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Comparative Study
. 2024 Mar 29;16(4):534.
doi: 10.3390/v16040534.

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

Supaporn Wacharapluesadee  1   2 , Nattakarn Thippamom  1 , Piyapha Hirunpatrawong  1   2 , Khwankamon Rattanatumhi  1 , Spencer L Sterling  2   3 , Wiparat Khunnawutmanotham  1 , Kirana Noradechanon  4 , Patarapol Maneeorn  4 , Rome Buathong  5 , Leilani Paitoonpong  1   6 , Opass Putcharoen  1   6
Affiliations
Comparative Study

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

Supaporn Wacharapluesadee et al. Viruses. .

Abstract

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.

Keywords: PCR; coronaviruses; pan-CoV PCR; reservoir host; surveillance.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The primer alignment with 70 CoV sequences represents all four genera of CoVs. (A,B) The target regions of W-CoV PCR and X-CoV PCR were at position 14,370–14,750 and 14,255–14,927, respectively (aligned to HCoV-229E, accession No. NC_002645.1). (C,D) The target regions of Q-CoV PCR were at position 17,480–17,820. The figures were created using Geneious Prime® 2024.0.2 (Auckland, New Zealand).
Figure 2
Figure 2
Capillary electrophoresis results of PCR products using the QIAxcel system. From three pan-CoV PCR protocols using QIAxcel. M: the QIAxcel size marker, 15–5000 bp; Lanes 1–4: the assay was performed using Q-CoV PCR and positive samples were alphacoronavirus from bat rectal swab, Pigeon-dominant Coronavirus from pigeon oral swab, HCoV-229E from human nasopharyngeal swab, and SARS-CoV-2 from wastewater sample, respectively. Lanes 5–8: the assay was performed using W-CoV PCR and positive samples were alphacoronavirus from bat, Anser fabalis coronavirus NCN2 from duck rectal swab, HCoV-229E from human nasopharyngeal swab, and HCoV-OC43 from wastewater sample, respectively. Lanes 9–12: the assay was performed using X-CoV PCR and positive samples were alphacoronavirus from bat, gammacoronavirus from Little Egret, HCoV-229E from human nasopharyngeal swab, and HCoV-229E from wastewater sample, respectively. NC = Negative control. PC = Positive control.
Figure 3
Figure 3
The chromatogram of the positive PCR product amplified using (A) W-CoV PCR, (B) X-CoV PCR, (C) Q-CoV PCR, and (D) X-CoV PCR for bat alphacoronavirus, SARS-CoV-2, pigeon-dominant coronavirus, and deltacoronavirus, respectively. The specimen source is in parentheses.
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