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

Abstract

Background and AimsCOVID‐19 morbidity and mortality varied globally through the pandemic. We studied the relationship of SARS‐CoV‐2 variants of concern (VOC) with COVID‐19 severity and mortality among hospitalized patients in Pakistan.MethodsA retrospective review of clinical, laboratory, and vaccination data of 197 COVID‐19 adult patients at the Aga Khan University Hospital, Karachi between April 2021, and February 2022 was performed. SARS‐CoV‐2 VOC identified in respiratory samples were analyzed. Univariate and multivariate analysis was conducted to identify factors associated with COVID‐19 outcomes.ResultsThe median age of cases was 55 years and 51.8% were males. Twenty‐four percent of females were pregnant. Of COVID‐19 cases, 48.2% had nonsevere disease, while 52.8% had severe/critical disease. Hypertension (48%) and diabetes mellitus (41%) were common comorbids. SARS‐CoV‐2 VOC identified comprised; Omicron (55.3%), Beta (14.7%), Alpha (13.7%), Delta (12.7%), and Gamma (3.6%) variants. Most (59.7%) study subjects were unvaccinated. Of vaccines, 88% had received inactivated virus COVID‐19 vaccines. Increased risk of severe disease was associated with age ≥50 years (odds ratio [OR]: 5.73; 95% confidence interval [CI]: [2.45–13.7]), as well as with diabetes mellitus (OR: 4.24; 95% CI: [1.82–9.85]). Full vaccination (OR: 0.25; 95% CI: [0.11–0.58]) or infection with Omicron (OR: 0.42; 95% CI: [0.23–0.74]) was associated with reduced disease severity. The risk of mortality increased with age ≥50 years (OR: 5.07; 95% CI: [1.92–13.42]) and a history of myocardial infarction (OR: 5.11; 95% CI: [1.45–17.93]) whilst, infection with Omicron was found to reduce the risk (OR: 0.22; 95% CI: [0.10–0.53]).ConclusionOur study describes the relationship between the severity of COVID‐19, in‐hospital mortality in relation to SARS‐CoV‐2 variants, and the impact of COVID‐19 vaccination in Pakistan. Outcomes were more favorable in younger individuals, after vaccinations and with Omicron variant infections. Most cases received inactivated virus vaccines therefore these data highlight the protection provided against severe COVID‐19.

A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population

“…Wuhan S, M, and N repertoires were compared against 16 variants (B.1, Alpha, five Delta, and nine Omicron) to identify epitopes that were lost, gained, or altered in estimated HLA binding affinity between variants ( Figure 2 ). In general, a balanced number of epitopes were lost and gained for all variants; however, BA.1.1 M, BA.4 N, B.1.1.7 S, and BQ.1.1 S repertoires sustained greater epitope loss than gain ( Figures 2A–C , 3 , bottom ), which may contribute to explaining the increased transmission and breakthrough cases seen in these subvariants ( 39 , 40 ). Additionally, spike epitopes in the early variants (B.1 and B.1.1.7) and Omicron VOCs experienced a greater number of epitopes predicted to have reduced binding affinity than increased affinity.…”

Influence of Seasonality and Public-Health Interventions on the COVID-19 Pandemic in Northern Europe

“…It is worth noting that this spread and its repercussions were not uniform and had many geographical, temporal and demographic variations. They were also heavily influenced by the nature of the RNA virus itself, which was characterised by a successive series of prevalent mutations, each having different levels of disease severity and communicability [14,16].…”