Validation of polyester nasal swabs for post-mortem SARS-CoV-2 diagnosis in Karachi, Pakistan: a prospective surveillance analysis

Background The COVID-19 pandemic has significantly impacted global health, with low- and middle-income countries (LMICs) facing unique healthcare challenges. Polyester nasal swabs stored in dry tubes have emerged as a cost-effective and scalable method for routine testing of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2). We aimed to assess the prevalence of SARS-CoV-2 among deceased individuals in an urban slum in Karachi, Pakistan, using dry and wet polyester nasal swabs, and to validate their use for post-mortem detection of the virus. Methods We conducted a prospective observational study from July 2022 to August 2023 in a low-income setting. We collected nasal samples from 350 deceased individuals based on community death alerts using dry polyester and wet swabs with transport media. These were then processed for SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR), with the positive samples sequenced on the Illumina platform to identify circulating variants. We also performed a comparative analysis between dry and wet swab methods for diagnostic performance. Results Of the 350 samples, 21 (6.0%) tested positive for SARS-CoV-2. Males accounted for 15/21 (71.4%) of positive cases, with the majority aged 60 and above (n/N = 12/21, 57.1%). The Omicron (22F) variant was the most prevalent, detected in 16/21 (76%) cases. The diagnostic performance of wet swabs showed a sensitivity of 76.19%, while dry swabs were more accurate, with a sensitivity of 90.48%, achieving a diagnostic odds ratio of 3120.5. Conclusions Our study demonstrated the feasibility and effectiveness of using dry polyester nasal swabs for post-mortem detection of SARS-CoV-2 in resource-constrained settings. These findings emphasise the method’s potential for monitoring respiratory infectious diseases and guiding public health strategies in LMICs.