Authors; Joyce Namulondo, John T Kayiwa,  Joseph Mutyaba, Wavamunno Samuel, Nicholas Owor, Jocelyn Kiconco, Bakamutumaho Barnanbas, Julius Lutwama**
Abstract
Viruses are the commonest pathogens in Severe Acute Respiratory Infections. 
Background
Respiratory infections are one of the leading causes of death in developing countries. Viruses too are the leading pathogens in severe acute respiratory infection (SARI). Influenza virus has been shown to contribute 11.2% in respiratory samples collected in Uganda and 8.5% in SARI samples collected.  Influenza AH1N1 and AH3N2 are the commonly circulating Influenza A subtypes and B Yamagata and B Victoria the B lineages \cite{Yang_2018}. The majority (91.5%) of these SARI samples in Ugandan influenza surveillance sites are negative for influenza and their etiology is not known\cite{Cummings_2016}. In neighboring Kenya, Respiratory Syncytial virus was the most prevalent virus in acute respiratory infections after influenza and  Streptococcus pneumoniae the most common bacterial pathogen in ARI among children \cite{Feikin_2012}.  Moreover Enteroviruses, Rhinoviruses, RSV and Adenoviruses are shown to be the common pathogens in fatal cases of acute respiratory infections \cite{Njuguna_2017}\cite{Jain_2015}\cite{Feikin_2012}. In Uganda,non-influenza viruses were seen to contribute to influenza-like-illnesses and their etiology established \cite{Balinandi_2013}. The clear etiology and prevalence of non-influenza respiratory pathogens in SARI to-date has not been established. We therefore set out to identify the etiology and  prevalence of non-influenza respiratory pathogens in Severe Acute Respiratory Infections in Uganda. We hypothesized that viral pathogens RSV, human metapneumovirus and adenovirus may be the predominant non-influenza pathogens among patients with severe acute respiratory infections at the border towns of Uganda. However, it is also possible that bacterial pathogens particularly Streptococcus pneumoniae may be prevalent in SARI cases in these settings.
Methods
Total nucleic acids were extracted from 177 samples using the QIAamp viral RNA mini extraction kit (Qiagen, Australia). Multiplex RT-PCR was done FTD-33TM kit (Fast track Diagnostics, USA) which can detect up to 33 viral and bacterial pathogens using the ABI 7500 Fast Real Time PCR machine (Applied Biosystems). Samples with a crossover threshold (Ct) value of <38 were considered positive for this study.
Results
A total of 177 SARI samples were tested for non-influenza respiratory pathogens.
Viral Results
For the non-influenza respiratory viruses, 63(35.6%) were RSV, 49(27.7%) Rhinoviruses, 29(16.4%) Enteroviruses, 26(17.7%) Human Adenoviruses, 22(12.4%) Human parainfluenza virus 3, 12(6.8%) influenza C, 9(5.1%) Human parainfluenza virus 4, 9(5.1) Human bocavirus, and 9(5.1%) Human parainfluenza virus, 8(4.5%) Human metapneumovirus, 7(4%) COR43, 5(2.8%) COR63, 4(2.3%) Human parechovirus, 2(1.1%) HKUI, 1(0.6%) COR229, 1(0.6%) Human parainfluenza virus 2 and 0(0%) Human parainfluenza virus 1.
Bacterial Results
The main circulating bacteria were 130(73.4%) Streptococcus pneumonia, 96(54.2%) Moraxella catarrhalis, 41(23.2%) Staphylococcus aureus, 12(6.8%) Klebsiella pneumonia, 8(4.5%) Haemophillus influenza B, 2(1.1%) Bordetella pertussis and 1(0.6%) Chlamydia pneumonia.
Viral etiology of non-influenza viruses in SARI cases by age