Molecular Characterization and Phylogenetic Analysis of the Hemagglutinin 1 Protein of Human Influenza A Virus Subtype H1N1 Circulating in Kenya During 2007-2008

Abstract

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.

In SilicoIdentification of Highly Conserved Epitopes of Influenza A H1N1, H2N2, H3N2, and H5N1 with Diagnostic and Vaccination Potential

“…However, for all of the subtypes, with the exception of H2N2, the protein in which the greatest number of epitopes has been described is HA, with the following percentages: H1N1 50.7%, H3N2 52.2%, and H5N1 67.7%. This finding is similar to observations made by Bulimo and Cols in 2012 [ 46 ]. Interestingly, M2 is the protein for which fewer epitopes have been described, even though the M2 protein has been one of the main targets in studies focusing on vaccine development in the last few years [ 47 – 50 ].…”

“…In the case of the HA membrane protein, the majority of the consensus epitopes identified were located in the globular region (HA1); thus, we can infer that this region in general and, more specifically, the region close to the sialic acid-binding site show a greater degree of conservation than the stem region. These findings are different than those reported by Bulimo et al in Kenya in 2012 [ 46 ] in a study that was completed during the 2007-2008 season; however, they support those findings reported by Iba et al [ 60 ] in a study completed with the H3N2 strain with globular region epitopes with greater antigenic overlap than those found in the stem region. These findings emphasize the importance of conserving the cellular recognition region of the virus.…”

Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009–2012

“…Nasopharyngeal (NP) specimens were retrieved from archives of the respiratory virus surveillance program in the Department of Emerging Infectious Diseases (DEID) of the United States Army Medical Research Unit-Kenya (USAMRU-K) [ 13 ]. These approximately 10000 archived NP specimens were collected from a study population comprising persons from two months of age onwards who attended outpatient clinics in the hospitals involved in the USAMRU-K respiratory virus surveillance; presenting with influenza like illnesses symptoms.…”

“…The surveillance network comprised Mbagathi, Isiolo, Alupe, Kericho, Kisi, Malindi, and Port Reitz district hospitals, as well as the New Nyanza General provincial hospital [ 13 ]. These hospitals represent disparate geographic regions and population demographics across the country and were delineated into Central, Northern, Western, Highlands and Coastal regions of Kenya, respectively.…”

“…These hospitals represent disparate geographic regions and population demographics across the country and were delineated into Central, Northern, Western, Highlands and Coastal regions of Kenya, respectively. Inclusion criteria consisted of being an outpatient aged at least 2 months and having influenza-like-illness (ILI) symptoms [ 13 ]. Clinical parameters and symptoms including recent history of ILI, cough, sore throat, difficulty in breathing, chills, nasal stuffiness, runny nose, sputum production, headache, joint pain, fatigue, diarrhea, vomiting and bleeding were documented.…”