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Virol Sin
. 2024 Feb 3:S1995-820X(24)00010-5.
doi: 10.1016/j.virs.2024.01.010. Online ahead of print. Quantitative and qualitative subgenomic RNA profiles of SARS-CoV-2 in respiratory samples: a comparison between Omicron BA.2 and non-VOC-D614G
Zigui Chen 1 , Rita Way Yin Ng 1 , Grace Lui 2 , Lowell Ling 3 , Agnes Sy Leung 4 , Chit Chow 5 , Siaw Shi Boon 1 , Wendy Cs Ho 1 , Maggie Haitian Wang 6 , Renee Wan Yi Chan 4 , Albert Martin Li 4 , David Shu Cheong Hui 7 , Paul Kay Sheung Chan 8
Affiliations
The SARS-CoV-2 Omicron variants are notorious for their transmissibility, but little is known about their subgenomic RNA (sgRNA) expression. This study applied RNA-seq to delineate the quantitative and qualitative profiles of canonical sgRNA of 118 respiratory samples collected from patients infected with Omicron BA.2 and compared with 338 patients infected with non-variant of concern (non-VOC)-D614G. A unique characteristic profile depicted by the relative abundance of 9 canonical sgRNAs was reproduced by both BA.2 and non-VOC-D614G regardless of host gender, age and presence of pneumonia. Remarkably, such profile was lost in samples with low viral load, suggesting a potential application of sgRNA pattern to indicate viral activity of individual patient at a specific time point. A characteristic qualitative profile of canonical sgRNAs was also reproduced by both BA.2 and non-VOC-D614G. The presence of a full set of canonical sgRNAs carried a coherent correlation with crude viral load (AUC = 0.91, 95% CI 0.88-0.94), and sgRNA ORF7b was identified to be the best surrogate marker allowing feasible routine application in characterizing the infection status of individual patient. Further potentials in using sgRNA as a target for vaccine and antiviral development are worth pursuing.
Keywords: Coronavirus; Non-VOC-D614G; Omicron BA.2; RNA-seq; SARS-CoV-2; Subgenomic.
. 2024 Feb 3:S1995-820X(24)00010-5.
doi: 10.1016/j.virs.2024.01.010. Online ahead of print. Quantitative and qualitative subgenomic RNA profiles of SARS-CoV-2 in respiratory samples: a comparison between Omicron BA.2 and non-VOC-D614G
Zigui Chen 1 , Rita Way Yin Ng 1 , Grace Lui 2 , Lowell Ling 3 , Agnes Sy Leung 4 , Chit Chow 5 , Siaw Shi Boon 1 , Wendy Cs Ho 1 , Maggie Haitian Wang 6 , Renee Wan Yi Chan 4 , Albert Martin Li 4 , David Shu Cheong Hui 7 , Paul Kay Sheung Chan 8
Affiliations
- PMID: 38316363
- DOI: 10.1016/j.virs.2024.01.010
The SARS-CoV-2 Omicron variants are notorious for their transmissibility, but little is known about their subgenomic RNA (sgRNA) expression. This study applied RNA-seq to delineate the quantitative and qualitative profiles of canonical sgRNA of 118 respiratory samples collected from patients infected with Omicron BA.2 and compared with 338 patients infected with non-variant of concern (non-VOC)-D614G. A unique characteristic profile depicted by the relative abundance of 9 canonical sgRNAs was reproduced by both BA.2 and non-VOC-D614G regardless of host gender, age and presence of pneumonia. Remarkably, such profile was lost in samples with low viral load, suggesting a potential application of sgRNA pattern to indicate viral activity of individual patient at a specific time point. A characteristic qualitative profile of canonical sgRNAs was also reproduced by both BA.2 and non-VOC-D614G. The presence of a full set of canonical sgRNAs carried a coherent correlation with crude viral load (AUC = 0.91, 95% CI 0.88-0.94), and sgRNA ORF7b was identified to be the best surrogate marker allowing feasible routine application in characterizing the infection status of individual patient. Further potentials in using sgRNA as a target for vaccine and antiviral development are worth pursuing.
Keywords: Coronavirus; Non-VOC-D614G; Omicron BA.2; RNA-seq; SARS-CoV-2; Subgenomic.