Viral burden and diversity in acute respiratory tract infections in hospitalized children in wet and dry zones of Sri Lanka

Abstract

The present study was done to identify the viral diversity, seasonality and burden associated with childhood acute respiratory tract infection (ARTI) in Sri Lanka. Nasopharyngeal aspirates (NPA) of hospitalized children (1 month-5 years) with ARTI were collected in 2 centers (wet and dry zones) from March 2013 to August 2014. Respiratory viral antigen detection by immunofluorescence assay (IFA) was used to identify the infecting viruses. IFA negative 100 NPA samples were tested for human metapeumovirus (hMPV), human bocavirus and corona viruses by polymerase chain reaction. Of the 443 and 418 NPAs, 37.2% and 39.4% were positive for any of the 8 different respiratory viruses tested from two centers studied. Viral co-infection was detected with respiratory syncytial virus (RSV) in both centers. Peak viral detection was noted in the wet zone from May-July 2013 and 2014 and in the dry zone from December-January 2014 suggesting a local seasonality for viral ARTI. RSV showed a clear seasonality with a direct correlation of monthly RSV infections with rainy days in the wet zone and an inverse correlation with temperature in both centers. The case fatality rate was 2.7% for RSV associated ARTI. The overall disability adjusted life years was 335.9 and for RSV associated ARTI it was 241.8. RSV was the commonly detected respiratory virus with an annual seasonality and distribution in rainy seasons in the dry and wet zones of Sri Lanka. Identifying the virus and seasonality will contribute to employ preventive measures and reduce the empirical use of antibiotics in resource limited settings.

Fig 1. A map of Sri Lanka with sampling sites (THA and THG), number of children recruited in each center (n) and patient draining area.

THA–Teaching hospital, Anuradhapura; THG–Teaching hospital, Gampola.

Fig 2. Monthly distribution of ARTIs in children less than 5 years in THA and THG from March 2013 to August 2014.

ARTI–Acute respiratory tract infection; THA–Teaching hospital, Anuradhapura; THG–Teaching hospital, Gampola.

Fig 3. Pattern of distribution of viral ARTIs in children less than 5 years in THA from March 2013 to August 2014.

ARTI–Acute respiratory tract infection; THA–Teaching hospital, Anuradhapura; RSV–Respiratory syncytial virus; PIV-1, 2 & 3 –Parainfluenza virus 1, 2 & 3; Ad V–Adenovirus; Inf-A–Influenza A; Inf-B–Influenza B; hMPV–Human metapneumovirus.

Fig 4. Pattern of distribution of viral ARTIs in children less than 5 years in THG from March 2013 to August 2014.

ARTI–Acute respiratory tract infection; THG–Teaching hospital, Gampola; RSV–Respiratory syncytial virus; PIV-1, 2 & 3 –Parainfluenza virus 1, 2 & 3; Ad V–Adenovirus; Inf-A–Influenza A; Inf-B–Influenza B; hMPV–Human metapneumovirus.

Fig 5. Pattern of RSV associated ARTI with climatic factors in THA and THG from March 2013 to August 2014.

ARTI–Acute respiratory tract infection; THA–Teaching hospital, Anuradhapura; THG–Teaching hospital, Gampola; RSV–Respiratory syncytial virus; PIV-1, 2 & 3 –Parainfluenza virus 1, 2 & 3; Ad V–Adenovirus; Inf-A–Influenza A; Inf-B–Influenza B; hMPV–Human metapneumovirus. Climatic factors analyzed–mean monthly relative humidity (%), mean monthly temperature, mean monthly number of rainy days.

Fig 6. Incidence/100000-person years for RSV, PIV-1, PIV-2 and PIV-3, AV, Inf-A, Inf-B, and hMPV infections for different age groups of children with ARTI compared to overall incidence of these viruses despite the age categories.

ARTI–Acute respiratory tract infection; RSV–Respiratory syncytial virus; PIV-1, 2 & 3 –Parainfluenza virus 1, 2 & 3; Ad V–Adenovirus; Inf-A–Influenza A; Inf-B–Influenza B; hMPV–Human metapneumovirus.