Prevalence and seasonality of common viral respiratory pathogens, including Cytomegalovirus in children, between 0–5 years of age in KwaZulu-Natal, an HIV endemic province in South Africa

Abstract

BackgroundAcute respiratory tract infections contribute significantly to morbidity and mortality among young children in resource-poor countries. However, studies on the viral aetiology of acute respiratory infections, seasonality and the relative contributions of comorbidities such as immune deficiency states to viral respiratory tract infections in children in these countries are limited.MethodsA retrospective analysis of laboratory test results of upper or lower respiratory specimens of children between 0 and 5 years of age collected between 1st January 2011 and 31st July 2015 from hospitals in KwaZulu-Natal, South Africa. Respiratory specimens were tested for viral respiratory pathogens using multiplex polymerase chain reaction (PCR), HIV testing was performed either by serological or PCR methods. Cytomegalovirus (CMV) respiratory infection was determined using the CMV R-gene PCR kit.ResultsIn total 2172 specimens were analysed, of which 1175 (54.1%) were from males. The median age was 3.0 months (interquartile range [IQR] 1–7). Samples from the lower respiratory tract accounted for 1949 (89.7%) of all specimens. Respiratory multiplex PCR results were positive in 834 (45.7%) specimens. Respiratory syncytial virus (RSV) was the most commonly detected virus in 316 (32.1%) patients, followed by adenovirus (ADV) in 215 (21.8%), human rhinovirus (Hrhino) in 152 (15.4%) and influenza A (FluA) in 50 (5.1%). A seasonal time series pattern was observed for ADV (winter peak), enterovirus (EV) (autumn), human bocavirus (HBoV) (summer), and parainfluenza viruses 1 and 3 (PIV1 and 3) (spring). Stationary or untrended seasonal variation was observed for FluA (winter peak) and RSV (summer). HIV results were available for 1475 (67.9%) specimens; of these 348 (23.6%) were positive. CMV results were available for 714 (32.9%) specimens, of which 416 (58.3%) were positive. There was a statistically significant association between the coinfection of HIV and CMV with ADV.ConclusionsIn this study, we identified the most common respiratory viral pathogens detected among hospitalized children in KwaZulu-Natal. The coinfection between HIV and CMV was found to be associated with an increased risk of only adenovirus infection. Most viral pathogens showed a seasonal trend of occurrence. Our data has implications for the rational design of public health programmes.

High genotypic diversity of Rhinoviruses obtained from Tunisian children with severe acute respiratory infection

“…In the other hand, most cases occurred before sixmonths of age, particularly for HRV-A infection. Other studies corroborate the same finding such as in western China where the highest HRV infection rate was before six months' age [24] or in South Africa where 60.9% of positive cases were isolated from the same age group [27]. Meanwhile, other studies demonstrated that HRV infection occurs later, between 13 and 36 months [25,28].…”

The epidemiology of seasonal influenza after the 2009 influenza pandemic in Africa: a systematic review

“…A total of 22 papers from 13 countries have reported data on influenza and other respiratory pathogens including both viruses and bacteria 145 – 167 . From these, 13 studies reported data on respiratory pathogens among children < 5 years with SARI 145 , 146 , 149 , 151 , 153 , 155 , 156 , 161 , 162 , 165 – 167 , 218 , while 9 studied reported data on respiratory pathogens among other age groups 147 , 148 , 150 , 152 , 157 – 160 , 163 . The detection of respiratory virus varied considerably.…”

COVID-19 Shuts Doors to Flu but Keeps Them Open to Rhinoviruses

“…The continuous invasion and high diversity of rhinoviruses have been observed [ 138 ]. Rhinovirus activity has been detected in countries of all continents: Spain [ 139 ], Brazil [ 140 , 141 , 142 ], Argentina [ 143 ], France [ 125 ], Italy [ 10 , 144 ], the United Kingdom [ 116 ], Russia [ 145 ], Finland [ 146 , 147 ], Canada [ 148 ], the US [ 3 , 102 , 137 , 149 , 150 , 151 ], Australia [ 152 ], Vietnam [ 153 ], China [ 154 , 155 ], Hong Kong [ 156 ], Japan [ 157 ], Burundi [ 158 ], KwaZulu-Natal (a province of South Africa) [ 159 ], Tanzania [ 90 ], and many others, including Antarctica [ 160 ].…”