1887

Abstract

Here, the complete genome sequences for three hepatitis C virus (HCV) variants identified from China and belonging to genotype 6 are reported: km41, km42 and gz52557. Their entire genome lengths were 9430, 9441 and 9448 nt, respectively; the 5′ untranslated regions (UTRs) contained 341, 342 and 339 nt, followed by single open reading frames of 9045, 9045 and 9057 nt, respectively; the 3′ UTRs, up to the poly(U) tracts, were 41, 51 and 52 nt, respectively. Phylogenetic analyses showed that km41 is classified into subtype 6k and km42 into subtype 6n. Although gz52557 clustered distantly with subtype 6g, it appeared to belong to a distinct subtype. Analysis with 53 and 105 partial core and NS5B region sequences, respectively, representing 17 subtypes from 6a to 6q and three unassigned isolates of genotype 6 in co-analyses demonstrated that gz52557 was equidistant from all of these isolates, indicating that it belongs to a novel subtype. However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype.

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2006-03-01
2019-11-18
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vol. , part 3, pp. 629 – 634

Phylogenetic trees based on (a) sequences of 321 nt partial core region corresponding to nt 372–692 of the JK046 genome and (b) sequences of 468 nt partial E1 region corresponding to nt 840–1307 of the JK046 genome.

PCR primers.

Nucleotide similarities of km41, km42 and gz52557 to representative sequences from subtypes 6a–6q and three sequences with their subtypes unassigned.

Partial sequences of the core and NS5B regions of the HCV isolates classified within genotype 6 and analysed in Fig. 2.

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