RNA viruses in community-acquired childhood pneumonia in semi-urban Nepal; a cross-sectional study

Abstract

Background: Pneumonia is among the main causes of illness and death in children <5 years of age. There is a need to better describe the epidemiology of viral community-acquired pneumonia (CAP) in developing countries.

Methods: From July 2004 to June 2007, we examined nasopharyngeal aspirates (NPA) from 2,230 cases of pneumonia (World Health Organization criteria) in children 2 to 35 months old recruited in a randomized trial of zinc supplementation at a field clinic in Bhaktapur, Nepal. The specimens were examined for respiratory syncytial virus (RSV), influenza virus type A (InfA) and B (InfB), parainfluenza virus types 1, 2 and 3 (PIV1, PIV2, and PIV3), and human metapneumovirus (hMPV) using a multiplex reverse transcriptase polymerase chain reaction (PCR) assay.

Results: We identified 919 virus isolates in 887 (40.0%) of the 2,219 NPA specimens with a valid PCR result, of which 334 (15.1%) yielded RSV, 164 (7.4%) InfA, 129 (5.8%) PIV3, 98 (4.4%) PIV1, 93 (4.2%) hMPV, 84 (3.8%) InfB, and 17 (0.8%) PIV2. CAP occurred in an epidemic pattern with substantial temporal variation during the three years of study. The largest peaks of pneumonia occurrence coincided with peaks of RSV infection, which occurred in epidemics during the rainy season and in winter. The monthly number of RSV infections was positively correlated with relative humidity (rs = 0.40, P = 0.01), but not with temperature or rainfall. An hMPV epidemic occurred during one of the three winter seasons and the monthly number of hMPV cases was also associated with relative humidity (rs = 0.55, P = 0.0005).

Conclusion: Respiratory RNA viruses were detected from NPA in 40% of CAP cases in our study. The most commonly isolated viruses were RSV, InfA, and PIV3. RSV infections contributed substantially to the observed CAP epidemics. The occurrence of viral CAP in this community seemed to reflect more or less overlapping micro-epidemics with several respiratory viruses, highlighting the challenges of developing and implementing effective public health control measures.

Figure 1

Study profile for children 2 to 35 months of age included in a study of viral community-acquired pneumonia in Bhaktapur, Nepal, from July 2004 to June 2007. Severe malnutrition was defined as <70% NCHS (National Center for Health Statistics) median weight for height. Severe anemia was defined as hemoglobin <7 g/dl.

Figure 2

Monthly number of community-acquired pneumonia cases and cases with a positive virus PCR in children aged 2 to 35 months identified at a field clinic in Bhaktapur, Nepal, from July 2004 to June 2007.

Figure 3

Monthly number of viral isolates in nasopharyngeal specimens from 2,219 cases with community-acquired pneumonia in children 2 to 35 months of age identified at a field clinic in Bhaktapur, Nepal, from July 2004 to June 2007. Parainfluenza 2 isolates were not included in the graph due to few positive cases.

Figure 4

Monthly number of RSV infections in children aged 2 to 35 months with community-acquired pneumonia from 29 June 2004 to 30 June 2007, in Bhaktapur, Nepal, depicted with monthly variation of relative humidity, rainfall and temperature. The mean daily measurement for the month was used for relative humidity and temperature, while rainfall was calculated as the total measurement for the month.