Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations
Novel SARS-CoV-2 variants have multiple mutations that may impact molecular diagnostics. The markedly conserved S2 subunit may be utilized to detect new variants. A comparison of 694 specimens (2019–2022) in Thailand using a commercial RT-PCR kit and the kit in combination with S2 primers and a prob...
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| Format: | Article |
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MDPI AG
2024-02-01
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| Series: | Tropical Medicine and Infectious Disease |
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| Online Access: | https://www.mdpi.com/2414-6366/9/2/50 |
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| author | Teerada Ponpinit Yutthana Joyjinda Weenassarin Ampoot Siriporn Yomrat Phatthamon Virojanapirom Chanida Ruchisrisarod Abhinbhen W. Saraya Pasin Hemachudha Thiravat Hemachudha |
| author_facet | Teerada Ponpinit Yutthana Joyjinda Weenassarin Ampoot Siriporn Yomrat Phatthamon Virojanapirom Chanida Ruchisrisarod Abhinbhen W. Saraya Pasin Hemachudha Thiravat Hemachudha |
| author_sort | Teerada Ponpinit |
| collection | DOAJ |
| description | Novel SARS-CoV-2 variants have multiple mutations that may impact molecular diagnostics. The markedly conserved S2 subunit may be utilized to detect new variants. A comparison of 694 specimens (2019–2022) in Thailand using a commercial RT-PCR kit and the kit in combination with S2 primers and a probe was performed. Delayed amplification in ORF1ab was detected in one BA.4 omicron, whereas no amplification problem was encountered in the S2 target. There were no statistically significant differences in mean Ct value between the target genes (E, N, ORF1ab, and S2) and no significant differences in mean Ct value between the reagents. Furthermore, 230,821 nucleotide sequences submitted by 20 representative counties in each region (Jan–Oct 2022) have been checked for mutations in S2 primers and probe using PrimerChecker; there is a very low chance of encountering performance problems. The S2 primers and probe are still bound to the top five currently circulating variants in all countries and Thailand without mismatch recognition (Jun–Nov 2023). This study shows the possible benefits of detecting S2 in combination with simultaneously detecting three genes in a kit without affecting the Ct value of each target. The S2 subunit may be a promising target for the detection of SARS-CoV-2 variants with multiple mutations. |
| first_indexed | 2024-03-07T22:11:11Z |
| format | Article |
| id | doaj.art-83f7b7287a8d4910bc37663a5d4cb27c |
| institution | Directory Open Access Journal |
| issn | 2414-6366 |
| language | English |
| last_indexed | 2024-03-07T22:11:11Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Tropical Medicine and Infectious Disease |
| spelling | doaj.art-83f7b7287a8d4910bc37663a5d4cb27c2024-02-23T15:36:42ZengMDPI AGTropical Medicine and Infectious Disease2414-63662024-02-01925010.3390/tropicalmed9020050Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple MutationsTeerada Ponpinit0Yutthana Joyjinda1Weenassarin Ampoot2Siriporn Yomrat3Phatthamon Virojanapirom4Chanida Ruchisrisarod5Abhinbhen W. Saraya6Pasin Hemachudha7Thiravat Hemachudha8Thai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandThai Red Cross Emerging Infectious Diseases Health Science Centre, King Chulalongkorn Memorial Hospital, Bangkok 10330, ThailandNovel SARS-CoV-2 variants have multiple mutations that may impact molecular diagnostics. The markedly conserved S2 subunit may be utilized to detect new variants. A comparison of 694 specimens (2019–2022) in Thailand using a commercial RT-PCR kit and the kit in combination with S2 primers and a probe was performed. Delayed amplification in ORF1ab was detected in one BA.4 omicron, whereas no amplification problem was encountered in the S2 target. There were no statistically significant differences in mean Ct value between the target genes (E, N, ORF1ab, and S2) and no significant differences in mean Ct value between the reagents. Furthermore, 230,821 nucleotide sequences submitted by 20 representative counties in each region (Jan–Oct 2022) have been checked for mutations in S2 primers and probe using PrimerChecker; there is a very low chance of encountering performance problems. The S2 primers and probe are still bound to the top five currently circulating variants in all countries and Thailand without mismatch recognition (Jun–Nov 2023). This study shows the possible benefits of detecting S2 in combination with simultaneously detecting three genes in a kit without affecting the Ct value of each target. The S2 subunit may be a promising target for the detection of SARS-CoV-2 variants with multiple mutations.https://www.mdpi.com/2414-6366/9/2/50SARS-CoV-2spike S2 subunitmultiple mutationsdetection |
| spellingShingle | Teerada Ponpinit Yutthana Joyjinda Weenassarin Ampoot Siriporn Yomrat Phatthamon Virojanapirom Chanida Ruchisrisarod Abhinbhen W. Saraya Pasin Hemachudha Thiravat Hemachudha Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations Tropical Medicine and Infectious Disease SARS-CoV-2 spike S2 subunit multiple mutations detection |
| title | Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations |
| title_full | Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations |
| title_fullStr | Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations |
| title_full_unstemmed | Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations |
| title_short | Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations |
| title_sort | spike s2 subunit possible target for detecting novel sars cov 2 variants with multiple mutations |
| topic | SARS-CoV-2 spike S2 subunit multiple mutations detection |
| url | https://www.mdpi.com/2414-6366/9/2/50 |
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