Respiratory pathogens associated with sudden unexpected deaths during the COVID-19 pandemic in Gauteng, South Africa

Abstract

This study investigated sudden unexpected deaths (SUDs) and individuals found dead in Tshwane, South Africa, during the COVID-19 pandemic, with a focus on SARS-CoV-2 infection and co-infections. Cases of SUDs were admitted to the Pretoria Medico-Legal Laboratory and tested for SARS-CoV-2, revealing an overall positivity rate of 16%, peaking at 21.74% in December 2021 during Omicron’s emergence. The increase in SARS-CoV-2 positivity among SUD cases mirrored national COVID-19 trends, suggesting potential underreporting of COVID-19-related deaths. Demographic and statistical analysis identified significant risk factors; children (≥1-18 years) had higher odds of testing positive during Omicron (OR=5.7; p=0.013), likely due to an absence of vaccination in children under 12 and low vaccination rates in 12–18-year-olds and immune evasion of Omicron variants in previously infected individuals. These findings emphasise the need for enhanced surveillance to accurately quantify COVID-19’s impact on mortality, particularly in vulnerable populations. Post-mortem analysis examined SARS-CoV-2 persistence and co-infections. Among post COVID-19 SUD cases (January 2023–January 2024), SARS-CoV-2 was detected in 8% (8/100) of cases, with viral presence in the lung (12.5%) and brain (12.5%) tissues. Co-infections with human parainfluenza virus (HPIV 4, HPIV 2), human coronavirus NL63 (hCoV NL63), and human bocavirus (hBoV) were found in 37.5% of nasopharyngeal (NP) swab-positive cases but were absent in lung and brain-positive cases. The detection of SARS-CoV-2 in neurological and lung tissues highlights its potential role in SUDs, warranting further investigation. Genomic sequencing confirmed the presence of Omicron sub-lineages XBB 1.9.1 (brain tissue, NP swab), XBB 1.5 (NP swab), and XBB 1.5.81 (lung tissue) between March and June 2023. These findings align with dominant circulating lineages in South Africa and emphasise the need for variant surveillance in forensic investigations. Respiratory pathogen co-infections were detected in 86% (86/100) of SUD cases between January 2023 and January 2024. The most prevalent pathogens included human adenovirus (HAdV) (42.6%), significantly associated with SUD (IRR=11.0, p=0.019), human rhinovirus (HRV) (27.8%) (borderline association, IRR=7.50, p=0.051), and enterovirus (EV) (24.1%). Additionally, 51.6% of lung tissues tested positive for respiratory pathogens, including respiratory syncytial virus (RSV) and human parechovirus. Pathological findings in these cases included lung congestion, tracheal pus, haemorrhages, and fibrosis, indicating severe respiratory involvement. Analysis of co-infections and seasonality revealed that SARS-CoV-2-positive cases (17%) had the highest co-infection rates, particularly with HAdV (30.61%), EV (24.48%), and HRV (14.28%). The COVID-19 lockdown measures initially suppressed RSV and influenza A infections, but RSV cases resurged post-lockdown. Non-enveloped viruses (e.g., HAdV, HRV) were less affected by infection control measures due to their structural resistance. This study underscores the role of underreported SARS-CoV-2 infections in paediatric and adult SUDs and highlights the necessity of post-mortem surveillance. Continuous SARS-CoV-2 testing in SUD cases is essential for tracking emerging variants and mortality trends. A multidisciplinary approach integrating pathogen detection using molecular diagnostic methods and genome sequencing, clinical symptom analysis, and epidemiological investigations is critical for improving SUD forensic investigations and understanding the contribution of respiratory viruses in fatalities in South Africa.