Analysis of Echovirus 30 Isolates from Russia and New Independent States Revealing Frequent Recombination and Reemergence of Ancient Lineages▿

We studied two genome regions, VP1 and 3D, of 48 echovirus 30 (E30) isolates from Russia and the new independent states. In VP1, most isolates were similar to European strains reported earlier, and frequent change of circulating subgroups was noticed. We also observed, in 2003-2006, the reemergence of a group of E30 strains with a VP1 region very distant from most modern E30 strains and remotely similar to E30 isolates from the 1960s and the 1970s. A study of the 3D genome region detected multiple recombination events among the studied strains. Recombination presumably occurred every few years, and therefore, the study of a single VP1 genome region cannot accurately describe the phylogenetic history of the virus or predict pathogenetic properties of an isolate. In general, a comparison of the VP1 and 3D genome region phylogenies revealed, in some instances, virtually independent circulation of enterovirus genome fragments on a scale of years

Seroepidemiology and molecular epidemiology of enterovirus 71 in Russia.

Enterovirus 71 (EV71) is an emerging human pathogen causing massive epidemics of hand, foot and mouth disease with severe neurological complications in Asia. EV71 also circulates in Europe, however it does not cause large outbreaks. The reason for distinct epidemiological patterns of EV71 infection in Europe and Asia and the risk of EV71 epidemic in Europe and Russia remain unknown. Seroepidemiology of EV71 and molecular epidemiology of occasional EV71 isolates were studied to explore circulation of EV71 in Russia. In six regions of Russian Federation, seroprevalence of EV71 in sera collected in 2008 ranged from 5% to 20% in children aged 1-2 years and from 19% to 83% in children aged 3-5 years. The seroprevalence among elder children was significantly higher (41-83% vs. 19-27%) in Asian regions of Russia. EV71 strains identified in Russia in 2001-2011 belonged to subtypes C1 and C2, while genotype C4 that was causing epidemics in Asia since 1998 emerged in 2009 and became dominant in 2013

Sampling territories (shaded on the map), the number of sampled sera, sociogeographic conditions in the study regions, prevalence and mean geometric titers of antibodies to EV71 in children aged 1–2 and 3–5 years.

<p>Social and economic status of the regions is provided according to the official census and statistical data. Climate zone is indicated in accordance with Köppen classification. Dfb, warm summer continental, even annual rainfall; Dfc, continental subarctic, even annual rainfall; Dwb, warm summer continental, low winter rainfall. Isolations sites of EV71 strains presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097404#pone-0097404-g002" target="_blank">Fig. 2</a> are indicated with empty circles. Significance of Fisher's exact test comparing seroprevalence in younger and elder age groups is indicated above the bars of the seroprevalence graph; comparison regions are indicated by first letters. Only significant values are shown; * indicates p<0.05, ** p<0.01, *** p<0.001.</p

Phylogenetic tree of EV71 isolates from Russia and CIS (indicated in bold) and all GenBank sequences of EV71 genotype C that differ by over 1%.

<p>For Russian/CIS sequences, the isolate number is indicated, which refers to the sampling location indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097404#pone-0097404-g001" target="_blank">Fig. 1</a>. The tree was created using the complete VP1 genome region (891 nucleotides) and the Bayesian Markov Chain Monte Carlo algorithm implemented in Beast 1.7.5. Scale bar indicates time. Branches are colored according to isolation region indicated in the legend.</p

Environmental Surveillance for Poliovirus and Other Enteroviruses: Long-Term Experience in Moscow, Russian Federation, 2004–2017

Polio and enterovirus surveillance may include a number of approaches, including incidence-based observation, a sentinel physician system, environmental monitoring and acute flaccid paralysis (AFP) surveillance. The relative value of these methods is widely debated. Here we summarized the results of 14 years of environmental surveillance at four sewage treatment plants of various capacities in Moscow, Russia. A total of 5450 samples were screened, yielding 1089 (20.0%) positive samples. There were 1168 viruses isolated including types 1&#8722;3 polioviruses (43%) and 29 different types of non-polio enteroviruses (51%). Despite using the same methodology, a significant variation in detection rates was observed between the treatment plants and within the same facility over time. The number of poliovirus isolates obtained from sewage was roughly 60 times higher than from AFP surveillance over the same time frame. All except one poliovirus isolate were Sabin-like polioviruses. The one isolate was vaccine-derived poliovirus type 2 with 17.6% difference from the corresponding Sabin strain, suggesting long-term circulation outside the scope of the surveillance. For some non-polio enterovirus types (e.g., Echovirus 6) there was a good correlation between detection in sewage and incidence of clinical cases in a given year, while other types (e.g., Echovirus 30) could cause large outbreaks and be almost absent in sewage samples. Therefore, sewage monitoring can be an important part of enterovirus surveillance, but cannot substitute other approaches

Pressure for Pattern-Specific Intertypic Recombination between Sabin Polioviruses: Evolutionary Implications

Complete genomic sequences of a non-redundant set of 70 recombinants between three serotypes of attenuated Sabin polioviruses as well as location (based on partial sequencing) of crossover sites of 28 additional recombinants were determined and compared with the previously published data. It is demonstrated that the genomes of Sabin viruses contain distinct strain-specific segments that are eliminated by recombination. The presumed low fitness of these segments could be linked to mutations acquired upon derivation of the vaccine strains and/or may have been present in wild-type parents of Sabin viruses. These “weak” segments contribute to the propensity of these viruses to recombine with each other and with other enteroviruses as well as determine the choice of crossover sites. The knowledge of location of such segments opens additional possibilities for the design of more genetically stable and/or more attenuated variants, i.e., candidates for new oral polio vaccines. The results also suggest that the genome of wild polioviruses, and, by generalization, of other RNA viruses, may harbor hidden low-fitness segments that can be readily eliminated only by recombination

Vaccine-associated paralytic poliomyelitis in a child: fast transformation from Sabin-like virus to vaccine-derived poliovirus triggered an epidemiological response in two countries of the European region

Objectives: The detection of a vaccine-derived poliovirus (VDPV) requires an epidemiological assessment and response. Using repeated stool sampling from a child who is immunocompetent and was vaccinated against poliomyelitis with acute flaccid paralysis, a case of an extremely rapid evolution of Sabin-like poliovirus (PV) type 3 was traced in the child's body. Methods: The case was independently identified in two countries—Tajikistan and Russia. Stool samples for the study were also independently collected in two countries on different days from the onset of paralysis. Virological, serological, and molecular methods; full genome Sanger; and high-throughput sequencing were performed to characterize isolates. Results: PV isolates from samples collected on days 2, 3, and 14 contained eight, seven, and seven mutations in the VP1-coding region, respectively, and were classified as Sabin-like PV type 3. The isolates from samples collected on days 15 and 18 had 11 mutations and were classified as vaccine-derived PVs, which required an epidemiological response in the two countries. Conclusion: The results indicate the need to continue acute flaccid paralysis surveillance, maintain high vaccination coverage, and develop and introduce new effective, genetically stable PV vaccines