Molecular variations in Vibrio alginolyticus and V. harveyi in shrimp-farming systems upon stress

A study was performed to investigate the genomic variations in the shrimp farm isolates of Vibrio alginolyticus and V. harveyi when the isolates were subjected to environmental stress. Samples of shrimps, water and sediment were collected from Southern Indian coastal shrimp farms. Vibrio isolates were biochemically identified and confirmed using 16S rDNA and gyrB gene specific PCR. The bacterial strains were genotyped by PCR fingerprinting using GTG(5) and IS (Insertion Sequence) primers. Seven strains each of V. alginolyticus and V. harveyi were subjected to 10 passages through trypticase soya broth (TSB), which contained different NaCl concentrations (3, 6 and 8%) and trypticase soya agar (TSA). V. alginolyticus was also passaged through TSB with a 12% NaCl concentration. PCR fingerprinting, which was performed on the strains that were passaged through different salt concentrations, confirmed that V. alginolyticus and V. harveyi could affect the genomic variations, depending on the environmental conditions of the culture. The study highlights the complex genotypic variations that occur in Vibrio strains of tropical aquatic environment because of varied environmental conditions, which result in genetic divergence and/or probable convergence. Such genetic divergence and/or convergence can lead to the organismal adaptive variation, which results in their ability to cause a productive infection in aquatic organisms or generation of new strains.

Analysis of genetic characteristics and molecular variation of human rhinovirus strains isolated in Shenzhen during 2012 / 中华微生物学和免疫学杂志

Objective To analyze the genetic characteristics and molecular variation of human rhi-novirus strains isolated in Shenzhen.Methods RNA samples were extracted from nasopharyngeal swab samples collected from influenza-like subjects in Shenzhen and analyzed by fluorescent RT-PCR.The VP4-VP2 and VP1 gene regions of human rhinovirus strains were amplified by nested RT-PCR.Clustal W and MEGA programs were used to evaluate molecular variation of the human rhinovirus strains.Results Both human rhinovirus A and B were prevalent in Shenzhen during 2012.Human rhinoviruses A was the predomi-nant pathogen, including subtypes A47, A31, A90, A18 and so on.Two recombinant strains of human rhi-noviruses A47 and A31 were detected.The mutations scattered on the VP1 protein and varied in different subtypes.The receptor binding sites ( loop BC, DE and HI) in different subtypes showed polymorphism. Five out of twenty-five drug sensitivity sites ( I121V, L123M, V167I, Y189H and H259G) showed muta-tion.Conclusion Multiple subtypes of human rhinovirus were prevalent in Shenzhen and were in a state of constant recombination and variation.

Epidemic pattern and molecular variation of respiratory syncytial virus strains isolated in Shenzhen from year 2012 to 2013 / 中华微生物学和免疫学杂志

Objective To study the epidemic pattern and molecular variation of respiratory syncy-tial virus ( RSV) strains isolated in Shenzhen from year 2012 to 2013.Methods The clinical samples iso-lated from patients with influenza-like illness were analyzed by fluorescent RT-PCR to screen RSV positive strains.The C-terminal variable regions of genes encoding G proteins were amplified by nested RT-PCR. Molecular variation was analyzed by using Clustal W and MEGA softwares.Results RSV strains were wide-ly prevalent in Shenzhen from 2012 to 2013.Two epidemic peaks usually occurred in spring and summer/au-tumn of each year.The RSV isolates were subtyped into group A belonging to genotype NA1 and group B be-longing to genotype BAⅨ.Most of the mutations scattered at the C-terminal region of G protein.A few mu-tations caused the disappearance of certain glycosylation sites.A novel recombinant virus strain containing 24 inserted amino acids was identified in 2013, which was likely to be introduced into our country from abroad. Conclusion RSV strains were widely and continuously prevalent in Shenzhen, characterized by constant evolution and variation.

Molecular Variation and Distribution of Anopheles fluviatilis (Diptera: Culicidae) Complex in Iran

Anopheles fluviatilis James (Diptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 28S-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 28S-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination.