Epidemiology of seasonal influenza and other respiratory pathogens during the COVID-19 pandemic in Zambia.
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Date
2024
Authors
Nyahoda, Martin
Journal Title
Journal ISSN
Volume Title
Publisher
The University of Zambia
Abstract
Respiratory infections are among the leading causes of morbidity and mortality globally especially in Sub-Saharan Africa. In 2021, there were an estimated 344 million global incident episodes attributable to lower respiratory infections translating to an estimated 4350 episodes per 100,000
population resulting in an estimated 2.18 million deaths which was about 27.7 deaths per 100,000 population. Sub-Saharan Africa accounts for about 66.4% of deaths attributable to lower respiratory tract infections per 100,000 persons. In Zambia, severe acute respiratory infections are estimated at 6181 and ranked between 5th and 8th on the top 10 leading causes of death. Between 2019 and 2021, non-pharmaceutical interventions (NPIs) to limit the spread of COVID-19 were implemented globally which included hand washing, face masking, school closures, limiting public gatherings, remote working, hand sanitizing, physical distancing and travel restrictions. This resulted in a decline of respiratory infections especially influenza and respiratory syncytial virus subsequently leading to a decline of all age mortality attributable to lower respiratory infections by 16%. While scientific studies to establish the impact of COVID-19 associated NPIs on circulation of respiratory pathogens have been conducted in several countries globally, there was little knowledge on how the COVID-19 pandemic and its associated public health and social measures changed the epidemiology of influenza and other respiratory infections in Zambia. Therefore, the aim of this study was to determine the broad range of respiratory pathogens that were circulating in Zambia during the COVID-19 pandemic and determine the effects of age and location (rural or urban) on the likelihood of infection. Additionally, through systematic review and meta-analysis, the study sought to ascertain the burden of respiratory infections in Africa and
existing regional disparities. This study was retrospective using nasopharyngeal specimens that were collected national wide to test for SARS-CoV-2. After testing for SARS-CoV-2, selected specimens were tested for influenza A virus (IAV), influenza A(H1N1) virus (swine lineage) (IAV(H1N1) swl), influenza B virus (IBV), influenza C virus (IVC), human coronaviruses (HCoV) NL63, 229E, OC43 and HKU1, human parainfluenza viruses (HPIV) 1, 2, 3 and 4, human metapneumoviruses (HMPV) A and B, human rhinovirus (HRV), human respiratory syncytial viruses (HRSV) A and B, human adenovirus (HAdV), enterovirus (EV), human parechovirus (HPeV), human bocavirus (HBoV), Pneumocystis jirovecii, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae B, Staphylococcus aureus, Moraxella catarrhalis, Bordetella spp. (except Bordetella parapertussis), Klebsiella pneumoniae, Legionella pneumophila / Legionella longbeachae, Salmonella spp. and Haemophilus influenzae in order to
understand the profile of pathogens that continued to circulate between July 2020 and July 2021. Proportional age stratified convenient sampling was used to select a total of 128 specimens from children, adolescents, adults and the elderly collected from both urban and rural areas. The final sample consisted 88 from urban and 40 from rural areas collected from Lusaka, Luapula, Northen and Muchinga provinces. Using multiplex rRT-PCR, 128 nasopharyngeal specimens were tested for influenza and other respiratory pathogens. Overall, 71.1% (91/128) of samples tested positive for at least one respiratory pathogen. Staphylococcus aureus was the most prevalent respiratory pathogen detected accounting for 22.7% (29/128) followed by Klebsiella pneumoniae 20.3% (26/128). Influenza accounted for 13.3% (17/128). Of the 17 specimens testing positive for influenza, 16 were influenza A/(H1N1) while one specimen tested positive for influenza B. The prevalence of rhinovirus and respiratory syncytial virus was estimated at 3.1% (4/128) and 2.3% (3/128), respectively. Children, adolescents and the elderly accounted for the most influenza positive specimens 76.5% (13/17)
while 100% (3/3) specimens positive for Moraxella catarrhalis were all from children. All specimens that tested positive for Haemophilus influenzae (5/5) were from children and adolescents and 17 of the 29 specimens that tested positive for Staphylococcus aureus were also from the same age group. For co-infections, 52 specimens were found to be co-infected with at least 2 respiratory pathogens. Of the total co-infections, 11.5% (6/52) were virus-virus with adenovirus as the most co-infecting viral pathogen while virus-bacteria co-infections accounted for 48.1% (25/52) with Staphylococcus aureus as the most co-infecting bacterial pathogen. Bacterial respiratory pathogens were more predominant than viral pathogens during the study period. Compared to prevalence prior to the COVID-19 pandemic, a decrease for both viral and bacterial respiratory pathogens was observed. The results seem to suggest that the emergence of COVID-19 and its associated public health interventions may have altered the epidemiology of influenza and other respiratory pathogens in Zambia. Increase in age was associated with an increased risk of infection with adenovirus and SARS-CoV-2 adjusted odds ratio Exp (B) 1.026, CI (0.999-1.053) and 1.048, CI (1.004-1.094) respectively. Although results suggested that rural areas were associated with an increased risk of infection for Bordetella pertussis adjusted odds ratio 3.10, CI (0.667-4.208) and K. pneumoniae adjusted odds ratio 1.588, CI (0.615-4.097) including S. aureus adjusted odds ratio 1.362, CI (0.561-3.303), the results were not statistically significant. At the level of the African continent, overall pooled prevalence for viral respiratory pathogens was estimated at 56.6% (95% CI, 0.371-0.762, I 2 99.9%). Overall pooled prevalence for bacterial respiratory pathogens was estimated at 12.9% (95% CI, 0.122-0.137, I 2 99.8%). Rhinovirus and respiratory syncytial virus were the most prevalent pathogens with wide geographical spread across all African regions with 19.9% and 8.9% prevalence respectively. Generally, most studies in Africa were focused on viral respiratory pathogens. To fully understand the burden of
respiratory infections in Africa, there is need for more studies combining both viral and bacterial respiratory pathogens especially with the advent of multiplex PCR. Colonization and enhanced viral induced bacterial binding may have contributed to the persistence of bacterial respiratory infections more than viral pathogens. Co-infections were mostly observed in children because they may be still immunologically naïve and not able to take precautionary measures such as avoiding touching eyes and mouth including frequent hand washing. Although there were observed differences in the prevalence of infection between rural and urban areas, the differences were not statistically significant. Further, and location did not increase the likelihood of infection except for SARS-CoV-2 and adenovirus. Overall, this study demonstrated that with sustained non-pharmaceutical interventions, it is possible to reduce the number of respiratory infections and contribute to improved public health outcomes. Additionally, the high number of bacterial respiratory pathogens detected in this study provides impetus to strengthen efforts to contain these pathogens as they are known to contribute to severe disease and death.
Description
Thesis of Doctor of Philosophy in Epidemiology.