SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron coincident with consecutive pandemic waves in Pakistan

Abstract

Identification and monitoring of SARS-CoV-2 Variants of Concern/Interest (VOC/VOIs) is essential to guide public health measures. 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 highlight the predominance of the VOCs identified through a rapid PCR based approach. As this is important to inform a public health response, we propose that a mutation targeted approach can be a rapid, lower cost solution to aid tracking of known VOCs during pandemic waves.

Effectiveness of inactivated COVID-19 vaccines against SARS-CoV-2 infections among healthcare personnel in Pakistan: a test-negative, case-control study

“…During our study period, the predominant variants in Pakistan switched from alpha, beta and gamma in April to June (13,14) to the highly transmissible delta constituting up to 99% of the total genomes sequenced from July to September 2021 (22).…”

“…We report the effectiveness of BBIBP-CorV and CoronaVac vaccines against RT-PCR-confirmed COVID-19 infections among HCPs, four months into the vaccination drive at a large private healthcare system in Pakistan, with an existing robust employee surveillance system. Our study was conducted in the setting of the third and fourth waves of COVID-19 in Pakistan during which the alpha, beta, gamma, and delta variants were prevalent (13, 14).…”

The Burden of Omicron Variant in Pakistan: An Updated Review

“…However, the Omicron variation influx was linked to more frequent regular episodes but less severe COVID-19 ailments [20,30,31].…”

Two-Dose Vaccination Significantly Prolongs the Duration from Symptom Onset to Death: A Retrospective Study Based on 173,894 SARS-CoV-2 Cases in Khyber Pakhtunkhwa, Pakistan

“…The Alpha variant was first reported in Pakistan on 29 December 2020. It triggered a surge in cases in March 2021 [ 3 ] and dominated the total case numbers (82.5%) confirmed in April [ 4 ]. The Beta variant was first reported in the capital Islamabad around April 2021, and cases then rapidly increased in May and June [ 4 ].…”

“…It triggered a surge in cases in March 2021 [ 3 ] and dominated the total case numbers (82.5%) confirmed in April [ 4 ]. The Beta variant was first reported in the capital Islamabad around April 2021, and cases then rapidly increased in May and June [ 4 ]. On 3 May 2021, the Delta variant was also found [ 5 ].…”