed positive for Nf and 68% (63/93) showed all thermophilic amoeba culture. Ten raw water sources and 17 distribution water systems tested positive. The year 2017 showed the highest number of samples with Nf (n = 10) followed by nine samples in 2015. As climate change increases surface water temperatures, continued testing for Nf prevalence will be an important facet of water monitoring and will need to extend into locations farther north than the current most common range.

Survivability of Delta and Omicron variants of SARS-CoV-2 in wastewater.

Concerns of fecal-aerosol transmission of coronavirus disease 2019 (COVID-2019) coupled with increased transmissibility and disease severity of Delta and Omicron variants of concern (VOC) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), suggest studies on survival of VOC in wastewater are warranted. To the best of our knowledge, this is the first study to investigate the survivability of Delta and Omicron VOC in filtered and unfiltered raw wastewater, and secondary effluent at room temperature (23 °C). The time required for 90 % inactivation (T90) of Delta and Omicron VOC in unfiltered raw wastewater was calculated as 17.7 and 15.3 h, respectively. Rapid inactivation of VOC in wastewater and inability to isolate SARS-CoV-2 in wastewater suggest risks from fecal-aerosol transmission are low. Nevertheless, high transmissibility of VOC cautions overruling fecal-aerosol transmission of COVID-19. Future studies on survival of SARS-CoV-2 in wastewater should attempt viral culture by spiking feces collected from COVID-19 infected patients into wastewater to match the real-world scenario.

Wastewater-based epidemiology predicts COVID-19-induced weekly new hospital admissions in over 150 USA counties.

Although the coronavirus disease (COVID-19) emergency status is easing, the COVID-19 pandemic continues to affect healthcare systems globally. It is crucial to have a reliable and population-wide prediction tool for estimating COVID-19-induced hospital admissions. We evaluated the feasibility of using wastewater-based epidemiology (WBE) to predict COVID-19-induced weekly new hospitalizations in 159 counties across 45 states in the United States of America (USA), covering a population of nearly 100 million. Using county-level weekly wastewater surveillance data (over 20 months), WBE-based models were established through the random forest algorithm. WBE-based models accurately predicted the county-level weekly new admissions, allowing a preparation window of 1-4 weeks. In real applications, periodically updated WBE-based models showed good accuracy and transferability, with mean absolute error within 4-6 patients/100k population for upcoming weekly new hospitalization numbers. Our study demonstrated the potential of using WBE as an effective method to provide early warnings for healthcare systems.

First quantitative detection of tomato brown rugose fruit virus in wastewater in Louisiana.

We investigated the occurrence of tomato brown rugose fruit virus (ToBRFV) at a conventional wastewater treatment plant in Louisiana over a 13-month period, from March 2017 to March 2018. Influent, secondary effluent, and final effluent wastewater samples were collected monthly, and viruses were concentrated by the adsorption-elution method using an electronegative filter, followed by the detection using quantitative polymerase chain reaction. ToBRFV was detected in 10 (77 %) of 13 influent samples, 9 (69 %) of 13 in secondary effluent, and 6 (50 %) of 12 final effluents. The concentrations of ToBRFV in the influent samples ranged from 3.5 to 6.1 log10 copies/L and it was always higher than those in secondary or final effluents. Wastewater samples showed a high positive ratio of ToBRFV during fall and winter months. The findings highlight that routine monitoring of new viral indicator such as ToBRFV is necessary to understand its environmental distribution and correlation with pathogenic viruses. This is the first study providing quantitative data on the occurrence of ToBRFV in wastewater.

Wastewater surveillance of Mpox virus in Baltimore.

This study aimed to utilize wastewater surveillance for monitoring Mpox cases at a community level. Untreated wastewater samples were collected once a week from two wastewater treatment plants (A and B) in Baltimore City from July 27, 2022-September 22, 2022. The samples were concentrated via an adsorption-elution (AE) method and Polyethylene Glycol (PEG) precipitation method followed by quantitative polymerase chain reaction (qPCR). Monkeypox virus (MPXV) was detected in 89 % (8/9) samples from WWTP A and 55 % (5/9) samples from WWTP B with at least one concentration method. Higher detection rate in samples concentrated with PEG precipitation compared to AE method was observed, indicating that PEG precipitation is a more effective virus concentration method for MPXV. To our knowledge, this is the first study reporting the detection of MPXV in wastewater in Baltimore. The results highlight that wastewater surveillance could be used as a complementary early warning tool for monitoring future Mpox outbreaks.

Microbial assessment of water, sanitation, and hygiene (WaSH) in temporary and permanent settlements two years after Nepal 2015 earthquake.

Disaster-induced displacement often causes people to live in temporary settlements that have limited infrastructure and access to water, sanitation, and hygiene (WaSH). Reducing the risk of diarrheal diseases in such situations requires knowing how housing influences the presence of pathogens in water and the interaction between human settlements and exposure to pathogens. A cross-sectional study was conducted in May 2017 in two communities hard-hit by the Nepal 2015 earthquake: one recovered with newly reconstructed houses, and one recovered with residents still living in sheet metal temporary shelters constructed after the earthquake. We collected 60 water (30 drinking water and 30 cleaning water), 30 hand rinse, and 90 environmental swab samples (30 toilet handles, 30 utensils, and 30 water vessels) from selected households in each location and quantified 22 bacterial pathogens using microfluidic quantitative polymerase chain reaction (mfqPCR). A total of 59 samples were randomly selected for amplicon-based sequencing of the 16S rRNA, and it identified bacterial community profiles between these two settlements and their association with target genes of pathogenic bacteria. Target genes like uidA of Escherichia coli and the mip gene of Legionella pnuemophila showed significantly high frequency in specific sample types in temporary settlements than in permanent settlements. A significantly high concentration was observed in temporary settlements for Enterococcus spp. and S. typhimurium, specifically in swab samples. There was a sharp distinction of microbial community profiles between water and hand rinse samples with environmental swab samples, with a large abundance of potentially pathogenic bacteria in swab samples in both settlements. This observation highlighted that fomite could be an important transmission route for pathogens in rural settings and designing key interventions to target different stages of transmission pathways is essential. Overall findings from this study suggest that the recovered settlement with higher quality housing may be less impacted by fecal contamination than recovering settlements and that interventions should be designed to disrupt multiple transmission pathways to reduce pathogen exposure.

Monkeypox outbreak: Wastewater and environmental surveillance perspective.

Monkeypox disease (MPXD), a viral disease caused by the monkeypox virus (MPXV), is an emerging zoonotic disease endemic in some countries of Central and Western Africa but seldom reported outside the affected region. Since May 2022, MPXD has been reported at least in 74 countries globally, prompting the World Health Organization to declare the MPXD outbreak a Public Health Emergency of International Concern. As of July 24, 2022; 92 % (68/74) of the countries with reported MPXD cases had no historical MPXD case reports. From the One Health perspective, the spread of MPXV in the environment poses a risk not only to humans but also to small mammals and may, ultimately, spread to potent novel host populations. Wastewater-based surveillance (WBS) has been extensively utilized to monitor communicable diseases, particularly during the ongoing COVID-19 pandemic. It helped in monitoring infectious disease caseloads as well as specific viral variants circulating in communities. The detection of MPXV DNA in lesion materials (e.g. skin, vesicle fluid, crusts), skin rashes, and various body fluids, including respiratory and nasal secretions, saliva, urine, feces, and semen of infected individuals, supports the possibility of using WBS as an early proxy for the detection of MPXV infections. WBS of MPXV DNA can be used to monitor MPXV activity/trends in sewerage network areas even before detecting laboratory-confirmed clinical cases within a community. However, several factors affect the detection of MPXV in wastewater including, but not limited to, routes and duration time of virus shedding by infected individuals, infection rates in the relevant affected population, environmental persistence, the processes and analytical sensitivity of the used methods. Further research is needed to identify the key factors that impact the detection of MPXV biomarkers in wastewater and improve the utility of WBS of MPXV as an early warning and monitoring tool for safeguarding human health. In this review, we shortly summarize aspects of the MPXV outbreak relevant to wastewater monitoring and discuss the challenges associated with WBS.

Classifying Building Roof Damage Using High Resolution Imagery for Disaster Recovery.

Post-hurricane damage assessments are often costly and time-consuming. Remotely sensed data provides a complementary method of data collection that can be completed comparatively quickly and at relatively low cost. This study focuses on 15 Florida counties impacted by Hurricane Michael (2018), which had category 5 strength winds at landfall. The present study evaluates the ability of aerial imagery collected to cost-effectively measure blue tarps on buildings for disaster impact and recovery. A support vector machine model classified blue tarp, and parcels received a damage indicator based on the model's prediction. The model had an overall accuracy of 85.3% with a sensitivity of 74% and a specificity of 96.7%. The model results indicated approximately 7% of all parcels (27 926 residential and 4431 commercial parcels) in the study area as having blue tarp present. The study results may benefit jurisdictions that lacked financial resources to conduct on-the-ground damage assessments.

Association between Global Monkeypox Cases and Meteorological Factors.

The emergence of an outbreak of Monkeypox disease (MPXD) is caused by a contagious zoonotic Monkeypox virus (MPXV) that has spread globally. Yet, there is no study investigating the effect of climatic changes on MPXV transmission. Thus, studies on the changing epidemiology, evolving nature of the virus, and ecological niche are highly paramount. Determination of the role of potential meteorological drivers including temperature, precipitation, relative humidity, dew point, wind speed, and surface pressure is beneficial to understand the MPXD outbreak. This study examines the changes in MPXV cases over time while assessing the meteorological characteristics that could impact these disparities from the onset of the global outbreak. To conduct this data-based research, several well-accepted statistical techniques including Simple Exponential Smoothing (SES), Auto-Regressive Integrated Moving Average (ARIMA), Automatic forecasting time-series model (Prophet), and Autoregressive Integrated Moving Average with Explanatory Variables (ARIMAX) were applied to delineate the correlation of the meteorological factors on global daily Monkeypox cases. Data on MPXV cases including affected countries spanning from 6 May 2022, to 9 November 2022, from global databases and meteorological data were used to evaluate the developed models. According to the ARIMAX model, the results showed that temperature, relative humidity, and surface pressure have a positive impact [(51.56, 95% confidence interval (CI): -274.55 to 377.68), (17.32, 95% CI: -83.71 to 118.35) and (23.42, 95% CI: -9.90 to 56.75), respectively] on MPXV cases. In addition, dew/frost point, precipitation, and wind speed show a significant negative impact on MPXD cases. The Prophet model showed a significant correlation with rising MPXD cases, although the trend predicts peak values while the overall trend increases. This underscores the importance of immediate and appropriate preventive measures (timely preparedness and proactive control strategies) with utmost priority against MPXD including awareness-raising programs, the discovery, and formulation of effective vaccine candidate(s), prophylaxis and therapeutic regimes, and management strategies.

Remotely sensed measures of Hurricane Michael damage and adverse perinatal outcomes and access to prenatal care services in the Florida panhandle.

BACKGROUND: Studies of effects of hurricanes on perinatal outcomes often rely on approximate measures of exposure. This study aims to use observed damage from aerial imagery to refine residential building damage estimates, evaluate the population changes post landfall, and assess the associations between the extent of residential building damage and adverse perinatal outcomes and access to prenatal care (PNC) services.  METHODS: Vital statistics data from the Florida Department of Health's Office of Vital Statistics were used to align maternal geocoded address data to high-resolution imagery (0.5-foot resolution, true color with red, blue, and green bands) aerial photographs. Machine learning (support vector machines) classified residential roof damage across the study area. Perinatal outcomes were compared with the presence or absence of damage to the mother's home. Log-binomial regression models were used to compare the populations living in and outside of high-risk/damage areas, to assess the population changes after Hurricane Michael, and to estimate the associations between damage after Hurricane Michael and adverse perinatal outcomes/access to PNC services. A semi-parametric linear model was used to model time of first PNC visit and increase in damage. RESULTS: We included 8,965 women in analysis. Women with lower education and/or of Black or other non-White race/ethnicity were more likely to live in areas that would see high damage than other groups. Moreover, there was a greater proportion of births delivered by women living in the high-risk/damage area (> 25% damaged parcels after Michael) in the year before Michael than the year after Michael. Lastly, living in the area with relatively high damage increased the risk of having intermediate or inadequate PNC (adjusted Risk Ratio = 1.21, 95% CI: 1.03, 1.43), but not other adverse perinatal outcomes. CONCLUSIONS: Aerially observed damage data enable us to evaluate the impact of natural disasters on perinatal outcomes and access to PNC services based on residential building damage immediately surrounding a household. The association between the extent of damage and adverse perinatal outcomes should be further investigated in future studies.

Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin.

Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.

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.

Harmful algal bloom-related 311 calls, Cape Coral, Florida 2018-2019.

Harmful algal blooms (HABs) can adversely impact water quality and threaten human and animal health. People working or living along waterways with prolonged HAB contamination may face elevated toxin exposures and breathing complications. Monitoring HABs and potential adverse human health effects is notoriously difficult due to routes and levels of exposure that vary widely across time and space. This study examines the utility of 311 calls to enhance HAB surveillance and monitoring. The study focuses on Cape Coral, FL, USA, located along the banks of the Caloosahatchee River and Estuary and the Gulf of Mexico. The wider study area experienced a prolonged cyanobacteria bloom in 2018. The present study examines the relationship between weekly water quality characteristics (temperature, dissolved oxygen, pH, microcystin-LR) and municipal requests for information or services (algal 311 calls). Each 1 µg/L increase in waterborne microcystin-LR concentrations corresponded with 9% more algal 311 calls (95% confidence interval: 1.03-1.15, p = 0.002). The results suggest water quality monitoring and the 311 dispatch systems may be further integrated to improve public health surveillance.

SARS-CoV-2 shedding sources in wastewater and implications for wastewater-based epidemiology.

Wastewater-based epidemiology (WBE) approach for COVID-19 surveillance is largely based on the assumption of SARS-CoV-2 RNA shedding into sewers by infected individuals. Recent studies found that SARS-CoV-2 RNA concentration in wastewater (CRNA) could not be accounted by the fecal shedding alone. This study aimed to determine potential major shedding sources based on literature data of CRNA, along with the COVID-19 prevalence in the catchment area through a systematic literature review. Theoretical CRNA under a certain prevalence was estimated using Monte Carlo simulations, with eight scenarios accommodating feces alone, and both feces and sputum as shedding sources. With feces alone, none of the WBE data was in the confidence interval of theoretical CRNA estimated with the mean feces shedding magnitude and probability, and 63% of CRNA in WBE reports were higher than the maximum theoretical concentration. With both sputum and feces, 91% of the WBE data were below the simulated maximum CRNA in wastewater. The inclusion of sputum as a major shedding source led to more comparable theoretical CRNA to the literature WBE data. Sputum discharging behavior of patients also resulted in great fluctuations of CRNA under a certain prevalence. Thus, sputum is a potential critical shedding source for COVID-19 WBE surveillance.

Hurricane Michael and Adverse Birth Outcomes in the Florida Panhandle: Analysis of Vital Statistics Data.

OBJECTIVE: The aim of this study was to examine birth outcomes in areas affected by Hurricane Michael. METHODS: Vital statistics data of 2017-2019 were obtained from the state of Florida. Births occurring in the year before and after the date of Hurricane Michael (October 7, 2018) were used. Florida counties were divided into 3 categories reflecting extent of impact from Hurricane Michael. Birth outcomes including incidence of preterm birth (PTB), low birth weight (LBW), and small for gestational age (SGA) were also compared before and after Hurricane Michael. Spontaneous and indicated PTBs were distinguished based on previously published algorithms. Multiple regression was used to control for potential confounders. RESULTS: Both LBW (aRR 1.19, 95% CI: 1.07, 1.32) and SGA (aRR 1.11, 95% CI: 1.01, 1.21) were higher in the year after Michael than the year before in the most-affected area; a similar effect was not seen in other areas. A stronger effect was seen for exposure in the first trimester or in the 2 months after Michael than in the second or third trimester. CONCLUSION: Consistent with many previous studies, this study of Hurricane Michael found an effect on fetal growth.

Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal.

The applicability of wastewater-based epidemiology (WBE) has been extensively studied throughout the world with remarkable findings. This study reports the presence and reduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at two wastewater treatment plants (WWTPs) of Nepal, along with river water, hospital wastewater (HWW), and wastewater from sewer lines collected between July 2020 and February 2021. SARS-CoV-2 RNA was detected in 50%, 54%, 100%, and 100% of water samples from WWTPs, river hospitals, and sewer lines, respectively, by at least one of four quantitative PCR assays tested (CDC-N1, CDC-N2, NIID_2019-nCOV_N, and N_Sarbeco). The CDC-N2 assay detected SARS-CoV-2 RNA in the highest number of raw influent samples of both WWTPs. The highest concentration was observed for an influent sample of WWTP A (5.5 ± 1.0 log10 genome copies/L) by the N_Sarbeco assay. SARS-CoV-2 was detected in 47% (16/34) of the total treated effluents of WWTPs, indicating that biological treatments installed at the tested WWTPs are not enough to eliminate SARS-CoV-2 RNA. One influent sample was positive for N501Y mutation using the mutation-specific qPCR, highlighting a need for further typing of water samples to detect Variants of Concern. Furthermore, crAssphage-normalized SARS-CoV-2 RNA concentrations in raw wastewater did not show any significant association with the number of new coronavirus disease 2019 (COVID-19) cases in the whole district where the WWTPs were located, suggesting a need for further studies focusing on suitability of viral as well as biochemical markers as a population normalizing factor. Detection of SARS-CoV-2 RNA before, after, and during the peaking in number of COVID-19 cases suggests that WBE is a useful tool for COVID-19 case estimation in developing countries.

The importance of accessory protein variants in the pathogenicity of SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) with an estimated fatality rate of less than 1%. The SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 possess putative functions to manipulate host immune mechanisms. These involve interferons, which appear as a consensus function, immune signaling receptor NLRP3 (NLR family pyrin domain-containing 3) inflammasome, and inflammatory cytokines such as interleukin 1ß (IL-1ß) and are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins were observed across six continents of all complete SARS-CoV-2 proteomes based on the data reported before November 2020. A decreasing order of percentage of unique variations in the accessory proteins was determined as ORF3a > ORF8 > ORF7a > ORF6 > ORF10 > ORF7b across all continents. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. These findings suggest that the wide variations in accessory proteins seem to affect the pathogenicity of SARS-CoV-2.

Persistence and occurrence of SARS-CoV-2 in water and wastewater environments: a review of the current literature.

As the world continues to cope with the COVID-19 pandemic, emerging evidence indicates that respiratory transmission may not the only pathway in which the virus can be spread. This review paper aims to summarize current knowledge surrounding possible fecal-oral transmission of SARS-CoV-2. It covers recent evidence of proliferation of SARS-CoV-2 in the gastrointestinal tract, as well as presence and persistence of SARS-CoV-2 in water, and suggested future directions. Research indicates that SARS-CoV-2 can actively replicate in the human gastrointestinal system and can subsequently be shed via feces. Several countries have reported SARS-CoV-2 RNA fractions in wastewater systems, and various factors such as temperature and presence of solids have been shown to affect the survival of the virus in water. The detection of RNA does not guarantee infectivity, as current methods such as RT-qPCR are not yet able to distinguish between infectious and non-infectious particles. More research is needed to determine survival time and potential infectivity, as well as to develop more accurate methods for detection and surveillance.