A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity

Wastewater based epidemiology (WBE) is an important tool to fight against COVID-19 as it provides insights into the health status of the targeted population from a small single house to a large municipality in a cost-effective, rapid, and non-invasive way. The implementation of wastewater based surveillance (WBS) could reduce the burden on the public health system, management of pandemics, help to make informed decisions, and protect public health. In this study, a house with COVID-19 patients was targeted for monitoring the prevalence of SARS-CoV-2 genetic markers in wastewa-ter samples (WS) with clinical specimens (CS) for a period of 30 days. RT-qPCR technique was employed to target non-structural (ORF1ab) and structural-nucleocapsid (N) protein genes of SARS-CoV-2, according to a validated experimental protocol. Physiological, environmental, and biological parameters were also measured following the American Public Health Association (APHA) standard protocols. SARS-CoV-2 viral shedding in wastewater peaked when the highest number of COVID-19 cases were clinically diagnosed. Throughout the study period, 7450 to 23,000 gene copies/1000 mL were detected, where we identified 47 % (57/120) positive samples from WS and 35 % (128/360) from CS. When the COVID-19 patient number was the lowest (2), the highest CT value (39.4; i.e., lowest copy number) was identified from WS. On the other hand, when the COVID-19 patients were the highest (6), the lowest CT value (25.2 i.e., highest copy numbers) was obtained from WS. An advance signal of increased SARS-CoV-2 viral load from the COVID-19 patient was found in WS earlier than in the CS. Using customized primer sets in a traditional PCR approach, we confirmed that all SARS-CoV-2 variants identified in both CS and WS were Delta variants (B.1.617.2). To our knowledge, this is the first follow-up study to determine a temporal relationship be-tween COVID-19 patients and their discharge of SARS-CoV-2 RNA genetic markers in wastewater from a single house including all family members for clinical sampling from a developing country (Bangladesh), where a proper sewage system is lacking. The salient findings of the study indicate that monitoring the genetic markers of the SARS-CoV-2 virus in wastewater could identify COVID-19 cases, which reduces the burden on the public health system during COVID-19 pandemics.Peer reviewe

Wastewater-based epidemiological surveillance to monitor the prevalence of SARS-CoV-2 in developing countries with onsite sanitation facilities

Wastewater-based epidemiology (WBE) has emerged as a valuable approach for forecasting disease outbreaks in developed countries with a centralized sewage infrastructure. On the other hand, due to the absence of well-defined and systematic sewage networks, WBE is challenging to implement in developing countries like Bangladesh where most people live in rural areas. Identification of appropriate locations for rural Hotspot Based Sampling (HBS) and urban Drain Based Sampling (DBS) are critical to enable WBE based monitoring system. We investigated the best sampling locations from both urban and rural areas in Bangladesh after evaluating the sanitation infrastructure for forecasting COVID-19 prevalence. A total of 168 wastewater samples were collected from 14 districts of Bangladesh during each of the two peak pandemic seasons. RT-qPCR commercial kits were used to target ORF1ab and N genes. The presence of SARS-CoV-2 genetic materials was found in 98% (165/168) and 95% (160/168) wastewater samples in the first and second round sampling, respectively. Although wastewater effluents from both the marketplace and isolation center drains were found with the highest amount of genetic materials according to the mixed model, quantifiable SARS-CoV-2 RNAs were also identified in the other four sampling sites. Hence, wastewater samples of the marketplace in rural areas and isolation centers in urban areas can be considered the appropriate sampling sites to detect contagion hotspots. This is the first complete study to detect SARS-CoV-2 genetic components in wastewater samples collected from rural and urban areas for monitoring the COVID-19 pandemic. The results based on the study revealed a correlation between viral copy numbers in wastewater samples and SARS-CoV-2 positive cases reported by the Directorate General of Health Services (DGHS) as part of the national surveillance program for COVID-19 prevention. The findings of this study will help in setting strategies and guidelines for the selection of appropriate sampling sites, which will facilitate in development of comprehensive wastewater-based epidemiological systems for surveillance of rural and urban areas of low-income countries with inadequate sewage infrastructure.This research was supported by Water Aid Bangladesh, North South University, Dhaka, COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University (NSTU), Noakhali, Bangladesh, the International Training Network of Bangladesh University of Engineering and Technology (ITN-BUET) - Centre for Water Supply and Waste Management, and KTH Royal Institute of Technology, Sweden. We acknowledge the sincere help and support of the staff and volunteers of NSTU-COVID-19 Diagnostic Lab, Noakhali Science and Technology University, Bangladesh during the different phases of the study. PB and MTI acknowledge the Life Science Technology Platform, Science for Life Laboratory for the seed funding to initiate the wastewater-based epidemiological studies for SARS-CoV-2 in Bangladesh. We would also like to acknowledge the two anonymous reviewers for their critical comments as well as their thoughtful insights, which has significantly improved the manuscript.Peer reviewe

Synthesis of nano-crystallite hydroxyapatites in different media and a comparative study for estimation of crystallite size using Scherrer method, Halder-Wagner method size-strain plot, and Williamson-Hall model

Hydroxyapatite (HAp) [Ca10(PO4)6(OH)2] is remarkably similar to the hard tissue of the human body and the uses of this material in various fields in addition to the medical sector are increasing day by day. In this research, mustered oil, soybean oil, as well as coconut oil were employed as liquid media for synthesizing nanocrystalline HAp using a wet chemical precipitation approach. The X-ray diffraction (XRD) study verified the crystalline phase of the HAp in all the indicated media and discovered similarities with the standard database. Several prominent models such as the Scherrer's Method (SM), Halder-Wagner Method (HWM), linear straight-line method (LSLM), Williamson-Hall Method (W-M), Monshi Scherrer Method (MSM), Size-Strain Plot Method (SSPM), Sahadat-Scherrer Method (S–S) were applied for the determination of crystallite size. The stress, strain, and energy density were also computed from the above models. All the models, without the Linear straight-line technique of Scherrer's equation, resulted in an appropriate value of crystallite size for synthesized products. The calculated crystallite sizes were 6.5 nm for HAp in master oil using Halder-Wagner Method, and 143 nm for HAp in coconut oil using the Scherrer equation which were the lowest and the largest, respectively

Facile preparation of micro-porous biochar from Bangladeshi sprouted agricultural waste (corncob) via in-house built heating chamber for cationic dye removal

Herein, in-house built heating chamber aided facile preparation of biochar was carried out using Bangladeshi sprouted corncob as the precursor for removing methylene blue (MB). The corncob biomass (CCB) was pyrolyzed at 700 °C for 2hrs (heating rate: 10 °C/min) using the in-house built heating chamber in a muffle furnace, eliminating the necessity of pyrolytic chamber. The prepared corncob biochar (CCBC) was characterized for elemental composition, crystallinity (XRD), functional groups (ATR-FTIR), surface morphology-elemental composition (SEM-EDX), surface area (BET), surface charge (point of zero charge), particle size-stability (DLS-zeta potential) and thermal stability (STA). Adsorption efficacy of CCBC was investigated in batch experiment with MB dye as well as effect of various factors such as contact time (5–120 min), initial MB concentration (7–15 mg/L), pH (2–10) and adsorbent dosage (10–35 mg). Without any chemical treatment for activation, CCBC produced maximum adsorption capacity (Qmax) of 20.42mgg−1 at 25 °C. The adsorption behavior of MB by CCBC could be better understood by Langmuir isotherm and Pseudo-second order kinetic model as they were the best fitted isotherm and kinetic models. Thus, waste to treat waste, meaning agricultural wastes like corncob can easily be converted into effective adsorbent for treating dye bearing wastewater

Genome-wide study of globally distributed respiratory syncytial virus (RSV) strains implicates diversification utilizing phylodynamics and mutational analysis

Abstract Respiratory syncytial virus (RSV) is a common respiratory pathogen that causes mild cold-like symptoms and severe lower respiratory tract infections, causing hospitalizations in children, the elderly and immunocompromised individuals. Due to genetic variability, this virus causes life-threatening pneumonia and bronchiolitis in young infants. Thus, we examined 3600 whole genome sequences submitted to GISAID by 31 December 2022 to examine the genetic variability of RSV. While RSVA and RSVB coexist throughout RSV seasons, RSVA is more prevalent, fatal, and epidemic-prone in several countries, including the United States, the United Kingdom, Australia, and China. Additionally, the virus's attachment glycoprotein and fusion protein were highly mutated, with RSVA having higher Shannon entropy than RSVB. The genetic makeup of these viruses contributes significantly to their prevalence and epidemic potential. Several strain-specific SNPs co-occurred with specific haplotypes of RSVA and RSVB, followed by different haplotypes of the viruses. RSVA and RSVB have the highest linkage probability at loci T12844A/T3483C and G13959T/C2198T, respectively. The results indicate that specific haplotypes and SNPs may significantly affect their spread. Overall, this analysis presents a promising strategy for tracking the evolving epidemic situation and genetic variants of RSV, which could aid in developing effective control, prophylactic, and treatment strategies

Prediction of novel miRNA biomarker candidates for diagnostic and prognostic analysis of STAD and LIHC: An integrated in silico approach

Background: miRNAs are endogenous, non-coding and evolutionarily conserved RNA molecules. They have been found to be involved in the progression and proliferation of various cancers due to their contribution in post-transcriptional regulation. Stomach Adenocarcinoma (STAD) and Liver Hepatocellular Carcinoma (LIHC) are the two most common cancers of the upper intestinal tract. Our study aimed to evaluate the circulating miRNAs from both STAD and LIHC samples and to identify commonly dysregulated miRNAs as biomarkers to detect both cancers at the same time. Methods and materials: Common differentially expressed miRNAs (DEMs) from GEO and Bioexpress datasets were considered for initial processing in the analysis. Pathway analysis of the selected miRNAs through DIANA-miRpath tool, followed by survival analysis based on prognostic values through OncoLnc server led to the final biomarker candidates for diagnosis and prognosis of STAD and LIHC. An elaborate miRNA-gene-cancer network was set up for a specialized understanding of the selected DEMs corresponding to the specifically unique target genes and the cancer types. The gene ontology analysis was performed using BINGO to determine functional connotations of the differentially expressed genes (DEGs). Results: After a thorough analysis, we found that the 4 miRNAs: miR-183-5p, miR-203-3p, miR-126-3p and miR-25-3p could be potential prognostic biomarkers against both STAD and LIHC. The differentially expressed genes (DEGs) for these miRNAs were inferred through GEPIA and miRwalk v2.0. The miRNA-gene-cancer network revealed that the commonly deregulated miRNAs could influence the same genes and pathways altered by multiple cancers at the same time-in our case, STAD and LIHC. To support our claim, we showed the gene ontology analysis by BINGO, attesting the functional assignment of the DEGs behind metastasis and development of both the cancers. Conclusion: Our study evaluated a particularly effective avenue of identifying novel miRNA for both early diagnostic and prognostic purposes against more than one cancer

MicroRNAs expression analysis shows key affirmation of Synaptopodin-2 as a novel prognostic and therapeutic biomarker for colorectal and cervical cancers

MicroRNAs play a crucial role in tumorigenesis, tumor progression, and metastasis, and thus they contribute in development of different malignancies including cervical cancer (CC) and colorectal cancer (CRC). Through integrated strategies of computational biology, this study aims to identify prognostic biomarkers responsible for CRC and CC prognosis, and potential therapeutic agents to halt the progression of these cancers. Expression analysis of miRNA datasets of CRC and CC identified 17 differentially expressed miRNAs (DEMs). SYNPO2, NEGR1, FGF7, LIFR, RUNX1T1, CFL2, BNC2, EPHB2, PMAIP1, and CDC25A differentially expressed genes (DEGs) regulated by these DEMs were classified as candidate genes responsible for CRC and CC. Down-regulation of Synaptopodin-2 (SYNPO2) is involved in emergence and progression of these cancers by activating ER, PI3K/AKT, and EMT pathways as well as by suppressing DNA damage response, and cell cycle pathways. Higher methylation rate in promoter region of SYNPO2 could be a possible reason for lowering the expression of SYNPO2 in tumor stages. Hence, the lower expression of SYNPO2 is associated with poor prognosis of CRC and CC and could function as prognostic biomarker and therapeutic target. Fourteen transcription factors were recognized which can activate/inhibit the transcription of SYNPO2 and may be a potential target to regulate expression of SYNPO2 in CRC and CC. Retinoic acid and Estradiol were identified as putative therapeutic drugs for CRC and CC patients. This study will thus help in understanding the underlying molecular events in CRC and CC that may improve the detection of malignant lesions in primary screening and will broaden the clinical applications

A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity

Wastewater based epidemiology (WBE) is an important tool to fight against COVID-19 as it provides insights into the health status of the targeted population from a small single house to a large municipality in a cost-effective, rapid, and non-invasive way. The implementation of wastewater based surveillance (WBS) could reduce the burden on the public health system, management of pandemics, help to make informed decisions, and protect public health. In this study, a house with COVID-19 patients was targeted for monitoring the prevalence of SARS-CoV-2 genetic markers in wastewa-ter samples (WS) with clinical specimens (CS) for a period of 30 days. RT-qPCR technique was employed to target non-structural (ORF1ab) and structural-nucleocapsid (N) protein genes of SARS-CoV-2, according to a validated experimental protocol. Physiological, environmental, and biological parameters were also measured following the American Public Health Association (APHA) standard protocols. SARS-CoV-2 viral shedding in wastewater peaked when the highest number of COVID-19 cases were clinically diagnosed. Throughout the study period, 7450 to 23,000 gene copies/1000 mL were detected, where we identified 47 % (57/120) positive samples from WS and 35 % (128/360) from CS. When the COVID-19 patient number was the lowest (2), the highest CT value (39.4; i.e., lowest copy number) was identified from WS. On the other hand, when the COVID-19 patients were the highest (6), the lowest CT value (25.2 i.e., highest copy numbers) was obtained from WS. An advance signal of increased SARS-CoV-2 viral load from the COVID-19 patient was found in WS earlier than in the CS. Using customized primer sets in a traditional PCR approach, we confirmed that all SARS-CoV-2 variants identified in both CS and WS were Delta variants (B.1.617.2). To our knowledge, this is the first follow-up study to determine a temporal relationship be-tween COVID-19 patients and their discharge of SARS-CoV-2 RNA genetic markers in wastewater from a single house including all family members for clinical sampling from a developing country (Bangladesh), where a proper sewage system is lacking. The salient findings of the study indicate that monitoring the genetic markers of the SARS-CoV-2 virus in wastewater could identify COVID-19 cases, which reduces the burden on the public health system during COVID-19 pandemics.Peer reviewe