Increased circulation of hepatitis A virus genotype IIIA over the last decade in St Petersburg, Russia

Мукомолов, С. Л.; Kontio, Mia; Железнова, Н. В.; Jokinen, Sari; Sinayskaya, Eugenia; Stalevskaya, Anna; Davidkin, Irja

doi:10.1002/jmv.23378

Cited by 15 publications

(7 citation statements)

References 96 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Phylogenetic analysis showed that the subtype IA isolates were 93% homologous to the sequences isolated in the European part of Russia, which formed a single phylogenetic cluster. This is consistent with reports on hepatitis A virus genomic variants circulating in the European part of Russia [ 13 , 19 ]. The identified subtype IB strains had maximum homology with isolates from Egypt and Bulgaria, which indicated probable imported cases of hepatitis A infection [ 20 ].…”

Section: Resultssupporting

confidence: 93%

Sequencing of the VP1–2A Genome Segment for Hepatitis A Subtyping

Залесских¹,

Быстрова²

2020

Sovrem Tehnol Med

View full text Add to dashboard Cite

The aim of the study was to improve the VP1-2A sequencing method and facilitate the hepatitis A virus genotyping technique. Materials and Methods. Nucleic acids were extracted by using commercial kits for nucleic acid extraction and reverse transcription in a manual and automatic version. Primer sequences were selected using the DNASTAR software. Oligonucleotides were synthesized by the amidophosphite method followed by purification with polyacrylamide gel electrophoresis. The sought fragments of the genome were obtained with PCR. Commercial components were used to prepare the reaction mixture. The results were verified by agarose gel electrophoresis with ethidium bromide DNA staining. After amplification, the DNA fragments were purified by adsorption on silica columns. Sequence identification of the purified fragments was performed by the Sanger sequencing method. The obtained sequences of the VP1-2A fragment were analyzed by the MEGA 6 software package. The optimized technique for sequencing of the VP1-2A segment was tested with 171 clinical and environmental samples containing hepatitis A virus RNA. Results. The sequencing technique has been optimized at the stage of amplification of the variable VP1-2A structural genome segment. To obtain this result, we created original primer sequences and selected the polymerase reaction conditions (length, localization and annealing temperature, concentration of the primers and template). The sought fragment with a length of 249 nucleotide pairs was located between the 2988 th and 3237 th base pairs as per the reference HM175 strain. Using this optimized method of VP1-2A fragment sequencing, the hepatitis A genotype was detected in 76 from 171 samples containing hepatitis A virus RNA in the city of Nizhny Novgorod from 2000 to 2017. The prevalence of the IA subtype was found in 97% of cases (74 of 76 samples), and only 2 samples contained subtype IB. Conclusion. The sequencing technique optimized at the stage of VP1-2A fragment amplification allows one to determine the hepatitis A virus genotype, identify imported virus strains, and also establish an epidemiological relationship between different cases of the disease.

show abstract

Section: Resultssupporting

confidence: 93%

Sequencing of the VP1–2A Genome Segment for Hepatitis A Subtyping

Залесских¹,

Быстрова²

2020

Sovrem Tehnol Med

View full text Add to dashboard Cite

show abstract

“…Several HAV outbreaks due to consumption of berries and vegetables have been reported previously (Butot et al 2007 ). Reports on contamination of vegetables from several parts of the world (Mukomolov et al 2012 ; Hernández et al 1997 ; Felix-Valenzuela et al 2012 ) indicate the gravity of the situation.…”

Section: Discussionmentioning

confidence: 99%

HAV in fresh vegetables: a hidden health risk in district Mardan, Pakistan

et al. 2014

View full text Add to dashboard Cite

Hepatitis A is an acute inflammation of the liver caused by the hepatitis A virus (HAV) in human. The path of entry of HAV to the bloodstream is the epithelium of the intestine. Liver inflammation occurs when HAV multiplies within the hepatocytes and Kupffer cells of the liver. HAV is mostly transmitted by contaminated water, fruits and vegetables. The purpose of the current study was to evaluate fresh vegetables raised on the fecal contaminated water for the detection of HAV by PCR method. Twenty nine samples were collected from 13 different locations of district Mardan and screened for the presence of HAV. Village Bajowro near Takht Bhai was the most contaminated site having HAV in all vegetables grown over there. Water samples collected from this area proved to be contaminated with HAV. It may be concluded that fecal contaminated water is unsafe for irrigation because of the health risk associated with such practices.

show abstract

“…Results obtained give confidence the method can be sensibly applied to actual surveillance datasets. Examples of existing large molecular epidemiological databases include VNTR typing datasets of tuberculosis [22], spa typing datasets of MRSA [23] and short read sequencing datasets of hepatitis B, hepatitis A and norovirus [24]–[26]. Note that the relevant spatial information differs for these datasets; we might focus on place of residence for tuberculosis, but on hospital, ward or even bed for MRSA.…”

Section: Discussionmentioning

confidence: 99%

Finding Evidence for Local Transmission of Contagious Disease in Molecular Epidemiological Datasets

et al. 2013

View full text Add to dashboard Cite

Surveillance systems of contagious diseases record information on cases to monitor incidence of disease and to evaluate effectiveness of interventions. These systems focus on a well-defined population; a key question is whether observed cases are infected through local transmission within the population or whether cases are the result of importation of infection into the population. Local spread of infection calls for different intervention measures than importation of infection. Besides standardized information on time of symptom onset and location of cases, pathogen genotyping or sequencing offers essential information to address this question. Here we introduce a method that takes full advantage of both the genetic and epidemiological data to distinguish local transmission from importation of infection, by comparing inter-case distances in temporal, spatial and genetic data. Cases that are part of a local transmission chain will have shorter distances between their geographical locations, shorter durations between their times of symptom onset and shorter genetic distances between their pathogen sequences as compared to cases that are due to importation. In contrast to generic clustering algorithms, the proposed method explicitly accounts for the fact that during local transmission of a contagious disease the cases are caused by other cases. No pathogen-specific assumptions are needed due to the use of ordinal distances, which allow for direct comparison between the disparate data types. Using simulations, we test the performance of the method in identifying local transmission of disease in large datasets, and assess how sensitivity and specificity change with varying size of local transmission chains and varying overall disease incidence.

show abstract

Increased circulation of hepatitis A virus genotype IIIA over the last decade in St Petersburg, Russia

Cited by 15 publications

References 96 publications

Sequencing of the VP1–2A Genome Segment for Hepatitis A Subtyping

Sequencing of the VP1–2A Genome Segment for Hepatitis A Subtyping

HAV in fresh vegetables: a hidden health risk in district Mardan, Pakistan

Finding Evidence for Local Transmission of Contagious Disease in Molecular Epidemiological Datasets

Contact Info

Product

Resources

About