@article{fdi:010068202,
  title = {{T}argeted genomic enrichment and sequencing of {C}y{HV}-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections},
  author = {{H}ammoumi, {S}aliha and {V}allaeys, {T}. and {S}antika, {A}. and {L}eleux, {P}. and {B}orzym, {E}. and {K}lopp, {C}. and {A}varre, {J}ean-{C}hristophe},
  editor = {},
  language = {{ENG}},
  abstract = {{K}oi herpesvirus disease ({KHVD}) is an emerging disease that causes mass mortality in koi and common carp, {C}yprinus carpio{L}. {I}ts causative agent is {C}yprinid herpesvirus 3 ({C}y{HV}-3), also known as koi herpesvirus ({KHV}). {A}lthough data on the pathogenesis of this deadly virus is relatively abundant in the literature, still little is known about its genomic diversity and about the molecular mechanisms that lead to such a high virulence. {I}n this context, we developed a new strategy for sequencing full-length {C}y{HV}-3 genomes directly from infected fish tissues. {T}otal genomic {DNA} extracted from carp gill tissue was specifically enriched with {C}y{HV}-3 sequences through hybridization to a set of nearly 2 million overlapping probes designed to cover the entire genome length, using {KHV}-{J} sequence ({G}en{B}ank accession number {AP}008984) as reference. {A}pplied to 7 {C}y{HV}-3 specimens from {P}oland and {I}ndonesia, this targeted genomic enrichment enabled recovery of the full genomes with > 99.9% reference coverage. {T}he enrichment rate was directly correlated to the estimated number of viral copies contained in the {DNA} extracts used for library preparation, which varied between similar to 5000 and similar to 2x10(7). {T}he average sequencing depth was > 200 for all samples, thus allowing the search for variants with high confidence. {S}equence analyses highlighted a significant proportion of intra-specimen sequence heterogeneity, suggesting the presence of mixed infections in all investigated fish. {T}hey also showed that inter-specimen genetic diversity at the genome scale was very low (>99.95% of sequence identity). {B}y enabling full genome comparisons directly from infected fish tissues, this new method will be valuable to trace outbreaks rapidly and at a reasonable cost, and in turn to understand the transmission routes of {C}y{HV}-3.},
  keywords = {{C}yprinid herpesvirus 3 ; {G}enome ; {T}argeted genomic enrichment ; {M}ixed infection ; {V}ariability ; {INDONESIE} ; {POLOGNE}},
  booktitle = {},
  journal = {{PEERJ}},
  volume = {4},
  numero = {},
  pages = {e2516 [17 p.]},
  ISSN = {2167-8359},
  year = {2016},
  DOI = {10.7717/peerj.2516},
  URL = {https://www.documentation.ird.fr/hor/fdi:010068202},
}