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Volume 21, Number 4—April 2015
Dispatch

Candidate New Rotavirus Species in Sheltered Dogs, Hungary

Eszter Mihalov-Kovács, Ákos Gellért, Szilvia Marton, Szilvia L. Farkas, Enikő Fehér, Miklós Oldal, Ferenc Jakab, Vito Martella, and Krisztián BányaiComments to Author 
Author affiliations: Hungarian Academy of Sciences–Centre for Agricultural Research, Budapest, Hungary (E. Mihalov-Kovács, S. Marton, S.L. Farkas, E. Fehér, K. Bányai); Hungarian Academy of Sciences–Centre for Agricultural Research, Martonvásár, Hungary (Á. Gellért); University of Pécs, Pécs, Hungary (M. Oldal, F. Jakab); Università Aldo Moro di Bari, Valenzano, Italy (V. Martella)

Main Article

Table

Sequencing depth for the putative rotavirus I strains obtained by massively parallel sequencing*

Gene KE135/2012
 KE528/2012
Mapped read count Average coverage (X) Mapped read count Average coverage (X)
VP1 9632 478 1286 59
VP2 7762 455 860 46
VP3 6361 510 657 49
VP4 5887 436 716 47
VP6 4762 700 582 72
VP7 2841 594 258 45
NSP1 3677 450 561 62
NSP2 2980 529 401 64
NSP3 2528 523 176 32
NSP4 2272 586 229 51
NSP5 1098 387 249 72

*Total sequence reads to obtain genomic RNA sequence for KE135/2012 and KE 528/2012 were 1,591,803, and 144,747, respectively. The minimum overlap with the consensus sequences (i.e., the de novo assembled rotavirus I–specific consensus sequences) was 20 nt, the minimum identity was 80%. To improve the mapping results, the following gap penalties were applied for the dataset: mismatch cost = 2, insertion cost = 3, deletion cost = 3. After visual inspection of the sequence alignments and remapping onto the obtained gene sequence, a single consensus sequence was finalized for each genome segment.

Main Article

Page created: March 17, 2015
Page updated: March 17, 2015
Page reviewed: March 17, 2015
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