Genetic Diversity of Plasmodium falciparum Surface Protein 25, 230 and 48/45 Gene in Malaria Endemic, Mesoendemic and Epidemic Regions of Western Kenya Kevin O. Ochwedo1, 2*, Daibin Zhong3, Fredrick Otieno Ariri4, Wolfgang R. Mukabana1, 2, Antony C. A. Otieno1, Sidney O. Ogolla7, Harryson Atieli2, 6, Ming-Chieh Lee3, Shirley A. Onyango2, Pauline W. Orondo2, Benyl M. Ondeto1, 2, Collince J. Omondi1, 2, Andrew K. Githeko2,7, James W. Kazura5* and Yan Guiyan3* Author’s affiliations 1School of biological sciences, University of Nairobi. 2Sub-Saharan Africa International Centre for Excellence in Malaria Research. 3University of California, Irvine. 4School Physical and biological, Maseno University. 5Caste Western Reserve University. 6School of Public Health and Community Development, Maseno University. 7Climate and Human Health Research Unit, Centre for Global Health Research, Kenya Medical. Research Institute, Kisumu, Kenya.
Background: Transmission blocking vaccines (TBVs) are renewed hope in complementing other malaria control strategies aimed at reducing incidents and mortality rates. Leading TBV candidate such as Plasmodium falciparum surface protein 25 (Pfs25), immunogenic domain I (D1) of Pfs230 and domain III (D3) of Pfs48/45 must overcome hurdles of antigenic alterations which may render them allele-specific or ineffective. This study explored sequence variation among three genes from malaria-endemic and epidemic region of western Kenya and described drivers of the observed mutations. Methods: A total of 220 samples collected between 2018 and 2020 from malaria-endemic (Homa Bay and Chulaimbo) and epidemic (Kisii-highland) regions in western Kenya were genotyped. A comparison of the three genes based on their sequence diversity, genetic diversity indices, variants distribution and signature of selection were inferred from sequenced Pfs25, D1 of Pfs230 and D3 of Pfs48/45 gene was also inferred. Results: A total of 10, 6 and 2 polymorphic loci were detected across Pfs25, D1 of Pfs230 and D3 of Pfs48/45 gene respectively from malaria-endemic and epidemic region in western Kenya. Singleton variable sites and nonsynonymous changes each comprised of 60% of the observed changes in Pfs25 sequences from endemic and epidemic sites. Domain III of Pfs25 gene had the highest number (60%) mutated sites, of which all polymorphic loci were under a purifying selection. Two dimorphic loci pairs were under linkage disequilibrium whereas others (105 and 511) had a history of recombination. Nonsynonymous changes predominated all the 6 polymorphic sites with dimorphic codon G605S being pronounced in D1 of Pfs230. Apart from mutated codon K661 which was under a balancing selection the rest were under purifying selection. History of recombination was detected between sites 1813 and 1955 among the mutated sites. Two mutated sites resulting in nonsynonymous changes were observed in the D3 of Pfs48/45. The two mutations occurred in 18.75% of sequences, mutated codon L314I was pronounced across the three study sites. D3 of Pfs48/45 had a high conservation index and a low number of variants. Conclusion: The Pfs25, D1 of Pfs230 and D3 of Pfs48/45 gene from the endemic and epidemic region in Kenya revealed varying levels of genetic diversity. Within the fusion protein, D3 of Pfs48/45 gene is highly conserved and stable as a TBV candidate with less number of variants. Purifying and balancing selection, inbreeding and recombination were predicted as the cause and drivers sustaining these variations. With the observed low nucleotide diversity, the three antigens stand a chance as formidable TBV candidates. Keywords: Transmission blocking vaccines, Pfs25, Pfs230, Pfs48/45, Polymorphism, Selection, Linkage disequilibrium, Recombination