Robustness in population-structure and demographic-inference results derived from the Aedes aegypti SNP chip and whole-genome sequencing data.

The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya and Zika, which affect millions of people world-wide. Population genetics studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse Ae. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shot-gun sequencing approach using mosquitoes from the native (Africa) and invasive range (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic and phylogenetic analyses using the SNP chip were congruent with those derived from low coverage whole genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases, opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole genome sequencing for population genetic studies of Ae. aegypti that do not rely on full allelic frequency spectra. Whole genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.

Population Genetic Analysis of Aedes aegypti Mosquitoes From Sudan Revealed Recent Independent Colonization Events by the Two Subspecies.

Increases in arbovirus outbreaks in Sudan are vectored by Aedes aegypti, raising the medical importance of this mosquito. We genotyped 12 microsatellite loci in four populations of Ae. aegypti from Sudan, two from the East and two from the West, and analyzed them together with a previously published database of 31 worldwide populations to infer population structure and investigate the demographic history of this species in Sudan. Our results revealed the presence of two genetically distinct subspecies of Ae. aegypti in Sudan. These are Ae. aegypti aegypti in Eastern Sudan and Ae. aegypti formosus in Western Sudan. Clustering analysis showed that mosquitoes from East Sudan are genetically homogeneous, while we found population substructure in West Sudan. In the global context our results indicate that Eastern Sudan populations are genetically closer to Asian and American populations, while Western Sudan populations are related to East and West African populations. Approximate Bayesian Computation Analysis supports a scenario in which Ae. aegypti entered Sudan in at least two independent occasions nearly 70-80 years ago. This study provides a baseline database that can be used to determine the likely origin of new introductions for this invasive species into Sudan. The presence of the two subspecies in the country should be consider when designing interventions, since they display different behaviors regarding epidemiologically relevant parameters, such as blood feeding preferences and ability to transmit disease.

Assessment of genetic diversity of Plasmodium falciparum circumsporozoite protein in Sudan: the RTS,S leading malaria vaccine candidate.

BACKGROUND: The currently used malaria vaccine, RTS,S, is designed based on the Plasmodium falciparum circumsporozoite protein (PfCSP). The pfcsp gene, besides having different polymorphic patterns, can vary between P. falciparum isolates due to geographical origin and host immune response. Such aspects are essential when considering the deployment of the RTS,S vaccine in a certain region. Therefore, this study assessed the genetic diversity of P. falciparum in Sudan based on the pfcsp gene by investigating the diversity at the N-terminal, central repeat, and the C-terminal regions. METHODS: A cross-sectional molecular study was conducted; P. falciparum isolates were collected from different health centres in Khartoum State between January and December 2019. During the study period, a total of 261 febrile patients were recruited. Malaria diagnosis was made by expert microscopists using Giemsa-stained thick and thin blood films. DNA samples were examined by the semi-nested polymerase chain reaction (PCR). Single clonal infection of the confirmed P. falciparum cases, were used to amplify the pfcsp gene. The amplified amplicons of pfcsp have been sequenced using the Sanger dideoxy method. The obtained sequences of pfcsp nucleotide diversity parameters including the numbers of haplotypes (Hap), haplotypes diversity (Hapd), the average number of nucleotide differences between two sequences (p), and the numbers of segregating sites (S) were obtained. The haplotype networks were constructed using the online tcsBU software. Natural selection theory was also tested on pfcsp using Fuand Li's D, Fuand Li's F statistics, and Tajima's D test using DnaSP. RESULTS: In comparison with the different pfcsp reference strains, the Sudanese isolates showed high similarity with other African isolates. The results of the N-terminal region showed the presence of 2 different haplotypes with a Hapd of 0.425 ± 0.00727. The presence of the unique insertion of NNNGDNGREGKDEDKRDGNN was reported. The KLKQP motif was conserved in all the studied isolates. At the central repeat region, 11 haplotypes were seen with a Hapd of 0.779 ± 0.00097. The analysis of the genetic diversity in the C-terminal region showed the presence of 10 haplotypes with a Hapd of 0.457 ± 0.073. Several non-synonymous amino acids changes were also seen at the Th2R and the Th3R T-cell epitope regions including T317K, E317K, Q318E, K321N, I322K, T322K, R322K, K324Q, I327L, G352N, S354P, R355K, N356D, Q357E, and E361A. CONCLUSIONS: In this study, the results indicated a high conservation at the pfcsp gene. This may further contribute in understanding the genetic polymorphisms of P. falciparum prior to the deployment of the RTS,S vaccine in Sudan.

Emergence of the invasive malaria vector Anopheles stephensi in Khartoum State, Central Sudan.

The emergence of the Asian invasive malaria vector, Anopheles stephensi, has been identified in Khartoum, the capital city of Sudan. This is the first report that confirms the geographical expansion of this urban mosquito into Central Sudan. We urgently recommend the launch of a national entomological survey to determine the distribution of this invasive disease vector and to generate essential information about its bionomics and susceptibility to available malaria control measures.

Proteomics and Docking Study Targeting Penicillin-Binding Protein and Penicillin-Binding Protein2a of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Sudan.

Whole genome sequencing of methicillin-resistant Staphylococcus aureus (MRSA) strain isolated from Sudan has led to a great deal of information, which allows the identification and characterization of some pivotal proteins. The objective of this study was to investigate the penicillin-binding proteins, PBP and PBP2a, of SO-1977 strain to have insights about their physicochemical properties and to assess and describe the interaction of some phytochemicals against them in silico. PBP and PBP2a from MRSA's Sudan strain were found to be of great resemblance with some other strains. G246E single-nucleotide polymorphism was reported and identified in the allosteric binding site positioned in the non-penicillin-binding domain. The docked compounds demonstrated good binding energies and hydrogen bond interactions with residue Ser404 which plays crucial roles in ß-lactam activity. This finding would contribute significantly to designing effective ß-lactam drugs, to combat and treat ß-lactam-resistant bacteria in the future.