Gauri Awasthi

The development and rapid spread of chloroquine resistance (CQR) in Plasmodium falciparum have triggered the identification of several genetic target(s) in the P. falciparum genome. In particular, mutations in the Pfcrt gene, specifically, K76T and mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75 and 76), are considered to be highly related to CQR. These various mutations form several different haplotypes and Pfcrt gene polymorphisms and the global distribution of the different CQR- Pfcrt haplotypes in endemic and non-endemic regions of P. falciparum malaria have been the subject of extensive study. Despite the fact that the Pfcrt gene is considered to be the primary CQR gene in P. falciparum , several studies have suggested that this may not be the case. Furthermore, there is a poor correlation between the evolutionary implications of the Pfcrt haplotypes and the inferred migration of CQR P. falciparum based on CQR epidemiological surveillance data. The present paper aims to clarify the existing knowledge on the genetic basis of the different CQR- Pfcrt haplotypes that are prevalent in worldwide populations based on the published literature and to analyse the data to generate hypotheses on the genetics and evolution of CQR malaria.

Mutations in the Pfcrt gene that change the resulting amino acids and form different haplotypes are common and correlate with the prevalence of chloroquine resistant (CQR) field isolates of the malaria parasite, Plasmodium falciparum. This correlation provides opportunities to infer the global evolutionary history of CQ resistance by analysing CQR Pfcrt haplotype data. We collated data on the Pfcrt haplotypes from different global studies and performed evolutionary genetic analysis to present comprehensive and comparative information on the global distribution of five major CQR-Pfcrt haplotypes and evolutionary inter-relationships among 38 different countries. Using the haplotype diversity data, inter-continental genetic differentiation was also ascertained.

Comparative genomics and evolutionary analyses of conserved genes have enabled us to understand the complexity of genomes of closely related species. For example: β-globin gene present in human hemoglobin is one such gene that has experienced many genetic changes in many related taxa and produced more than 600 variants. One of the variant, HBS causes sickle-cell anemia in humans but offers protection against severe malaria due to Plasmodium falciparum. In the present study, we characterized and performed evolutionary comparative analyses of the ?-globin gene in different related and unrelated taxa to have a comprehensive view of its evolution. DNA and protein sequences of β-globin gene were downloaded from NCBI and characterized in detail in nine eutherian (Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus, Rattus norvegicus, Bos taurus, Canis familiaris, Equus caballus, Oryctolagus cuniculus), a dinosaurian (Gallus gallus) and a neopterygii (Danio rerio) taxa. Three more eutherian (Papio anubis, Ovis aries and Sus scrofa) taxa were included for an analysis at the protein level but not included at the gene level owing to lack of genomic information. Computational and phylogenetic analyses were performed using evolutionary comparative approach. Results of comparative and phylogenetic analyses revealed less conservation of genetic architecture of β-globin compared to its protein architecture in all eutherian taxa. Both dinosaurian and neopterygii taxa served as outgroups and varied at gene and protein levels. Most remarkably, all primates from eutherian taxa including P. anubis showed only nine codon position differences and an absolute similarity between H. sapiens and P. troglodytes. Absolute conservation of coding region in Equus caballus (horse) was observed. The results were discussed with an inference on the role of evolutionary forces in maintaining such close similarities and variations across closely related taxa. Further, the need to utilize more comparative approaches in understanding the disease causing genes' evolution in closely related taxa is hoped for.

Genome scan and genotype-phenotype association study offer excellent opportunities to unearth drug/vaccine targets in human pathogens including malaria parasites. A recently conducted such study in worldwide isolates in the most devastating malaria parasite Plasmodium falciparum has reported important genomic information on genetic basis of antimalarial resistance. Several unknown genes were also found to be under strong influence of natural selection. The findings provide important insights into the malaria parasite genome evolution in general and to use this information to develop more focused malaria control strategies, in particular.

Evolutionary analyses of genes conserved across taxa are keys to understand the complexity of gene and genome variation. Since malaria is a highly infectious human disease and its susceptibility in human is genetically controlled, characterization and evolutionary analyses of such genes are of prime importance to understand genetic mechanisms of disease susceptibility. In the present study we have characterized and performed comparative genomic analyses of the human Duffy gene responsible for malaria pathogenesis in nine different mammalian taxa. DNA sequences of human duffy gene were downloaded from public domain and have been characterized in detail and compared with eight other different mammalian taxa (Pan troglodytes, Macaca mulatta, Pongo pygmaeus, Rattus norvegicus, Mus musculus, Monodelphis domestica, Bos taurus and Canis familiaris). Comparative and evolutionary analyses were performed using statistical software and tools. We observed that the genetic architecture of this gene was entirely different across all the nine taxa and a close similarity between Homo sapiens and Pan troglodytes (chimpanzee) was evident for several aspects of this gene. Comparisons on several aspects, such as ratio of coding and non-coding regions, total gene length number and size of introns and difference of number of nucleotides in human and chimpanzees have revealed interesting features. Phylogenetic inferences based on the Duffy gene among nine different taxa were found to be different than other genes previously studied. Most remarkably, human and chimpanzee were only 0.75% different in this gene. The results were discussed on the similarities between human and chimpanzee and gain of introns in human-chimpanzee clade with an inference on the role of evolutionary forces (mainly natural selection) in maintaining such variations across closely-related mammalian taxa.

Understanding evolutionary genetic details of immune system genes responsible for infectious diseases is of prime importance concerning disease pathogenecity. Considering malaria as a devastating disease in the world including India, detail evolutionary understanding on human immune system gene is essential. The primary aim of this study was to initiate work on one such gene, the human CD36 gene responsible in malaria pathogenesis. DNA sequences of the human CD36 gene was retrieved from public domain and fine-scale details were characterized. Both comparative and evolutionary analyses were performed with sequences from six other taxa (5 mammalian one avian) where CD36 homologs are present. Different statistical analyses were also performed. Differential distribution in number and length of exons and introns was detected in CD36 gene across seven taxa. The CpG islands were also found to be distributed unevenly across the gene and taxa. Neighbour-joining tree was constructed and it was observed that the chimpanzee and human are diverged at the CD36 gene relatively recently. The chicken, Gallus gallus was found to be diverged from rest of the taxa significantly. Also copy number variation was observed across different taxa. Comparative genomic study of a human immune system gene CD36 show relationships among different taxa at the evolutionary level. The information can be of help to study genetic diversity in malaria endemic zones and to correlate it with malaria pathogenecity.

Coincidence of acute pancreatitis caused by hepatitis E virus (HEV) infection is rare. We report a case of severe acute pancreatitis in the course of acute hepatitis E in a 35-year-old man who presented with jaundice for 1 week. Serum was positive for IgM anti-HEV and negative for hepatitis A, B and C viruses. There was upper abdominal tenderness and fullness with absent bowel sounds. A diagnosis of acute pancreatitis was made and confirmed with elevated serum lipase 2,032 U/L and amylase 1,287 U/L. Two weeks after admission he had an increase in abdominal pain associated with oliguria and hemodynamic instability. Serum creatinine had increased and hemoglobin had dropped along with metabolic acidosis. Ultrasound showed hemorrhage into the pseudocyst, which was confirmed by contrast-enhanced computed tomography scan (which also ruled any pseudoaneurysm as the cause of bleed). He was hemodialysed and transfused blood. However, he developed refractory hypotension and did not respond to inotropes. After a rapid downhill course, he did not survive. Hepatitis E virus infection was complicated with the development of acute pancreatitis, which was severe with multiorgan failure and had a fatal outcome.