A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions. Ideally, this is accomplished under as low sequencing coverage as possible. Here we report our attempt to meet these goals with a novel library construction and library amplification methodology. In our approach, single-cell genomic DNA is first fragmented with saturated transposition to make a primary library that uniformly covers the whole genome by short fragments. The library is then amplified by a carefully optimized PCR protocol in a uniform and synchronized fashion for next-generation sequencing. Each step of the protocol can be quantitatively characterized. Our shallow sequencing data show that the library is tightly distributed and is useful for the determination of copy number variations.

Plague (Yersinia pestis) and zoonotic cutaneous leishmaniasis (Leishmania major) are two rodent-associated diseases which are vectored by fleas and phlebotomine sand flies, respectively. In Central Asia, the great gerbil (Rhombomys opimus) serves as the primary reservoir for both diseases in most natural foci. The systemic insecticide fipronil has been previously shown to be highly effective in controlling fleas and sand flies. However, the impact of a fipronil-based rodent bait, on flea and sand fly abundance, has never been reported in Central Asia. A field trial was conducted in southeastern Kazakhstan to evaluate the efficacy of a 0.005% fipronil bait, applied to gerbil burrows for oral uptake, in reducing Xenopsylla spp. flea and Phlebotomus spp. sand fly abundance. All active gerbil burrows within the treated area were presented with ~120 g of 0.005% fipronil grain bait twice during late spring/early summer (June 16, June 21). In total, 120 occupied and 14 visited gerbil colonies were surveyed and treated, and the resulting application rate was minimal (~0.006 mg fipronil/m2). The bait resulted in 100% reduction in Xenopsylla spp. flea abundance at 80-days post-treatment. Gravid sand flies were reduced ~72% and 100% during treatment and at week-3 post-treatment, respectively. However, noticeable sand fly reduction did not occur after week-3 and results suggest environmental factors also influenced abundance significantly. In conclusion, fipronil bait, applied in southeastern Kazakhstan, has the potential to reduce or potentially eliminate Xenopsylla spp. fleas if applied at least every 80-days, but may need to be applied at higher frequency to significantly reduce the oviposition rate of Phlebotomus spp. sand flies. Fipronil-based bait may provide a means of controlling blood-feeding vectors, subsequently reducing disease risk, in Central Asia and other affected regions globally.

Puumala orthohantavirus (PUUV) causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS) commonly diagnosed in Europe. The majority of HFRS cases in the European part of Russia are diagnosed in the Volga Federal District, which includes the Republic of Tatarstan (RT). The current study aims to analyze the genetic variability of PUUV in Pre-Kama region of the RT bounded by the Volga, Kama, and Vyatka rivers. In 2017, bank voles were caught in seven isolated forest traps in the Pre-Kama region and for the 26 PUUV-positive samples, the partial small (S), medium (M), and large (L) genome segment sequences were obtained and analyzed. It was determined that all identified PUUV strains belong to the Russian (RUS) genetic lineage; however, the genetic distance between strains is not directly correlated with the geographical distance between bank vole populations. One of the identified strains has S and L segments produced from one parental strain, while the M segment was supplied by another, suggesting that this strain could be the reassortant. We suggest that the revealed pattern of the PUUV strains distribution could be the result of a series of successive multidirectional migratory flows of the bank voles to the Pre-Kama region in the postglacial period.

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