Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19
Introduction: The coronavirus disease 2019 (COVID-19) wave has fluctuated erratically around the globe over the past three years of the pandemic, sometimes declining and at other times surging. The cases of infection in India have remained low, despite the continued surge of Omicron sub-lineages re...
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The Journal of Infection in Developing Countries
2023-04-01
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| Series: | Journal of Infection in Developing Countries |
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| Online Access: | https://jidc.org/index.php/journal/article/view/17628 |
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| author | Suresh Kumar Sahdev Choudhary Sharad Thakur Arbind Kumar Sanjay Kumar |
| author_facet | Suresh Kumar Sahdev Choudhary Sharad Thakur Arbind Kumar Sanjay Kumar |
| author_sort | Suresh Kumar |
| collection | DOAJ |
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Introduction: The coronavirus disease 2019 (COVID-19) wave has fluctuated erratically around the globe over the past three years of the pandemic, sometimes declining and at other times surging. The cases of infection in India have remained low, despite the continued surge of Omicron sub-lineages reported in a few countries. In this study, we determined the presence of the circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains in the population of Kangra District, Himachal Pradesh, India.
Methodology: In vitro diagnostic real-time reverse transcriptase polymerase chain reaction (RT-qPCR) was performed using Tata MD CHECK RT-PCR Omisure kit (Tata Medical and Diagnostics Limited, Maharashtra, India), to detect the presence of Omicron in target samples. A total of 400 samples were analyzed in this study; 200 each for the second and third waves, respectively. The S gene target failure (SG-TF) and S gene mutation amplification (SG-MA) primer-probe sets were used.
Results: Our results corroborated that during the third wave, SG-MA amplification was noted, while amplification of SG-TF was not, and vice versa in the case of the second wave, indicating that all the tested patients were infected with the Omicron variant during the third wave, while Omicron was absent during the second wave.
Conclusions: This study added more information about the prevalence of Omicron variants during the third wave in the chosen area, and it projected a use of in vitro RT-qPCR method for rapid prospective determination of the prevalence of the variant of concern (VOC) in developing countries with limited sequencing facility.
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| format | Article |
| id | doaj-art-129cbd4ab485402ebe4e4c2f1a873ea8 |
| institution | Kabale University |
| issn | 1972-2680 |
| language | English |
| publishDate | 2023-04-01 |
| publisher | The Journal of Infection in Developing Countries |
| record_format | Article |
| series | Journal of Infection in Developing Countries |
| spelling | doaj-art-129cbd4ab485402ebe4e4c2f1a873ea82025-08-20T03:48:47ZengThe Journal of Infection in Developing CountriesJournal of Infection in Developing Countries1972-26802023-04-01170410.3855/jidc.17628Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19Suresh Kumar0Sahdev Choudhary1Sharad Thakur2Arbind Kumar3Sanjay Kumar4COVID-19 Testing Facility, D & NT Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, IndiaCOVID-19 Testing Facility, D & NT Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, IndiaCOVID-19 Testing Facility, D & NT Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, IndiaCOVID-19 Testing Facility, D & NT Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, IndiaCSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India Introduction: The coronavirus disease 2019 (COVID-19) wave has fluctuated erratically around the globe over the past three years of the pandemic, sometimes declining and at other times surging. The cases of infection in India have remained low, despite the continued surge of Omicron sub-lineages reported in a few countries. In this study, we determined the presence of the circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains in the population of Kangra District, Himachal Pradesh, India. Methodology: In vitro diagnostic real-time reverse transcriptase polymerase chain reaction (RT-qPCR) was performed using Tata MD CHECK RT-PCR Omisure kit (Tata Medical and Diagnostics Limited, Maharashtra, India), to detect the presence of Omicron in target samples. A total of 400 samples were analyzed in this study; 200 each for the second and third waves, respectively. The S gene target failure (SG-TF) and S gene mutation amplification (SG-MA) primer-probe sets were used. Results: Our results corroborated that during the third wave, SG-MA amplification was noted, while amplification of SG-TF was not, and vice versa in the case of the second wave, indicating that all the tested patients were infected with the Omicron variant during the third wave, while Omicron was absent during the second wave. Conclusions: This study added more information about the prevalence of Omicron variants during the third wave in the chosen area, and it projected a use of in vitro RT-qPCR method for rapid prospective determination of the prevalence of the variant of concern (VOC) in developing countries with limited sequencing facility. https://jidc.org/index.php/journal/article/view/17628COVID-19SARS-CoV-2Omicronreal RT-PCRthird wave |
| spellingShingle | Suresh Kumar Sahdev Choudhary Sharad Thakur Arbind Kumar Sanjay Kumar Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19 Journal of Infection in Developing Countries COVID-19 SARS-CoV-2 Omicron real RT-PCR third wave |
| title | Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19 |
| title_full | Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19 |
| title_fullStr | Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19 |
| title_full_unstemmed | Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19 |
| title_short | Surveillance of omicron variant in Kangra District of Himachal Pradesh, India during the 3rd disease wave of COVID-19 |
| title_sort | surveillance of omicron variant in kangra district of himachal pradesh india during the 3rd disease wave of covid 19 |
| topic | COVID-19 SARS-CoV-2 Omicron real RT-PCR third wave |
| url | https://jidc.org/index.php/journal/article/view/17628 |
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