Variants Specific Clinical Characteristics of SARS-CoV-2: A Cross-Sectional Study in Khyber Pakhtunkhwa, Pakistan

Abstract

Background: SARS-CoV-2 has evolved into multiple variants with potential differences in transmissibility, pathogenicity, and clinical presentation. Understanding variant-specific symptom profiles is essential for improving surveillance, diagnosis, and clinical management, particularly in resource-limited settings where genomic sequencing is limited. Objective: To compare the clinical characteristics associated with Alpha, Beta, Gamma, and Delta SARS-CoV-2 variants among PCR-confirmed COVID-19 cases in Khyber Pakhtunkhwa, Pakistan. Methods: A cross-sectional observational study was conducted at the Public Health Reference Laboratory, Khyber Medical University, using PCR-confirmed COVID-19 cases recorded between 2020 and 2023. SARS-CoV-2 variants were identified using mutation-specific PCR assays. Clinical and demographic data were collected through structured telephone interviews based on the World Health Organization COVID-19 case report form. Descriptive statistics and inferential analyses including chi-square and Fisher–Freeman–Halton tests were performed using SPSS version 25, with statistical significance set at p<0.05. Results: Among 416 participants, the Delta variant accounted for the majority of infections (310; 74.5%), followed by Gamma (60; 14.4%), Alpha (36; 8.7%), and Beta (10; 2.4%). Delta infections were strongly associated with fever, cough, sore throat, body aches, and loss of smell and taste, each exceeding 94% prevalence. Gamma infections demonstrated high rates of fatigue, rigors, chills, rhinorrhea, and shortness of breath (>90%), whereas Beta infections showed prominent gastrointestinal symptoms including nausea and vomiting (70%). Alpha infections had the highest proportion of asymptomatic cases (27.8%). Conclusion: SARS-CoV-2 variants exhibited distinct clinical phenotypes in this population, with Delta characterized by respiratory and sensory symptoms, Gamma by systemic inflammatory manifestations, and Beta by gastrointestinal involvement. Recognition of variant-specific symptom clusters may support improved clinical detection and epidemiological surveillance in settings with limited genomic sequencing capacity.