SARS-CoV-2 Variants Detection Strategies in Wastewater Samples Collected in the Bangkok Metropolitan Region

Tangwangvivat, Ratanaporn; Wacharapluesadee, Supaporn; Pinyopornpanish, Papassorn; Petcharat, Sininat; Hearn, Suthida Muangnoicharoen; Thippamom, Nattakarn; Phiancharoen, Chadaporn; Hirunpatrawong, Piyapha; Duangkaewkart, Phattra; Supataragul, Ananporn; Chaiden, Chadaporn; Wechsirisan, Wiriyachayon; Wandee, Nantaporn; Srimuang, Krongkan; Paitoonpong, Leilani; Buathong, Rome; Klungthong, Chonticha; Pawun, Vichan; Hinjoy, Soawapak; Putcharoen, Opass; Iamsirithaworn, Sopon

doi:10.3390/v15040876

Cited by 4 publications

(4 citation statements)

References 31 publications

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“…Successful detection and discrimination of all six Omicron subvariants in a single assay was a challenge that limited previous studies. − Our Omicron triplex assay is advantageous because, by utilizing three target mutations, all six Omicron subvariants (BA.1/BA.3, BA.2/XBB, and BA.4/BA.5) can be discriminated. Additionally, our triplex assay only requires a commonly available PCR instrument, uses fewer reagents, and is more versatile and cost-effective.…”

Section: Resultsmentioning

confidence: 99%

“…Using combinations of the HV 69–70 deletion, N501Y, and T478K targets to detect Omicron can broaden the range of Omicron subvariants detected, but this assay is not capable of differentiating BA.1 from BA.4/5 . Additionally, targeting two mutations in the N gene and the two mutations E484A and S477N in the S gene can detect all Omicron subvariants, but these assays cannot differentiate among all the subvariants, because these mutations are shared by all the Omicron subvariants. , …”

Section: Resultsmentioning

confidence: 99%

“… 29 Additionally, targeting two mutations in the N gene and the two mutations E484A and S477N in the S gene can detect all Omicron subvariants, but these assays cannot differentiate among all the subvariants, because these mutations are shared by all the Omicron subvariants. 30 , 31 …”

Section: Resultsmentioning

confidence: 99%

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Quantification and Differentiation of SARS-CoV-2 Variants in Wastewater for Surveillance

et al. 2023

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Wastewater surveillance plays an important role in the monitoring of infections of SARS-CoV-2 at the community level. We report here the determination of SARS-CoV-2 and differentiation of its variants of concern in 294 wastewater samples collected from two major Canadian cities from May 2021 to March 2023. The overall method of analysis involved extraction of the virus and viral components using electronegative membranes, in situ stabilization and concentration of the viral RNA onto magnetic beads, and direct analysis of the viral RNA on the magnetic beads. Multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays, targeting specific and naturally selected mutations in SARS-CoV-2, enabled detection and differentiation of the Alpha, Beta, Gamma, Delta, and Omicron variants. An Omicron triplex RT-qPCR assay targeting three mutations, HV 69−70 deletion, K417N, and L452R, was able to detect and differentiate the Omicron BA.1/BA.3, BA.2/XBB, and BA.4/5. This assay had efficiencies of 90−104% for all three mutation targets and a limit of detection of 28 RNA copies per reaction. Analyses of 294 wastewater samples collected over a two-year span showed the concentrations and trends of Alpha, Beta, Gamma, Delta, and Omicron variants as they emerge in two major Canadian cities participating in the wastewater surveillance program. The trends of specific variants were consistent with clinical reports for the same period. At the beginning of each wave, the corresponding variants were detectable in wastewater. For example, RNA concentrations of the BA.2 variant were as high as 10 4 copies per 100 mL of wastewater collected in January 2022, when approximately only 50−60 clinical cases of BA.2 infection were reported in Canada. These results show that the strategy and highly sensitive assays for the variants of concern in wastewater are potentially useful for the detection of newly emerging SARS-CoV-2 variants and other viruses for future community biomonitoring.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Quantification and Differentiation of SARS-CoV-2 Variants in Wastewater for Surveillance

et al. 2023

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“…Viral RNA from nasopharyngeal swabs from humans, as well as rectal and oral swabs from bats and birds, was extracted with the MagPurix ® Viral RNA Extraction Kit (Zinexts Life Science Corp., New Taipei, Taiwan). Viral RNA from wastewater samples was extracted with the ZR Urine RNA Isolation Kit™ (Zymo Research, Murphy Ave, Irvine, CA, USA), as previously published [ 30 ]. Briefly, 40 mL of wastewater was transferred to a fresh 50 mL centrifuge tube containing glass beads (HiMedia, Kennett Square, PA, USA) and was homogenized using a sample disruption instrument (FastPrep-24TM 5G, MP Biomedicals, Irvine, CA, USA) for 60 s at 6 m/s.…”

Section: Methodsmentioning

confidence: 99%

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Wacharapluesadee,

Thippamom,

Hirunpatrawong

et al. 2024

Viruses

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Emerging coronaviruses (CoVs) are understood to cause critical human and domestic animal diseases; the spillover from wildlife reservoirs can result in mild and severe respiratory illness in humans and domestic animals and can spread more readily in these naïve hosts. A low-cost CoV molecular method that can detect a variety of CoVs from humans, animals, and environmental specimens is an initial step to ensure the early identification of known and new viruses. We examine a collection of 50 human, 46 wastewater, 28 bat, and 17 avian archived specimens using 3 published pan-CoV PCR assays called Q-, W-, and X-CoV PCR, to compare the performance of each assay against four CoV genera. X-CoV PCR can detect all four CoV genera, but Q- and W-CoV PCR failed to detect δ-CoV. In total, 21 (42.0%), 9 (18.0%), and 21 (42.0%) of 50 human specimens and 30 (65.22%), 6 (13.04%), and 27 (58.70%) of 46 wastewater specimens were detected using Q-, W-, and X-CoV PCR assays, respectively. The X-CoV PCR assay has a comparable sensitivity to Q-CoV PCR in bat CoV detection. Combining Q- and X-CoV PCR assays can increase sensitivity and avoid false negative results in the early detection of novel CoVs.

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Co-occurrence of SARS-CoV-2 variants in rivers and sewage in India and Brazil

Thompson,

Leal,

da Silva Faustino

et al. 2025

Science of The Total Environment

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SARS-CoV-2 Variants Detection Strategies in Wastewater Samples Collected in the Bangkok Metropolitan Region

Cited by 4 publications

References 31 publications

Quantification and Differentiation of SARS-CoV-2 Variants in Wastewater for Surveillance

Quantification and Differentiation of SARS-CoV-2 Variants in Wastewater for Surveillance

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Co-occurrence of SARS-CoV-2 variants in rivers and sewage in India and Brazil

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