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The widespread use of the oral poliovaccine from Sabin strains (tOPV) radically reduced poliomyelitis incidence worldwide. However, OPV became a source of neurovirulent vaccine-derived polioviruses (VDPVs). Currently, circulating type 2 VDPVs (cVDPV2) are the leading cause of poliomyelitis. The novel OPV type 2 vaccine (nOPV2), based on genetically modified Sabin strain with increased genetic stability and reduced risk of cVDPV formation, has been used to combat cVDPV2 outbreaks, including one in Tajikistan in 2021. In order to identify the importation of cVDPV2 and nOPV2-derivates, stool samples from 12,127 healthy migrant children under 5 years of age arriving from Tajikistan were examined in Russia (March 2021–April 2022). Viruses were isolated in cell culture and identified via intratype differentiation RT-PCR, VP1 and whole-genome sequencing. cVDPV2 isolates closely related with the Tajikistan one were isolated from two children, and nOPV2-derived viruses were detected in specimens from 106 children from 37 regions of Russia. The duration of nOPV2 excretion ranged from 24 to 124 days post-vaccination. nOPV2 isolates contained 27 mutations per genome (0.36%) on average, with no critical genetic changes, which confirms the genetic stability of nOPV2 during field use. The possibility of epidemiologically significant poliovirus introduction into polio-free countries has been confirmed. The screening of special populations, including migrants, is required to maintain epidemiological well-being. [ABSTRACT FROM AUTHOR]

Dugbe virus (DUGV) is a tick-borne arbovirus first isolated in Nigeria in 1964. It has been detected in many African countries using such diverse methods as serological tests, virus isolation, and molecular detection. In Senegal, reports of DUGV isolates mainly occurred in the 1970s and 1980s. Here, we report a contemporary detection of three novel DUGV isolates upon screening of a total of 2877 individual ticks regrouped into 844 pools. The three positive pools were identified as Amblyomma variegatum, the main known vector of DUGV, collected in the southern part of the country (Kolda region). Interestingly, phylogenetic analysis indicates that the newly sequenced isolates are globally related to the previously characterized isolates in West Africa, thus highlighting potentially endemic, unnoticed viral transmission. This study was also an opportunity to develop a rapid and affordable protocol for full-genome sequencing of DUGV using nanopore technology. The results suggest a relatively low mutation rate and relatively conservative evolution of DUGV isolates. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID‐19) has become pandemic since March 11, 2020. Thus, development and integration in clinics of fast and sensitive diagnostic tools are essential. The aim of the study is a development and evaluation of a one‐step quantitative reverse transcription‐polymerase chain reaction (RT‐qPCR) assay (COVID‐19 Amp) for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) detection with an armored positive control and internal controls constructed from synthetic MS2‐phage‐based RNA particles. The COVID‐19 Amp assay limit of detection was 103 copies/ml, the analytical specificity was 100%. A total of 109 biological samples were examined using COVID‐19 Amp and World Health Organization (WHO)‐based assay. Discordance in nine samples was observed (negative by the WHO‐based assay) and discordant samples were retested as positive according to the results obtained from the Vector‐PCRrv‐2019‐nCoV‐RG assay. The developed COVID‐19 Amp assay has high sensitivity and specificity, includes virus particles‐based controls, provides the direct definition of the SARS‐CoV‐2 RdRp gene partial sequence, and is suitable for any hospital and laboratory equipped for RT‐qPCR. Highlights: One‐step RT‐qPCR assay (COVID‐19 Amp) contains an armored positive control (ARC+) and an armored internal control (ICS) constructed from synthetic MS2‐phage‐based RNA particles.Displays high specificity and selectivity rendering it a powerful diagnostic testSuitable for any hospital and laboratory equipped for RT‐qPCR. [ABSTRACT FROM AUTHOR]

This chapter reports a library preparation protocol for efficient high-throughput sequencing of double-stranded RNA viruses. The protocol consists of four main steps, viz., enzyme treatment, precipitation using lithium chloride, full-length amplification of cDNAs, and tailing adapters for high-throughput sequencing. This protocol will be useful for all double-stranded RNA viruses and for all of the high-throughput sequencing platforms.