HCV Sequence Alignments

• The web alignments have been manually optimized, and contain only one sequence from one patient. Please note that for most genes, only sequences that cover the entire gene are included. Exceptions are both UTRs and the complete genome, where this rule would result in the loss of too many sequences. Very similar or epidemiologically related groups have also been reduced to one sequence, with the exception of the 5' UTR where sequences that are nearly identical but almost certainly not epidemiologically related were not removed; this region is so conserved that few sequences would have remained. Sequences that are not genotyped are also not included, but sequences that have a genotype but no subtype are; however, no consensus sequences were made for these.
• The reference alignments contain approximately 4 representatives of each clade, and are useful for classifying new sequences.
• The consensus sequences are only available for genotypes for which the alignment contains at least three sequences. The original sequences are also included in the consensus sequence files. The consensus sequences consist of upper- and lower case letters; the lowercase indicates that the consensus is not unanimous. Please note that the parameters used to generate these consensus sequences are set so that gaps are avoided where possible; i.e., if a consensus is based on 50 sequences of which 49 have a gap but one has a valid residue code, the consensus will contain that code.

* The year associated with a specific alignment refers to until the end of that year, so '2008' contains sequences published in 2008. The Compendia are published the year after the sequences were published, and 2008 alignment appears in the 2009 compendium.