tetano
Editor, Senior Moderator
Bull Exp Biol Med
. 2022 Jun 23.
doi: 10.1007/s10517-022-05524-0. Online ahead of print.
Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
M L Filipenko[SUP] 1 [/SUP], I P Oskorbin[SUP] 2 [/SUP], D V Shamovskaya[SUP] 2 [/SUP], E A Kharpov[SUP] 2 [/SUP], A A Stepanov[SUP] 2 [/SUP], V V Romanov[SUP] 3 [/SUP], V V Kuznetsov[SUP] 3 [/SUP], U A Boyarskikh[SUP] 2 [/SUP], A A Kechin[SUP] 2 [/SUP], E V Pechkovsky[SUP] 4 [/SUP], A B Krivoruchko[SUP] 5 [/SUP], A M Ivanov[SUP] 5 [/SUP], N E Kushlinskii[SUP] 6 [/SUP], V V Vlasov[SUP] 2 [/SUP]
Affiliations
Abstract
We developed a new test system to detect the omicron variant of SARS-CoV-2 using allele-specific reverse transcription PCR and estimated the frequency of its detection in patients living in the Novosibirsk Region. Clinical samples were divided into 3 groups: samples collected from December 1 to December 30, 2021 (group 1; n=66), from December 30, 2021 to January 10, 2022 (group 2; n=20), and from January 11 to January 22, 2022 (group 3; n=101). Based on the identification of 5 mutations specific to SARS-CoV-2 (B.1.1.529), two systems of oligonucleotide primers and probes were developed for detecting this coronavirus genotype in clinical samples. Limit of detection (LOD[SUB]95[/SUB]) was 4×10[SUP]3[/SUP] genome equivalents per 1 ml of clinical sample for the first test system and 2×10[SUP]3[/SUP] for the for the second test system. The omicron variant of SARS-CoV-2 was absent in group 1 of studied samples, but was detected in 20% (4/20) of group 2 samples and 88% of group 2 samples collected within less than 2 weeks of January 2022. Using developed test system, we showed that in less than 2 weeks the omicron variant has become dominant in patients, which confirms previously published data on its exceptional contagiousness.
Keywords: SARS-CoV 2; allele-specific reverse transcription PCR (AS-RT-PCR); coronavirus; mutations; omicron variant.
. 2022 Jun 23.
doi: 10.1007/s10517-022-05524-0. Online ahead of print.
Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
M L Filipenko[SUP] 1 [/SUP], I P Oskorbin[SUP] 2 [/SUP], D V Shamovskaya[SUP] 2 [/SUP], E A Kharpov[SUP] 2 [/SUP], A A Stepanov[SUP] 2 [/SUP], V V Romanov[SUP] 3 [/SUP], V V Kuznetsov[SUP] 3 [/SUP], U A Boyarskikh[SUP] 2 [/SUP], A A Kechin[SUP] 2 [/SUP], E V Pechkovsky[SUP] 4 [/SUP], A B Krivoruchko[SUP] 5 [/SUP], A M Ivanov[SUP] 5 [/SUP], N E Kushlinskii[SUP] 6 [/SUP], V V Vlasov[SUP] 2 [/SUP]
Affiliations
- PMID: 35737161
- DOI: 10.1007/s10517-022-05524-0
Abstract
We developed a new test system to detect the omicron variant of SARS-CoV-2 using allele-specific reverse transcription PCR and estimated the frequency of its detection in patients living in the Novosibirsk Region. Clinical samples were divided into 3 groups: samples collected from December 1 to December 30, 2021 (group 1; n=66), from December 30, 2021 to January 10, 2022 (group 2; n=20), and from January 11 to January 22, 2022 (group 3; n=101). Based on the identification of 5 mutations specific to SARS-CoV-2 (B.1.1.529), two systems of oligonucleotide primers and probes were developed for detecting this coronavirus genotype in clinical samples. Limit of detection (LOD[SUB]95[/SUB]) was 4×10[SUP]3[/SUP] genome equivalents per 1 ml of clinical sample for the first test system and 2×10[SUP]3[/SUP] for the for the second test system. The omicron variant of SARS-CoV-2 was absent in group 1 of studied samples, but was detected in 20% (4/20) of group 2 samples and 88% of group 2 samples collected within less than 2 weeks of January 2022. Using developed test system, we showed that in less than 2 weeks the omicron variant has become dominant in patients, which confirms previously published data on its exceptional contagiousness.
Keywords: SARS-CoV 2; allele-specific reverse transcription PCR (AS-RT-PCR); coronavirus; mutations; omicron variant.