Aetiologic agent of acute upper respiratory infection in human influenza and sars-Cov-2 negative cases in Tanzania

Abstract

ABSTRACT Background: Viral aetiologies are among the most frequent causes of respiratory disease in both children and adults worldwide. The annual epidemics causes estimated 290,000 to 650,000 deaths and 3 to 5 million cases of serious respiratory illness globally. There are several respiratory pathogens that cause acute respiratory infections (ARIs), however adequate data on aetiologic agents are lacking. Objective: To determine aetiological agent of ARI among patient tested negative for human influenza and SARS-CoV-2 in Tanzania. Method: This was a retrospective cross-sectional study carried out using archived nasopharyngeal swab samples of patients confirmed of SARS-CoV-2 and Human Influenza virus tested negative. The study was conducted at National Public Health Laboratory (NPHL), samples were collected from 27 sentinel site from October 2023 to March 2024. Total nucleic acid (RNA and DNA) were extracted using Qiagen-QIA/80204 All-Prep DNA/RNA Mini Kit. The profiling of genomes of pathogen was quantified using Illumina Miseq reagents kit and DNA libraries were sequenced using the Illumina sequencer. Results: A total of 172 patient samples were include in this study of which 89% (153/172) were positive with at least one pathogen detected. A high proportion 84.9% (146/172) of samples had bacteria pathogen, 18.0% (31/172) viral pathogen and 18.6% (32/172) had fungi. A total of 406 of respiratory pathogen were detected. S. pneumoniae was the predominant bacterial pathogen 78.2% (115/147) detected while Human rhinovirus 38.7% (12/31) was the prevalent virus. Individuals aged between 18 and 64 had 3.1 times the odds of having ARI caused by single pathogen (aOR 3.1, 95%CI: 1.1–8.8) compared to patients aged ≥65 years while the odds of having ARI due multiple pathogens for the same age group (aOR 6.1, 95%CI: 2.3–16.3) were 6.1 times higher than those aged ≥ 65 years.. Conclusion: The study found a high proportion of other pathogens causing ARI. Particularly S. pneumoniae were the predominant cause with Human rhinovirus emerged as the prevalent viral cause of ARI. Age played a significant role in susceptibility to respiratory infections.