Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South Africa
Introduction: Death due to infectious diseases is a major problem worldwide, particularly in developing countries, due to the lack of medical care and poor socioeconomic factors contributing to the disease. In South Africa, the medicolegal death investigation of sudden unexpected deaths (SUD) in the...
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Elsevier
2025-03-01
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| Series: | International Journal of Infectious Diseases |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1201971224007860 |
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| author | Miss Gadean Brecht Miss Caitlin MacIntyre Dr Servaas Rossouw Prof Marietjie Venter |
| author_facet | Miss Gadean Brecht Miss Caitlin MacIntyre Dr Servaas Rossouw Prof Marietjie Venter |
| author_sort | Miss Gadean Brecht |
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| description | Introduction: Death due to infectious diseases is a major problem worldwide, particularly in developing countries, due to the lack of medical care and poor socioeconomic factors contributing to the disease. In South Africa, the medicolegal death investigation of sudden unexpected deaths (SUD) in the young and adults with COVID-19 and other respiratory infections has not been well studied. The underreported cases of suspecting COVID-19 deaths during the pandemic were owed to the lack of molecular autopsies.The objective of the study was to describe the incidence and variants of COVID-19 and other respiratory pathogens in sudden unexplained deaths in Tshwane, South Africa, the site of the first identified Omicron cases. We also looked at pulmonary involvement associated with respiratory viruses with extra pulmonary manifestations, specifically neurological manifestations since this have been associated with COVID-19. Methods: SUD cases were admitted at the Pretoria Medico Legal Laboratory (January 2023- January 2024). Prospective sampling of post-mortem specimens was done to identify infectious pathogens. Brain and lung tissues and nasopharyngeal (NP) swabs were tested for SARS-CoV-2, and NP swabs were screened using the FTD®-21 kit to identify respiratory pathogens. In total, 100 cases (82 adults, 8 children, and 10 infants) were collected, 10% (10/100) of the deceased participants tested positive for SARS-CoV-2 on NP swabs and in two of the cases (1/10 tested positive on the brain specimen and 1/10 tested positive on a lung specimen). Positive SARS-CoV-2 cases were further characterized by genomic sequencing to define the variants involved. Results and Discussion: The full genome (98% coverage) was recovered from the brain of a 7 y/o female and was identified as XBB 1.9 lineage. The low coverage (<55%) across other specimens makes it difficult to fully conclude the lineage, however XBB1.5, XBB1.9 and BA.2 were the identified Omicron lineages. Common respiratory pathogens (hCoV NL63, hCoV 0C43, HAdV, HRV, EV, HPIV 2, HPIV 4, IAV, HBoV, HMPV A and B) were detected in 76% (76/100) of cases in upper respiratory tract specimens, while Influenza (H1N1) (2009), HBoV, HPeV and SARS-CoV-2 were detected in the lower respiratory tract specimens. Conclusion: This study highlights the need for medico-legal investigation and further ancillary testing in South Africa, to better understand sudden infectious diseases deaths in children and adults. The recovery of SARS-CoV-2 in post-mortem brain and lung tissues suggests a role of SARS-CoV-2 in unexplained deaths. Whole genome sequencing identified sub-lineages of the Omicron variant in cases with little or no known medical history of individuals who died unexpectedly. The evidence of SARS-COV-2 Omicron sub-lineages in unexplained deaths in South Africa where Omicron was thought not to cause severe disease is a reminder that SARS-CoV-2, Influenza, and other common respiratory viruses should be investigated in unexplained deaths. |
| format | Article |
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| language | English |
| publishDate | 2025-03-01 |
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| series | International Journal of Infectious Diseases |
| spelling | doaj-art-8600c02e33014de28b8483d119d5a0eb2025-08-20T02:00:41ZengElsevierInternational Journal of Infectious Diseases1201-97122025-03-0115210771110.1016/j.ijid.2024.107711Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South AfricaMiss Gadean Brecht0Miss Caitlin MacIntyre1Dr Servaas Rossouw2Prof Marietjie Venter3Centre for Emerging and Reemerging Arbo and Respiratory virus research, Department of Medical Virology, Faculty of Health, University of Pretoria, South AfricaCentre for Emerging and Reemerging Arbo and Respiratory virus research, Department of Medical Virology, Faculty of Health, University of Pretoria, South Africa; Emerging Viral Threats, One Health Surveillance and Vaccines (EViTOH) division, Infectious disease, and Oncology Research Institute (IDORI), University of the Witwatersrand, South AfricaDepartment of Forensic Medicine, Faculty of Health Sciences, University of Pretoria, South AfricaCentre for Emerging and Reemerging Arbo and Respiratory virus research, Department of Medical Virology, Faculty of Health, University of Pretoria, South Africa; Emerging Viral Threats, One Health Surveillance and Vaccines (EViTOH) division, Infectious disease, and Oncology Research Institute (IDORI), University of the Witwatersrand, South AfricaIntroduction: Death due to infectious diseases is a major problem worldwide, particularly in developing countries, due to the lack of medical care and poor socioeconomic factors contributing to the disease. In South Africa, the medicolegal death investigation of sudden unexpected deaths (SUD) in the young and adults with COVID-19 and other respiratory infections has not been well studied. The underreported cases of suspecting COVID-19 deaths during the pandemic were owed to the lack of molecular autopsies.The objective of the study was to describe the incidence and variants of COVID-19 and other respiratory pathogens in sudden unexplained deaths in Tshwane, South Africa, the site of the first identified Omicron cases. We also looked at pulmonary involvement associated with respiratory viruses with extra pulmonary manifestations, specifically neurological manifestations since this have been associated with COVID-19. Methods: SUD cases were admitted at the Pretoria Medico Legal Laboratory (January 2023- January 2024). Prospective sampling of post-mortem specimens was done to identify infectious pathogens. Brain and lung tissues and nasopharyngeal (NP) swabs were tested for SARS-CoV-2, and NP swabs were screened using the FTD®-21 kit to identify respiratory pathogens. In total, 100 cases (82 adults, 8 children, and 10 infants) were collected, 10% (10/100) of the deceased participants tested positive for SARS-CoV-2 on NP swabs and in two of the cases (1/10 tested positive on the brain specimen and 1/10 tested positive on a lung specimen). Positive SARS-CoV-2 cases were further characterized by genomic sequencing to define the variants involved. Results and Discussion: The full genome (98% coverage) was recovered from the brain of a 7 y/o female and was identified as XBB 1.9 lineage. The low coverage (<55%) across other specimens makes it difficult to fully conclude the lineage, however XBB1.5, XBB1.9 and BA.2 were the identified Omicron lineages. Common respiratory pathogens (hCoV NL63, hCoV 0C43, HAdV, HRV, EV, HPIV 2, HPIV 4, IAV, HBoV, HMPV A and B) were detected in 76% (76/100) of cases in upper respiratory tract specimens, while Influenza (H1N1) (2009), HBoV, HPeV and SARS-CoV-2 were detected in the lower respiratory tract specimens. Conclusion: This study highlights the need for medico-legal investigation and further ancillary testing in South Africa, to better understand sudden infectious diseases deaths in children and adults. The recovery of SARS-CoV-2 in post-mortem brain and lung tissues suggests a role of SARS-CoV-2 in unexplained deaths. Whole genome sequencing identified sub-lineages of the Omicron variant in cases with little or no known medical history of individuals who died unexpectedly. The evidence of SARS-COV-2 Omicron sub-lineages in unexplained deaths in South Africa where Omicron was thought not to cause severe disease is a reminder that SARS-CoV-2, Influenza, and other common respiratory viruses should be investigated in unexplained deaths.http://www.sciencedirect.com/science/article/pii/S1201971224007860 |
| spellingShingle | Miss Gadean Brecht Miss Caitlin MacIntyre Dr Servaas Rossouw Prof Marietjie Venter Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South Africa International Journal of Infectious Diseases |
| title | Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South Africa |
| title_full | Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South Africa |
| title_fullStr | Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South Africa |
| title_full_unstemmed | Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South Africa |
| title_short | Respiratory pathogens associated with sudden unexpected deaths during and post COVID-19 pandemic in Gauteng, South Africa |
| title_sort | respiratory pathogens associated with sudden unexpected deaths during and post covid 19 pandemic in gauteng south africa |
| url | http://www.sciencedirect.com/science/article/pii/S1201971224007860 |
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