No abstract

Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3–14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing.

The problem of the discrepancy between serotypes of the circulating strains of hepatitis B virus and serotype of the HBsAg in the vaccine is discussed. The results of published scientific studies show that hepatitis B vaccines containing HBsAg serotype ad provide good, but not optimal, protection against heterologous serotypes of the virus. The authors conclude that the use of vaccines containing HBsAg serotype typical for given territory is a priority. Further in-depth studies on this issue are needed to clarify the available scientific evidence.

The article presents the results of analysis of reported incidence of acute and chronic hepatitis С in Russian Federation. Detailed description of current epidemiological characteristics of acute and chronic hepatitis С in various Federal regions and in different age groups is provided. The authors discuss the most probable transmission routs of HCV and its genotype distribution in Russia. Critical problems of laboratory diagnosis and hepatitis С surveillance are reviewed. There is an urgent need for introduction of HCV RNA as a routine confirmatory test for acute and chronic hepatitis С as well as introduction of Viral Hepatitis Registry for HCV patients throughout the entire territory of the Russian Federation.

No abstract