tetano
Editor, Senior Moderator
J Med Virol
. 2023 Jul;95(7):e28914.
doi: 10.1002/jmv.28914. Accelerating pandemic response with the emergency Omicron RT-PCR test: A comprehensive solution for COVID-19 diagnosis and tracking
Hsing-Yi Chung[SUP] 1 2 [/SUP], Ming-Jr Jian[SUP] 1 [/SUP], Chih-Kai Chang[SUP] 1 [/SUP], Jung-Chung Lin[SUP] 3 [/SUP], Kuo-Ming Yeh[SUP] 3 [/SUP], Chien-Wen Chen[SUP] 4 [/SUP], Shan-Shan Hsieh[SUP] 1 [/SUP], Kuo-Sheng Hung[SUP] 5 [/SUP], Chi-Sheng Chen[SUP] 1 [/SUP], Sheng-Hui Tang[SUP] 1 [/SUP], Cherng-Lih Perng[SUP] 1 [/SUP], Feng-Yee Chang[SUP] 3 [/SUP], Chih-Hung Wang[SUP] 6 [/SUP], Yi-Jen Hung[SUP] 7 [/SUP], Hung-Sheng Shang[SUP] 1 [/SUP]
Affiliations
The Omicron variant of concern (VOC) has surged in many countries and replaced the previously reported VOC. To identify different Omicron strains/sublineages on a rapid, convenient, and precise platform, we report a novel multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) method in one tube based on the Omicron lineage sequence variants' information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subvariants were used in a PCR-based assay for rapid identification of Omicron sublineage genotyping in 1000 clinical samples. Several characteristic mutations were analyzed using specific primers and probes for the spike gene, del69-70, and F486V. To distinguish Omicron sublineages (BA.2, BA.4, and BA.5), the NSP1:141-143del in the ORF1a region and D3N mutation in membrane protein occurring outside the spike protein region were analyzed. Results from the real-time PCR assay for one-tube accuracy were compared to those of whole genome sequencing. The developed PCR assay was used to analyze 400 SARS-CoV-2 positive samples. Ten samples determined as BA.4 were positive for NSP1:141-143del, del69-70, and F486V mutations; 160 BA.5 samples were positive for D3N, del69-70, and F486V mutations, and 230 BA.2 samples were without del69-70. Screening these samples allowed the identification of epidemic trends at different time intervals. Our novel one-tube multiplex PCR assay was effective in identifying Omicron sublineages.
Keywords: BA.2; BA.4; BA.5; D3N; F486V; NSP1:141-143del; Omicron; SARS-CoV-2; del69-70; epidemiological surveillance; variant of concern genotyping.
. 2023 Jul;95(7):e28914.
doi: 10.1002/jmv.28914. Accelerating pandemic response with the emergency Omicron RT-PCR test: A comprehensive solution for COVID-19 diagnosis and tracking
Hsing-Yi Chung[SUP] 1 2 [/SUP], Ming-Jr Jian[SUP] 1 [/SUP], Chih-Kai Chang[SUP] 1 [/SUP], Jung-Chung Lin[SUP] 3 [/SUP], Kuo-Ming Yeh[SUP] 3 [/SUP], Chien-Wen Chen[SUP] 4 [/SUP], Shan-Shan Hsieh[SUP] 1 [/SUP], Kuo-Sheng Hung[SUP] 5 [/SUP], Chi-Sheng Chen[SUP] 1 [/SUP], Sheng-Hui Tang[SUP] 1 [/SUP], Cherng-Lih Perng[SUP] 1 [/SUP], Feng-Yee Chang[SUP] 3 [/SUP], Chih-Hung Wang[SUP] 6 [/SUP], Yi-Jen Hung[SUP] 7 [/SUP], Hung-Sheng Shang[SUP] 1 [/SUP]
Affiliations
- PMID: 37394776
- DOI: 10.1002/jmv.28914
The Omicron variant of concern (VOC) has surged in many countries and replaced the previously reported VOC. To identify different Omicron strains/sublineages on a rapid, convenient, and precise platform, we report a novel multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) method in one tube based on the Omicron lineage sequence variants' information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subvariants were used in a PCR-based assay for rapid identification of Omicron sublineage genotyping in 1000 clinical samples. Several characteristic mutations were analyzed using specific primers and probes for the spike gene, del69-70, and F486V. To distinguish Omicron sublineages (BA.2, BA.4, and BA.5), the NSP1:141-143del in the ORF1a region and D3N mutation in membrane protein occurring outside the spike protein region were analyzed. Results from the real-time PCR assay for one-tube accuracy were compared to those of whole genome sequencing. The developed PCR assay was used to analyze 400 SARS-CoV-2 positive samples. Ten samples determined as BA.4 were positive for NSP1:141-143del, del69-70, and F486V mutations; 160 BA.5 samples were positive for D3N, del69-70, and F486V mutations, and 230 BA.2 samples were without del69-70. Screening these samples allowed the identification of epidemic trends at different time intervals. Our novel one-tube multiplex PCR assay was effective in identifying Omicron sublineages.
Keywords: BA.2; BA.4; BA.5; D3N; F486V; NSP1:141-143del; Omicron; SARS-CoV-2; del69-70; epidemiological surveillance; variant of concern genotyping.