Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples
Background: Respiratory droplets are the main way in which the COVID-19 pandemic’s causal agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), spreads. Angiotensin-converting enzyme 2 (ACE2) receptors, especially in lung cells, allow the virus to enter host cells. However, ACE2 expre...
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2025-05-01
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| author | Vrushali D. Patil Rashmi Chowdhary Anvita Gupta Malhotra Jitendra Singh Debasis Biswas Rajnish Joshi Jagat Rakesh Kanwar |
| author_facet | Vrushali D. Patil Rashmi Chowdhary Anvita Gupta Malhotra Jitendra Singh Debasis Biswas Rajnish Joshi Jagat Rakesh Kanwar |
| author_sort | Vrushali D. Patil |
| collection | DOAJ |
| description | Background: Respiratory droplets are the main way in which the COVID-19 pandemic’s causal agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), spreads. Angiotensin-converting enzyme 2 (ACE2) receptors, especially in lung cells, allow the virus to enter host cells. However, ACE2 expression in intestinal cells has sparked worries about possible fecal transfer, particularly in poor-sanitation areas like India. Methods: Between July 2021 and July 2024, clinical (nasopharyngeal, saliva, and stool samples) and sewage samples were collected from outpatient departments and sewage treatment plants (STPs), respectively, from the high-population-density area under study in order to investigate SARS-CoV-2 transmission. Results: This proof-of-concept study analyzed clinical samples from <i>n</i> = 60 COVID-19-positive patients at a central Indian tertiary care hospital and <i>n</i> = 156 samples from hospital STPs. Variants of SARS-CoV-2 were found using qRT-PCR and Next-Generation Sequencing (NGS). Of the <i>n</i> = 37 qRT-PCR-positive patients who gave their assent, 30% had stool samples that tested positive for viral RNA. In 70% of positive NP and 65% of positive saliva samples, along with two stool samples from immunocompromised patients, the live virus was identified using Vero E6 cell lines. Although 18% of the tests reported qRT-PCR-positive results, no live virus was detected in sewage samples despite NGS validation. The detection of SARS-CoV-2 in the absence of confirmed clinical cases may indicate the silent circulation of the virus within the community, suggesting that sewage surveillance can serve as an early warning system before an outbreak occurs. Conclusions: These findings provide critical insights into the importance of continuous environmental surveillance, silent virus circulation, changes in viral epidemiology throughout the years, and strategies to mitigate coronavirus outbreaks. |
| format | Article |
| id | doaj-art-d095ddaade8944a5bf1385c58f027df4 |
| institution | DOAJ |
| issn | 1999-4915 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj-art-d095ddaade8944a5bf1385c58f027df42025-08-20T03:12:09ZengMDPI AGViruses1999-49152025-05-0117572610.3390/v17050726Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental SamplesVrushali D. Patil0Rashmi Chowdhary1Anvita Gupta Malhotra2Jitendra Singh3Debasis Biswas4Rajnish Joshi5Jagat Rakesh Kanwar6Department of Biochemistry, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Biochemistry, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Translation Medicine, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Translation Medicine, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of General Medicine, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Biochemistry, All India Institute of Medical Sciences, Bhopal 462020, IndiaBackground: Respiratory droplets are the main way in which the COVID-19 pandemic’s causal agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), spreads. Angiotensin-converting enzyme 2 (ACE2) receptors, especially in lung cells, allow the virus to enter host cells. However, ACE2 expression in intestinal cells has sparked worries about possible fecal transfer, particularly in poor-sanitation areas like India. Methods: Between July 2021 and July 2024, clinical (nasopharyngeal, saliva, and stool samples) and sewage samples were collected from outpatient departments and sewage treatment plants (STPs), respectively, from the high-population-density area under study in order to investigate SARS-CoV-2 transmission. Results: This proof-of-concept study analyzed clinical samples from <i>n</i> = 60 COVID-19-positive patients at a central Indian tertiary care hospital and <i>n</i> = 156 samples from hospital STPs. Variants of SARS-CoV-2 were found using qRT-PCR and Next-Generation Sequencing (NGS). Of the <i>n</i> = 37 qRT-PCR-positive patients who gave their assent, 30% had stool samples that tested positive for viral RNA. In 70% of positive NP and 65% of positive saliva samples, along with two stool samples from immunocompromised patients, the live virus was identified using Vero E6 cell lines. Although 18% of the tests reported qRT-PCR-positive results, no live virus was detected in sewage samples despite NGS validation. The detection of SARS-CoV-2 in the absence of confirmed clinical cases may indicate the silent circulation of the virus within the community, suggesting that sewage surveillance can serve as an early warning system before an outbreak occurs. Conclusions: These findings provide critical insights into the importance of continuous environmental surveillance, silent virus circulation, changes in viral epidemiology throughout the years, and strategies to mitigate coronavirus outbreaks.https://www.mdpi.com/1999-4915/17/5/726coronavirusenvironmental surveillancenext-generation sequencingoutbreak preventionsilent circulationimmunocompromised patients |
| spellingShingle | Vrushali D. Patil Rashmi Chowdhary Anvita Gupta Malhotra Jitendra Singh Debasis Biswas Rajnish Joshi Jagat Rakesh Kanwar Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples Viruses coronavirus environmental surveillance next-generation sequencing outbreak prevention silent circulation immunocompromised patients |
| title | Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples |
| title_full | Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples |
| title_fullStr | Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples |
| title_full_unstemmed | Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples |
| title_short | Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples |
| title_sort | uncovering sars cov 2 molecular epidemiology across the pandemic transition insights into transmission in clinical and environmental samples |
| topic | coronavirus environmental surveillance next-generation sequencing outbreak prevention silent circulation immunocompromised patients |
| url | https://www.mdpi.com/1999-4915/17/5/726 |
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