title: Large-scale whole genome sequencing identifies country-wide spread of an emerging G9P[8] rotavirus strain in Hungary, 2012.
abstract: With the availability of rotavirus vaccines routine strain surveillance has been launched or continued in many countries worldwide. In this study relevant information is provided from Hungary in order to extend knowledge about circulating rotavirus strains. Direct sequencing of the RT-PCR products obtained by VP7 and VP4 genes specific primer sets was utilized as routine laboratory method. In addition we explored the advantage of random primed RT-PCR and semiconductor sequencing of the whole genome of selected strains. During the study year, 2012, we identified an increase in the prevalence of G9P[8] strains across the country. This genotype combination predominated in seven out of nine study sites (detection rates, 45-83%). In addition to G9P[8]s, epidemiologically major strains included genotypes G1P[8] (34.2%), G2P[4] (13.5%), and G4P[8] (7.4%), whereas unusual and rare strains were G3P[8] (1%), G2P[8] (0.5%), G1P[4] (0.2%), G3P[4] (0.2%), and G3P[9] (0.2%). Whole genome analysis of 125 Hungarian human rotaviruses identified nine major genotype constellations and uncovered both intra- and intergenogroup reassortment events in circulating strains. Intergenogroup reassortment resulted in several unusual genotype constellations, including mono-reassortant G1P[8] and G9P[8] strains whose genotype 1 (Wa-like) backbone gene constellations contained DS1-like NSP2 and VP3 genes, respectively, as well as, a putative bovine-feline G3P[9] reassortant strain. The conserved genomic constellations of epidemiologically major genotypes suggested the clonal spread of the re-emerging G9P[8] genotype and several co-circulating strains (e.g., G1P[8] and G2P[4]) in many study sites during 2012. Of interest, medically important G2P[4] strains carried bovine-like VP1 and VP6 genes in their genotype constellation. No evidence for vaccine associated selection, or, interaction between wild-type and vaccine strains was obtained. In conclusion, this study reports the reemergence of G9P[8] strains across the country and indicates the robustness of whole genome sequencing in routine rotavirus strain surveillance.
authors.affiliation: Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: Renáta
authors.initials: R
authors.lastname: Dóró
authors.affiliation: Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: Eszter
authors.initials: E
authors.lastname: Mihalov-Kovács
authors.affiliation: Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: Szilvia
authors.initials: S
authors.lastname: Marton
authors.affiliation: University of Debrecen, Debrecen, Hungary.
authors.forename: Brigitta
authors.initials: B
authors.lastname: László
authors.affiliation: University of Szeged, Szeged, Hungary.
authors.forename: Judit
authors.initials: J
authors.lastname: Deák
authors.affiliation: University of Pécs, Pécs, Hungary.
authors.forename: Ferenc
authors.initials: F
authors.lastname: Jakab
authors.affiliation: Laboratory Ltd., Debrecen, Hungary.
authors.forename: Ágnes
authors.initials: Á
authors.lastname: Juhász
authors.affiliation: University of Pécs, Pécs, Hungary.
authors.forename: Péter
authors.initials: P
authors.lastname: Kisfali
authors.affiliation: University of Bari, Bari, Italy.
authors.forename: Vito
authors.initials: V
authors.lastname: Martella
authors.affiliation: University of Pécs, Pécs, Hungary.
authors.forename: Béla
authors.initials: B
authors.lastname: Melegh
authors.affiliation: Combined Szent István and Szent László Hospital, Budapest, Hungary.
authors.forename: Péter
authors.initials: P
authors.lastname: Molnár
authors.affiliation: Hungarian National Public Health and Medical Officer Service, Miskolc, Hungary.
authors.forename: Ildikó
authors.initials: I
authors.lastname: Sántha
authors.affiliation: Markusovszky Hospital, Szombathely, Hungary.
authors.forename: Ferenc
authors.initials: F
authors.lastname: Schneider
authors.affiliation: Hungarian Academy of Sciences, Budapest, Hungary. Electronic address: bkrota@hotmail.com.
authors.forename: Krisztián
authors.initials: K
authors.lastname: Bányai
mesh_terms: D036022:Capsid Proteins / Q000235:genetics; D021821:Communicable Diseases, Emerging; D016679:Genome, Viral; D005838:Genotype; D062305:Geographic Mapping; D049674:History, 21st Century; D006801:Humans; D006814:Hungary / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D011159:Population Surveillance; D012401:Rotavirus / Q000145:classification / Q000235:genetics*; D012400:Rotavirus Infections / Q000453:epidemiology* / Q000266:history / Q000821:virology*; D017422:Sequence Analysis, DNA; D062211:Spatio-Temporal Analysis
chemical_list: D036022:Capsid Proteins
keywords: Genotype; Rotavirus; Surveillance; Whole genome sequencing