Epidemiology and Molecular Characterization of Influenza Viruses Isolated From Children Admitted At the Kenyatta National Hospital in April-July 2008

Abstract

Background: 20% of deaths in children are caused by respiratory infections. Acute respiratory infections (ARIs), have both bacterial and viral aetiologies. Influenza viruses cause highly contagious respiratory diseases. In Kenya, three studies focusing on influenza-like-illness and severe acute respiratory illness are ongoing. Despite these surveillance programmes, little is known regarding the epidemiology and molecular characteristics of influenza viruses found in children at the KenyattaNational Hospital (KNH).

Objective: To determine the epidemiology and molecular characteristics of influenza viruses from children at the Kenyatta National Hospital during the April-July 2008 period.

Methodology: Throat swabs were collected from 388 consenting patients. Swabs were inoculated onto monolayers of cultured MDCK cellsto isolate influenza viruses. The virus isolates were identified by HA/HAI assays. Viral RNA was extracted from isolates followed by RT-PCR amplification of the haemagglutinin gene.Nucleotide sequences were determined by the Sanger dideoxy termination method on an ABI 3500xL genetic analyzer. The nucleotide sequences were aligned to similar sequences from GenBank, and phylogeny inferred using Bayesian methods.

Results: Twenty viruses consisting of 19 (95%) influenza B viruses and 1 (5%) seasonal influenza A/H1N1 were detected from the 388 patient samples. HAI titres for both A and B viruses ranged between 320-1280 with both vaccine strains showing a titre of 320. Viruses were detected mostly in 1year olds (11; 55%), patients with LRTI (14; 70%) and in the month of June (9; 45%). The nucleotide sequences displayed had 97-98%similarities to other 2008 influenza sequences. Phylogenetic analyses of seasonal influenza A/H1N1 clustered together with 2008 regional sequences while influenza B also clustered with 2008 sequences. Influenza A sequence showed substitutions at one antigenic site (198-Sb), while 3 antigenic sites (150loop, 160loop and 190 – Helix) on influenza B also had substitutions when compared to the 2008 vaccine strains.

Conclusion: In 2008, influenza viruses were common in 1year oldsat KNH. Infection rates were highest in the month of June. Viruses isolated in the study period were genetically similar to those isolated elsewhere. Amino acid changes in the Kenyan isolates did not adversely affect the immunogenicity of the 2008 vaccine.