Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings

Abstract

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<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.

SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction–based assays in Addis Ababa, Ethiopia

“…Therefore, real-time RT-PCR genotyping is being considered as a practical solution for identifying SARS-CoV-2 variants. It has become pivotal to track SARS-CoV-2 variants to ensure a rapid public health response because the finding of this study is in concordance with other similar studies [16] , [17] , [18] , [19] , [20] .…”

Exploring the relationship between SARS‐CoV‐2 variants, illness severity at presentation, in‐hospital mortality and COVID‐19 vaccination in a low middle‐income country: A retrospective cross‐sectional study

“…The correlation between COVID‐19 severity and SARS‐CoV‐2 variants has been a topic of significant discussion with limited information in the context of Pakistan. Our study was conducted through the pandemic waves in Pakistan characterized by ancestral followed by G clade, Alpha, and then Delta followed by Omicron variants 14,15 . We found a large proportion of patients were unvaccinated and nearly half the COVID‐19 admissions developed critical disease.…”

“…The CT (crossing threshold) value of each positive SARS‐CoV‐2 sample was noted. The cases chosen for review were those for whom SARS‐CoV‐2 VOC testing had been conducted as part of a WHO supported genomic surveillance effort 15 …”

“…Isolates were screened for VOC; Alpha, Beta, Gamma, Delta, and Omicron lineage associated mutations using a PCR‐based approach 15 …”

“…G, L, and S clade SARS‐CoV‐2 strains were shown to be present in the first wave of COVID‐19 in Pakistan between March and August 2020 14 . Alpha variants were identified in January 2021 and there was a shift in the predominance of VOC from Alpha to Delta variants between April and July 2021, and then from Delta to Omicron variants between December and February 2022 15–17 . The Omicron variant wave reached its peak in Pakistan in January 2022, resulting in the highest number of cases since the beginning of the pandemic 1,16 …”