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Albert Johannes Buitenhuis

Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies

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The high mutation rate of RNA viruses enables the generation of a genetically diverse viral population, termed a quasispecies,
within a single infected host. This high in-host genetic diversity enables an RNA virus to adapt to a diverse
array of selective pressures such as host immune response and switching between host species. The negative-sense,
single-stranded RNA virus, viral haemorrhagic septicaemia virus (VHSV), was originally considered an epidemic virus
of cultured rainbow trout in Europe, but was later proved to be endemic among a range of marine fish species in the
Northern hemisphere. To better understand the nature of a virus quasispecies related to the evolutionary potential
of VHSV, a deep-sequencing protocol specific to VHSV was established and applied to 4 VHSV isolates, 2 originating
from rainbow trout and 2 from Atlantic herring. Each isolate was subjected to Illumina paired end shotgun sequencing
after PCR amplification and the 11.1 kb genome was successfully sequenced with an average coverage of
0.5–1.9 × 106 sequenced copies. Differences in single nucleotide polymorphism (SNP) frequency were detected both
within and between isolates, possibly related to their stage of adaptation to host species and host immune reactions.
The N, M, P and Nv genes appeared nearly fixed, while genetic variation in the G and L genes demonstrated presence
of diverse genetic populations particularly in two isolates. The results demonstrate that deep sequencing and analysis
methodologies can be useful for future in vivo host adaption studies of VHSV.
TidsskriftVeterinary Research
Antal sider12
StatusUdgivet - 8 jan. 2016

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