Rapid investigation of hepatitis A virus outbreak by single strand conformation polymorphism analysis

The application of single strand conformation polymorphism (SSCP) analysis in determining Hepatitis E virus intra-host diversity

Genetic heterogeneity of RNA populations influences virus pathogenesis, epidemiology and evolution. Therefore, accurate information regarding virus genetic structure is highly important for both diagnostic and scientific purposes. For the Hepatitis E virus (HEV), the causal agent of hepatitis in humans, the intra-host population structure has been poorly investigated, mainly using the less sensitive RFLP-based approach. The objective of this study was to assess the suitability and the accuracy of single strand conformation polymorphism (SSCP) analysis, a well-established tool in genetic variation research, for the characterization of HEV quasispecies. The analysis was conducted on 50 clones of five swine isolates and 30 clones of three human HEV isolates. To identify and quantify the sequence variants present in each HEV isolate, 348bp long fragments of the amplified conserved ORF2 region were separated by cloning. Ten clones per isolate were subjected to SSCP and sequenced in a parallel experiment. The results show a high correlation of SSCP haplotype profiling with the sequencing results, confirming the sensitivity and reliability of this simple, rapid and low cost approach in the characterization of HEV quasispecies.

Single-strand conformation polymorphism analysis for differentiating phytoplasma strains

Single-strand conformation polymorphism (SSCP) analysis is a sensitive and rapid technique for detecting DNA polymorphisms and mutations in PCR-amplified fragments. Due to its technical simplicity, it is widely used as a screening tool in various investigations, ranging from clinical diagnosis of human hereditary diseases to the characterization of microbial communities. This method can also be used successfully on phytoplasmas as a tool for the detection of molecular variability in conserved housekeeping genes such as 16S rRNA and tuf, as well as in more variable genes, revealing the presence of polymorphisms undetected by routine RFLP analyses. The reliability of SSCP has been confirmed by multiple alignments and phylogenetic analyses of representative sequences showing different SSCP profiles. However, it is not broadly applied in phytoplasma research yet. The technique provides an inexpensive, convenient, and sensitive method for determining sequence variation and to differentiate phytoplasma strains, and is particularly suitable for epidemiological studies or as a fast screening, typing tool when dealing with a large number of field samples.

Hepatitis A virus: serology and molecular diagnostics

The diagnosis of hepatitis A virus (HAV) infection is based on the detection of anti-HAV IgM. Shortcomings of this serological approach include the persistence of IgM after normalization of liver enzymes or its detection during polyclonal activation of the immune system due to unrelated viral infection or autoimmune diseases. Molecular diagnosis of HAV along with anti-HAV IgG avidity measurement are helpful in case of positive IgM where laboratory evidence of acute hepatitis is absent and there is no epidemiologic link to other cases. Molecular epidemiology allows us to determine whether viruses from different locations are related to each other and provides further understanding of viral epidemiology by identifying sources and transmission modes. It has been demonstrated that the rapid turnover of HAV strains in low-endemicity countries is caused by their introduction by travelers. Growing sequence databases allow for the identification of geographic origin of viral strains. Collaboration between surveillance laboratories, including database sharing, should be promoted for deeper investigation of outbreaks and improved prevention approaches.