A longitudinal survey for genome-based identification of SARS-CoV-2 in sewage water in selected lockdown areas of Lahore city, Pakistan; a potential approach for future smart lockdown strategy

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has affected more than 15 million people and, as of 22 July 2019, caused deaths of more than 0.6 million individuals globally. With the excretion of SARS-CoV-2 in the stool of symptomatic and asymptomatic COVID-19 patients, its genome detection in the sewage water can be used as a powerful epidemiological tool to predict the number of positive cases in a population. This study was conducted to detect SARS-CoV-2 genome in sewage water during the lockdown. Sewage samples, from 28 pre-selected sites, were collected on alternate days from 13-25 July, 2020 from two selected areas [Johar Town (n = 05) and Township (n = 23)], where smart lockdown were implemented by the government authorities on 9th July, 2020. Genomic RNA was extracted and the SARS-CoV-2 was detected and quantified using commercially available kit through Real-Time PCR. Out of 28, sixteen samples were positive on day one while 19, 17, 23, 17, 05 and 09 samples were positive on day 3, 5, 7, 9, 11, and 13, respectively. These results indicate the decreasing viral copy load with the passage of time however few sites did not followed a clear pattern indicating the complexities in sewage water based surveillance i.e time of sampling. Hourly sampling from two sites for 24 hours also revealed the impact of time sampling time on detection of SARS-CoV-2 genome in sewage pipelines and lift/disposal stations. Results of current study indicate a possible role of sewage-based COVID-19 surveillance in monitoring and execution of smart lockdowns.

Occurrence of various viruses and recent evidence of SARS-CoV-2 in wastewater systems

“…From March 20 to April 9, 2020, among samples collected from various locations in 17 districts, 21/78 (26.9%) were positive ( Sharif ), and Lahore samples were collected on alternate days between July 13 to 25, 2020. We found that 22/28 (78.6%) of the positive samples ( Yaqub et al, 2020 ) from Wuhan Pulmonary Hospital, China, were collected after the initial identification of 2019-NCoV. Moreover, 4/15 (26.7%) ( Zhang et al, 2020 ) samples collected from Zhongnan Hospital of Wuhan University from January 20 to February 9, 2020, were positive.…”

“…SARS-CoV2 quantitative analysis done by RT-qPCR Filtration & PEG centrifugation ORF1ab Total of 78 untreated wastewater samples analysed 21/78 (26.9%) samples detected positive NA ( $author1$ et al, 18] </id><AuthGrp><Author><in>S.</in><dl> </dl><au>Sharif</au></Author></AuthGrp> ) Various locations Pakistan Lahore Viral RNA genome recovered from concentrated wastewater samples using BSL-3 of IM, UVAS. SARS-CoV2 quantitative analysis done by RT-qPCR Centrifugation (4 °C for 15 minutes) ORF1ab Total of 28 untreated wastewater samples analysed 22/28 (78.6%) samples detected positive 2.67 × 10 2 to 3.60 × 10 4 ( Yaqub et al, 2020 ) ChinaWuhan SARS-CoV2 quantitative analysis done by RT-qPCR NA NA Total of 42 untreated stool samples analysed 28/42 (66.67%) samples detected positive NA ( Chen et al, 2020 ) China SARS-CoV2 quantitative analysis done by RT-qPCR Centrifugation (56 °C for 30 minutes inactivation) ORF1ab Total of 15 untreated stool samples analysed 4/15 (26.7%) samples detected positive 0.05 to 1.87 × 10 5 ( Zhang et al, 2020 ) Wuhan Not Detected = (ND); Not Available = (NA). …”

“…SARS-CoV-2 RNA is shed in body fluids, such as faeces, saliva, and sputum, and these fluids are often disposed of via wastewater systems ( Holshue et al, 2020 , Mallapaty, 2020 ). To date, studies have identified SARS-CoV-2 in the wastewater systems of different countries, including Australia ( Ahmed et al, 2020 ), France ( Wurtzer et al, 2020 ), Italy ( La Rosa et al, 2020 ), the Netherlands ( Medema et al, 2020 ), Spain ( Randazzo et al, 2020 ), the Czech Republic ( Mlejnkova et al, 2020 ), Japan ( Haramoto et al, 2020 ), Turkey ( Kocamemi et al, 2020 ), Israel ( Or et al, 2020 ), India ( Kumar et al, 2020 ), Pakistan, ( Sharif, , Yaqub et al, 2020 ), China ( Chen et al, 2020 , Zhang et al, 2020 ) and the USA ( Wu et al, 2020 ). Based on these studies, clear evidence of the presence of SARS-CoV-2 in sewage is available, and this transmission pathway increases the risk of human exposure to the virus.…”

Preparing for COVID-2x: Urban Planning Needs to Regard Urological Wastewater as an Invaluable Communal Public Health Asset and Not as a Burden

“…This changed dramatically in February 2020 when COVID-19 had been declared a pandemic. Since then, the sewage testing for fragments of the SARS-CoV-2 has been successfully deployed and proven in value as an early detection tool and employed by public health authorities throughout Europe including Belgium [64], England [65], France [66], Germany [67], Hungary [68], Italy [69], the Netherlands [70], Russia [71], Spain [72,73], Switzerland [74], and Turkey [75,76], The same technique was also employed in other parts of the globe such as Hong Kong [77], Israel [78,79], India [80], Pakistan [81], Saudi Arabia [82], Brazil [83,84], Chile [85], Mexico [86], the USA [87,88] and Australia [89,90].…”

A novel RdRp-based colorimetric RT-LAMP assay for rapid and sensitive detection of SARS-CoV-2 in clinical and sewage samples from Pakistan

“…The said study has a major limitation that it relies on conventional Real-time reverse transcriptase (rRT-PCR) method. Moreover, the authors have tested sewage water from only a single source ( Yaqub et al, 2020 ).…”