SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron Coincident with Consecutive Pandemic Waves in Pakistan

Identification and monitoring of SARS-CoV-2 Variants of Concern/Interest (VOC/VOIs) can aid public health measures to reduce COVID-19. We report the surveillance of VOCs circulating in Karachi during the pandemic between April 2021 and February 2022. We screened 2150 SARS-CoV-2 PCR positive samples received at the AKUH Clinical Laboratories. VOC was identified using a PCR-based approach targeting lineage-specific mutations using commercially available assays. Of the SARS-CoV-2 PCR positive samples, 81.7% had VOC/VOI, while 18.3% were undetermined. Alpha variants were predominant at 82.5% and 40.3% of the cases in April and May 2021. Beta variants increased in May (29%) and June (42%) and then reduced to 6% by July. Gamma variant cases were at 14.5% and 9% in May and June, respectively. Delta variants first detected in May, increased to comprise 66% of all variants by July, remaining dominant in August, September, October, and November 2021 at 88%, 91%, 91% and 85% respectively. Omicron (BA.1) variants emerged in December, rising to 42% of cases with an increase to 81% by January 2022 and then reducing to 45% in February 2022. Delta variant prevalence was coincident with increased hospital admissions and mortality. The Omicron variant surge was associated with increased daily infections but limited COVID-19 severity. We successfully identified predominant VOCs during the COVID-19 waves using a targeted PCR based approach. We propose this to be a rapid, lower cost method to be used with genome based variant identification especially in low-resource settings to inform a public health response.

Note:
Funding Information: This work received support through a University Research Council Grant, Aga Khan University, Pakistan, Higher Education Commission Pakistan, Rapid Research Grant-236 and the World Health Organization, Pakistan.

Conflict of Interests: The authors have no conflicts of interest to declare.

Ethical Approval: This study received approval from the Ethical Review Committee, The Aga Khan University (AKU).

Keywords: SARS-CoV-2, VOC, Surveillance, Pakistan

Suggested Citation: Suggested Citation

Nasir, Asghar and Bashir Aamir, Uzma and Kanji, Akbar and Samreen, Azra and Ansar, Zeeshan and Ghanchi, Najia and Raza Bukhari, Ali and Masood, Kiran Iqbal and Islam, Nazneen and Ghani, Samina and Syed, Technical Support officer Asi and Wassan, Mansoor and Mahmood, Syed Faisal and Hasan, Zahra, SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron Coincident with Consecutive Pandemic Waves in Pakistan. Available at SSRN: https://ssrn.com/abstract=4109998