The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya

The emergence and establishment of SARS-CoV-2 variants of concern presented a major global public health crisis across the world. There were six waves of SARS-CoV-2 cases in Kenya that corresponded with the introduction and eventual dominance of the major SARS-COV-2 variants of concern, excepting the first 2 waves that were both wild-type virus. We estimate that more than 1000 SARS-CoV-2 introductions occurred in the two-year epidemic period (March 2020 - September 2022) and a total of 930 introductions were associated with variants of concern namely Beta (n=78), Alpha(n=108), Delta(n=239) and Omicron (n=505). A total of 29 introductions were associated with A.23.1 variant that circulated in high frequencies in Uganda and Rwanda. The actual number of introductions is likely to be higher than these conservative estimates due to limited genomic sequencing. Our data suggested that cryptic transmission was usually underway prior to the first real-time identification of a new variant, and that multiple introductions were responsible. Following emergence of each VOC and subsequent introduction, transmission patterns were associated with hotspots of transmission in Coast, Nairobi and Western Kenya and follows established land and air transport corridors. Understanding the introduction and dispersal of major circulating variants and identifying the sources of new introductions is important to inform public health control strategies within Kenya and the larger East-African region. Border control and case finding reactive to new variants is unlikely to be a successful control strategy.

Genetic diversity of nontuberculous mycobacteria among symptomatic tuberculosis negative patients in Kenya.

Background: Non-Tuberculous Mycobacteria (NTM) transmission to humans occurs through inhalation of dust particles or vaporized water containing NTM leading to pulmonary manifestations. NTM infections are often misdiagnosed for tuberculosis (TB) due to their similar clinical and radiological manifestations. Aims and Objectives: We, therefore, performed a species-level identification of NTM in symptomatic TB negative patients through sequencing of the hsp65 gene. Materials and Methods: We conducted a cross-sectional study at the National Tuberculosis Reference Laboratory in the period between January to November 2020. One hundred and sixty-six mycobacterial culture-positive samples that tested negative for TB using capilia underwent Polymerase Chain Reaction targeting the hsp65 gene. Isolates showing a band with gel electrophoresis at 441 bp position were sequenced using Sanger technology. Geneious software was used to analyze the obtained sequences, and the National Center for Biotechnology Information gene database identified NTM species for each isolate. A phylogenetic tree was constructed from the DNA sequences and evolutionary distances computed using the general time-reversible method. Pearson chi-square was used to determine the association between NTM infection and participants' characteristics. Results: Our study identified 43 different NTM species. The dominant NTM belonged to Mycobacterium avium complex 37 (31%). Slow-growing NTM were the majority at 86 (71%) while rapid-growing NTM were 36 (29%). A significant association (P<0.05) was observed for regions and age, while patient type had a weak likelihood of NTM infection. Conclusion: Our study characterized the diversity of NTM in Kenya for the first time and showed that species belonging to M. Avium Complex are the most prevalent in the country.

Amino acid sequence analysis and identification of mutations in the NS gene of 2009 influenza A (H1N1) isolates from Kenya.

Although the important role of the nonstructural (NS) gene of influenza A virus in virulence and replication is well-established, the knowledge about the extent of variation in the NS gene of 2009 influenza A (H1N1) viruses in Kenya and Africa is scanty. This study analysed the NS gene of 31 isolates from Kenya in order to obtain a more detailed knowledge about the genetic variation of NS gene of 2009 influenza A (H1N1) isolates from Kenya. A comparison with the vaccine strain and viruses isolated elsewhere in Africa was also made. The amino acid sequences of the non-structural protein, NS1 of the viruses from this study and the vaccine strain revealed 18 differences. Conversely, the nuclear export protein (NEP) of the isolates in this study had 11 differences from the vaccine strain. Analysis of the NS1 protein showed only one fixed amino acid change I123V which is one of the characteristics of clade 7 viruses. In the NEP, the amino acid at position 77 was the most mutable with 9 (39%) of all mutations seen in this protein. A mutation A115T which is a characteristic of clade 5 viruses was noted in the isolates from Lagos, Nigeria. The study shows a substantial number of mutations in the NS gene that has not been reported elsewhere and gives a glimpse of the evolution of this gene in the region.