Tracking Sars-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings
Bibliographic Data
| ID | 19592974 |
|---|---|
| Authors | Asghar Nasir (Aga Khan University, corresponding author), Uzma Bashir Aamir (World Health Organization - Pakistan, corresponding author), Akbar Kanji (0000-0003-1862-3102, Aga Khan University, corresponding author), Ali Raza Bukhari (0000-0001-7878-8959, Aga Khan University, corresponding author), Zeeshan Ansar (Aga Khan University, corresponding author), Najia Karim Ghanchi (Aga Khan University, corresponding author), Kiran Iqbal Masood (0000-0002-5391-2834, Aga Khan University, corresponding author), Azra Samreen (Aga Khan University, corresponding author), Nazneen Islam, Nazneen Naher Islam (Aga Khan University, corresponding author), Samina Ghani (Aga Khan University, corresponding author), M Asif Syed (Government of Pakistan, corresponding author), Mansoor Wassan (Government of Pakistan, corresponding author), Syed Faisal Mahmood (0000-0002-3390-7659, Aga Khan University, corresponding author), Zahra Hasan (0000-0001-7580-372X, Aga Khan University, corresponding author) |
| Editors | Vijaykrishna Dhanasekaran |
| Year | 2023 |
| Volume | 3 |
| Issue | 6 |
| Pages | e0001896 |
| Publication date | 2023-06-01 |
| Open Access | Yes |
| Type | ARTICLE |
| Venue | PLOS Global Public Health (JOURNAL) |
| Journal identifiers | ISSN: 2767-3375 • E-ISSN: 2767-3375 |
| Publisher | Public Library of Science (PLoS) (PUBLISHER) |
| DOI | 10.1371/journal.pgph.0001896 |
| PMID | 37262051 |
| OpenAlex | W4379057078 |
| Language | EN |
| Citations received | 2 |
| References cited | 17 |
COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p
2019-20 coronavirus outbreak · Biology · Delta · Disease · Gene · Mutation · Outbreak · Pandemic · Medicine · SARS-CoV-2 and COVID-19 Research · SARS-CoV-2 detection and testing · Viral Infections and Outbreaks Research · Genetics · Internal Medicine · Virology
| Citations per year | 1 |
|---|---|
| Citation span | 2024 - 2025 (2) |
| Highly cited | No |