Epidemiology of 2009 pandemic influenza A virus subtype H1N1 among Kenyans aged 2 months to 18 years, 2009-2010.

BACKGROUND: The US Army Medical Research Unit-Kenya (USAMRU-K) conducts surveillance for influenza-like illness (ILI) in Kenya. We describe the temporal and geographic progression of A(H1N1)pdm09 as it emerged in Kenya and characterize the outpatient population with A(H1N1)pdm09 infection. METHODS: We included patients with ILI aged 2 months to 18 years enrolled during June 2009-August 2010. Respiratory specimens were tested by real-time reverse-transcription polymerase chain reaction for influenza virus. Patients with A(H1N1)pdm09 infection were compared to those with seasonal influenza A virus infection and those with ILI who had no virus or a virus other than influenza virus identified (hereafter, "noninfluenza ILI"). RESULTS: Of 4251 patients with ILI, 193 had laboratory-confirmed A(H1N1)pdm09 infection. The first pandemic influenza case detected by USAMRU-K surveillance was in August 2009; peak activity nationwide occurred during October-November 2009. Patients with A(H1N1)pdm09 infection were more likely to be school-aged, compared with patients with seasonal influenza A virus infection (prevalence ratio [PR], 2.0; 95% confidence interval [CI], 1.3-3.1) or noninfluenza ILI (PR, 3.2; 95% CI, 2.4-4.3). CONCLUSIONS: USAMRU-K ILI surveillance detected the geographic and temporal distribution of pandemic influenza in Kenya. The age distribution of A(H1N1)pdm09 infections included more school-aged children, compared with seasonal influenza A virus infection and noninfluenza ILI.

Molecular characterization and phylogenetic analysis of the hemagglutinin 1 protein of human influenza A virus subtype H1N1 circulating in Kenya during 2007-2008.

BACKGROUND: Among influenza viruses, type A viruses exhibit the greatest genetic diversity, infect the widest range of host species, and cause the vast majority of cases of severe disease in humans, including cases during the great pandemics. The hemagglutinin 1 (HA1) domain of the HA protein contains the highest concentration of epitopes and, correspondingly, experiences the most intense positive selection pressure. OBJECTIVES: We sought to isolate and genetically characterize influenza A virus subtype H1N1 (A[H1N1]) circulating in Kenya during 2007-2008, using the HA1 protein. METHODS: Nasopharyngeal swab specimens were collected from patients aged ≥ 2 months who presented to 8 healthcare facilities in Kenya with influenza-like illness. We tested specimens for seasonal influenza A viruses, using real-time reverse-transcription polymerase chain reaction (RT-PCR). Viruses were subtyped using subtype-specific primers. Specimens positive for seasonal A(H1N1) were inoculated onto Madin-Darby canine kidney cells for virus isolation. Viral RNAs were extracted from isolates, and the HA1 gene was amplified by RT-PCR, followed by nucleotide sequencing. Nucleotide sequences were assembled using BioEdit and translated into amino acid codes, using DS Gene, version 1.5. Multiple sequence alignments were performed using MUSCLE, version 3.6, and phylogenetic analysis was performed using MrBayes software. RESULTS: We found that, similar to A/Brisbane/59/2007 (H1N1)-like virus, which was included in the southern hemisphere vaccine for the 2009 influenza season, all 2007 Kenyan viruses had D39N, R77K, T132V, K149R, and E277K amino acid substitutions, compared with A/Solomon Islands/3/2006 (H1N1)-like virus, a component of the southern hemisphere vaccine for the 2008 influenza season. However, the majority of 2008 viruses from Kenya also had R192K and R226Q substitutions, compared with A/Solomon Islands/3/2006 (H1N1)-like virus. These 2 changes occurred at the receptor binding site. The majority of the 2008 Kenyan isolates contained N187S, G189N, and A193T mutations, which differed from A/Brisbane/59/2007 (H1N1)-like virus. The A193T substitution is involved in binding the sialic acid receptor. Phylogenetically, the 2008 Kenyan isolates grouped into 2 clusters. The main cluster contained viruses with N187S and A193T changes; residue 187 is involved in receptor binding, whereas residue 193 is at antigenic site Sb. CONCLUSION: Overall, the major genetic variations that occurred in seasonal A(H1) viruses either affected receptor binding or altered epitopes at the immunodominant sites. These genetic variations in seasonal A(H1N1) isolated in Kenya during 2007-2008 highlight the importance of continuing surveillance and characterization of emerging drift variants of influenza virus in Africa.

A growing global network's role in outbreak response: AFHSC-GEIS 2008-2009.

A cornerstone of effective disease surveillance programs comprises the early identification of infectious threats and the subsequent rapid response to prevent further spread. Effectively identifying, tracking and responding to these threats is often difficult and requires international cooperation due to the rapidity with which diseases cross national borders and spread throughout the global community as a result of travel and migration by humans and animals. From Oct.1, 2008 to Sept. 30, 2009, the United States Department of Defense's (DoD) Armed Forces Health Surveillance Center Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) identified 76 outbreaks in 53 countries. Emerging infectious disease outbreaks were identified by the global network and included a wide spectrum of support activities in collaboration with host country partners, several of which were in direct support of the World Health Organization's (WHO) International Health Regulations (IHR) (2005). The network also supported military forces around the world affected by the novel influenza A/H1N1 pandemic of 2009. With IHR (2005) as the guiding framework for action, the AFHSC-GEIS network of international partners and overseas research laboratories continues to develop into a far-reaching system for identifying, analyzing and responding to emerging disease threats.