Influenza Virus Subtypes in Wild Birds within Selected Sites along the Major Migratory Fly-Ways in Kenya

Human influenza pandemics are rare but recurring events that have periodically affected humanity since ancient times. They are associated with a rapid surge, experienced globally, in the number of cases of respiratory illness and death. Three pandemics occurred during the previous century; the Spanish flu in 1918, the Asian flu in 1957 and the Hong Kong flu in 1968. The world is at risk of another pandemic. For almost two years, health experts have been monitoring a new and severe influenza virus, the highly pathogenic H5Nl strain. Since mid- 2003, this virus has caused the largest and most severe outbreaks of highly pathogenic disease ever recorded in poultry. The current H5Nl strain is a fastmutating and is found in multiple bird species. It is both epizootic and panzootic. Since 1~97, studies of H5Nl indicate that these viruses continue to evolve, with changes in antigenicity and internal gene structure with an expanded host range in avian species and the ability to infect other animal species with enhanced pathogenicity and increased environmental stability. Kenya is a part of the migratory bird fly-way from Europe and Western Asia. Surveillance along the flyway is essential to identify possible HPAI infection and the nature of infection in order to be able to predict possible spillover into human populations. Due to limited data on circulating Influenza strains in wild birds in Kenya, the study was initiated to determine what subtypes of avian influenza viruses are harbored by wild birds in four migration seasons between October 2005 to June 2009. Specimens were collected in 13 sites from 3,618 birds representing 150 species with majority of the specimens being collected from sandpipers, plovers and ducks. The specimens were screened for influenza A by real-time Reverse Transcriptase Polymerase Chain Reaction. All positive Influenza A specimens were further screened for the H5 subtype.Influenza A virus was detected in 1.68% (61/3618) of the all birds representing 23 different species. Of the 61 Influenza A virus positives 21 (34%) were from resident birds, 21 (34%) from paleartic migrants and 19 (32%) from intra African migrants. All the positives were detected during the migration period between October to April. Chi-square was used to determine if there was a significant difference in the number of positive samples in each of the 4 years and among the various categories of birds based on their migration patterns. This variation in prevalence was significant among the four year migration seasons. No highly pathogenic avian influenza viruses were detected during the study period. However, 1 low pathogenic avian influenza virus (LPAI) H12N2 and 4 LPAI H5 subtypes whose neuraminidase subtype was not established were detected in 4 bird species representing both resident and migratory species sampled in 3 sites. The findings demonstrate the potential for wild birds as reservoirs and disseminators of HPAI viruses to areas that may be free from the viruses. The study has given animal and public health experts a baseline of influenza virus activity in wild birds. The study should be strengthened and maintained to continuously monitor influenza virus subtypes circulating in wild birds. In addition to screening for H5 subtypes, other subtypes like the H7 should also be screened for as they are known to cause outbreaks in poultry and have been associated with disease in humans

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Human and entomologic investigations of chikungunya outbreak in Mandera, Northeastern Kenya, 2016.

Chikungunya is a reemerging vector borne pathogen associated with severe morbidity in affected populations. Lamu, along the Kenyan coast was affected by a major chikungunya outbreak in 2004. Twelve years later, we report on entomologic investigations and laboratory confirmed chikungunya cases in northeastern Kenya. Patient blood samples were received at the Kenya Medical Research Institute (KEMRI) viral hemorrhagic fever laboratory and the immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against chikungunya and dengue. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus, alphavirus and chikungunya specific primers were used to detect acute infections and representative PCR positive samples sequenced to confirm the circulating strain. Immature mosquitoes were collected from water-holding containers indoors and outdoors in the affected areas in northeastern Kenya. A total of 189 human samples were tested; 126 from Kenya and 63 from Somalia. 52.9% (100/189) tested positive for Chikungunya virus (CHIKV) by either IgM ELISA or RT-PCR. Sequence analysis of selected samples revealed that the virus was closely related to that from China (2010). 29% (55/189) of the samples, almost all from northeastern Kenya or with a history of travel to northern Kenya, tested positive for dengue IgM antibodies. Entomologic risk assessment revealed high house, container and Breteau indices of, 14.5, 41.9 and 17.1% respectively. Underground water storage tanks were the most abundant, 30.1%, of which 77.4% were infested with Aedes aegypti mosquitoes. These findings confirm the presence of active chikungunya infections in the northeastern parts of Kenya. The detection of dengue IgM antibodies concurrently with chikungunya virus circulation emphasizes on the need for improved surveillance systems and diagnostic algorithms with the capacity to capture multiple causes of arbovirus infections as these two viruses share common vectors and eco-systems. In addition sustained entomological surveillance and vector control programs targeting most productive containers are needed to monitor changes in vector densities, for early detection of the viruses and initiate vector control efforts to prevent possible outbreaks

Monoclonal Antibodies for Rift Valley Fever Virus Nucleocapsid: Application in IgG/IgM ELISA for Sero-Diagnosis

Introduction: Rift Valley fever virus (RVFV) belonging to the Phenuiviridae family is responsible for a zoonotic disease called Rift Valley fever (RVF). Currently, RVFV has spread from Africa to Asia, and due to its ability to cause high mortality rates, it has significantly impacted human health and economic development in many societies. Highly specific and sensitive systems for sero-diagnosis of RVFV infection are needed for clinical use. Method: BALB/c mice were immunized with recombinant RVFV nucleocapsid (rRVFV-N) protein and the spleen cells fused with SP2/0 myeloma cells to create hybridoma cell lines. The secreted monoclonal antibodies (MAbs) were purified and characterized. Enzyme-linked immunosorbent assay (ELISA) systems for the detection of IgG and IgM using the new MAbs were established and evaluated. Serum samples from 96 volunteers and 93 patients of suspected RVF from Kenya were tested compared with the ELISA systems based on inactivated viruses and the rabbit polyclonal antibody. Result: Three monoclonal antibodies against rRVFV-N protein were established. The performance of the MAb-based sandwich IgG ELISA and the IgM capture ELISA perfectly matched the ELISA systems using the inactivated virus or the polyclonal antibody. Conclusions: Recombinant RVFV-N protein-specific MAbs were developed and they offer useful tools for RVFV studies. The MAb-based ELISA systems for detecting IgG and IgM offer safe and useful options for diagnosing RVFV infections in humans

Phylogenetic relationships of Chikungunya virus strains.

The tree was inferred in MEGA version 7 using 1138 base pair data set that encompasses the capsid protein. The analysis involved 52 nucleotide sequences. The Kenyan dataset is in the red typeface.</p

Graph showing the number of samples received and the number positive for Chikungunya and Dengue, February–June 2016.

Graph showing the number of samples received and the number positive for Chikungunya and Dengue, February–June 2016.</p

Map of Kenya showing regions from which human samples were obtained for testing.

Map of Kenya showing regions from which human samples were obtained for testing.</p

The number of wet containers sampled indoors and outdoors and immature <i>Ae</i>. <i>aegypti</i> positivity rates.

The number of wet containers sampled indoors and outdoors and immature Ae. aegypti positivity rates.</p

A household serosurvey to estimate the magnitude of a dengue outbreak in Mombasa, Kenya, 2013.

Dengue appears to be endemic in Africa with a number of reported outbreaks. In February 2013, several individuals with dengue-like illnesses and negative malaria blood smears were identified in Mombasa, Kenya. Dengue was laboratory confirmed and an investigation was conducted to estimate the magnitude of local transmission including a serologic survey to determine incident dengue virus (DENV) infections. Consenting household members provided serum and were questioned regarding exposures and medical history. RT-PCR was used to identify current DENV infections and IgM anti-DENV ELISA to identify recent infections. Of 1,500 participants from 701 households, 210 (13%) had evidence of current or recent DENV infection. Among those infected, 93 (44%) reported fever in the past month. Most (68, 73%) febrile infected participants were seen by a clinician and all but one of 32 participants who reportedly received a diagnosis were clinically diagnosed as having malaria. Having open windows at night (OR = 2.3; CI: 1.1-4.8), not using daily mosquito repellent (OR = 1.6; CI: 1.0-2.8), and recent travel outside of Kenya (OR = 2.5; CI: 1.1-5.4) were associated with increased risk of DENV infection. This survey provided a robust measure of incident DENV infections in a setting where cases were often unrecognized and misdiagnosed