Abstract
Leishmania (Viannia) braziliensis is an important Leishmania species circulating in several Central and South American countries. Among Leishmania species circulating in Brazil, Argentina and Colombia, L. braziliensis has the highest genomic variability. However, genomic variability at the whole genome level has been only studied in Brazilian and Peruvian isolates; to date, no Colombian isolates have been studied. Considering that in Colombia, L. braziliensis is a species with great clinical and therapeutic relevance, as well as the role of genetic variability in the epidemiology of leishmaniasis, we analyzed and evaluated intraspecific genomic variability of L. braziliensis from Colombian and Bolivian isolates and compared them with Brazilian isolates. Twenty-one genomes were analyzed, six from Colombian patients, one from a Bolivian patient, and 14 Brazilian isolates downloaded from public databases. The results obtained of Phylogenomic analysis showed the existence of four well-supported clades, which evidenced intraspecific variability. The whole-genome analysis revealed structural variations in the somy, mainly in the Brazilian genomes (clade 1 and clade 3), low copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs) in all genomes analyzed. Interestingly, the genomes belonging to clades 2 and 3 from Colombia and Brazil, respectively, were characterized by low heterozygosity (~90% of SNP loci were homozygous) and regions suggestive of loss of heterozygosity (LOH). Additionally, we observed the drastic whole genome loss of heterozygosity and possible hybridization events in one genome belonging to clade 4. Unique/shared SNPs between and within the four clades were identified, revealing the importance of some of them in biological processes of L. braziliensis. Our analyses demonstrate high genomic variability of L. braziliensis in different regions of South America, mainly in Colombia and suggest that this species exhibits striking genomic diversity and a capacity of genomic hybridization; additionally, this is the first study to report whole-genome sequences of Colombian L. braziliensis isolates.
Highlights
Leishmania (Viannia) braziliensis is the most important Leishmania species associated with cases of cutaneous leishmaniasis and muco-cutaneous leishmaniasis in several Central and South American countries (Ramirez et al, 2016; Patino et al, 2017)
Considering the public health importance of leishmaniasis caused by L. braziliensis in Colombia and the role of genetic variability of the parasite in the epidemiology of the disease, the objective of this study was to perform a comprehensive analysis of whole genome sequencing (DNA-seq) to evaluate phylogenomic relationships among six Colombian clinical isolates and one Bolivian clinical isolate
The amplification and Sanger sequencing of Cytochrome b proteins (Cytb) and Hsp70 genes identified that the isolates included corresponded to L. braziliensis (Supplementary Table S1)
Summary
Leishmania (Viannia) braziliensis is the most important Leishmania species associated with cases of cutaneous leishmaniasis and muco-cutaneous leishmaniasis in several Central and South American countries (Ramirez et al, 2016; Patino et al, 2017) This species is characterized by its ability to cause distinct forms of tegumentary leishmaniasis in humans (Jirmanus et al, 2012; Meireles et al, 2017) and animals (De Oliveira et al, 2013; Brilhante et al, 2019), and for its variable infectivity, virulence, and response to anti-leishmanial therapy (Rego et al, 2018; Patino et al, 2019a). Few studies have examined this variability in whole genomes of New-World Leishmania species, such as L. braziliensis (Valdivia et al, 2015; Urrea et al, 2018; Bruna et al, 2019; Restrepo et al, 2019), because most of the research has focused on revealing the genome diversity of Old-World Leishmania species (Downing et al, 2011; Imamura et al, 2016; Ghouila et al, 2017; Franssen et al, 2020)
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