TABLE 1.

Coding mutations of serially passaged Core-NS2 SA13 (5a) JFH1-based recombinants^g

^aPositions are numbered according to the sequence of pSA13/JFH1 (24) (GenBank accession no. FJ393024). Corresponding H77 absolute reference numbers are given. Only positions with coding mutations present as a 50/50 quasispecies or dominant in at least one isolate are shown. Dashes indicate identity with original plasmid sequence. Positions with quasispecies are written with the dominant sequence in uppercase and the minor sequence in lowercase. The 50/50 quasispecies are shown with two uppercase letters. Shaded positions were introduced back into pSA13/JFH1_orig in different combinations. Positions shaded in black represent SA13/JFH1_orig cell culture-adaptive mutations described previously (24).

^bCommon 17th passage used for subsequent flask and plate lineage.

^cVirus stocks are designated according to their passage and the well number used to infect culture. Accordingly, a 31st-passage virus stock derived from well C5 of a 96-well plate is designated p31/C5.

^dAdapted virus stock received from the University of Birmingham (United Kingdom).

^ePositions of individual amino acid changes within the given HCV protein are shown as H77 absolute reference numbers.

^fHCV infectivity titers were determined as described in Materials and Methods. Peak infectivity titers are displayed as log₁₀ focus-forming units per milliliter.

^gIn addition to the mutations shown in the table, the following noncoding nucleotide changes (positions are given as H77 absolute reference numbers, GenBank accession no. AF009606) were observed in the ORFs of the various sequenced virus stocks: G350T, T791C, T2337T/C, T2405C/t, C2468T/c, T2636C, G2807C/g, C3881T/C, A3914G, A4367G, T5231C, T5648C/T, C5750T, T7202C, A7485G/A, T7540C, C7540A/c, T7932C, and A8573G.