Inventing Fictional Resistance from Real Data (Pt 2 of 2)

This particular example of HCV being devious was brought up to us by Federico Garcia – Thanks Federico!   He points out an interesting aspect of one of the most famous mutations in HCV.  S282T is a substitution in the NS5b gene, which results in resistance to sofosbuvir.  It is an example where we can accidently  “invent” HCV drug resistance when none is actually present.

So let’s dig into the weeds a bit.  First of all, Serine is potentially encoded by a number of different nucleotide combinations, but for HCV genotype 1a and 1b, and most other genotypes, the S is almost exclusively encoded by AGC, except in genotype 3, where it is usually AGT.  (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993261/).  This is not that weird – different organisms usually have an overall preference for which codon they use for a given amino acid, even if it is not obvious why.  And viruses tend to have preferences for which nucleotide triplet for any specific amino acids at any given location in their genome.

An odd thing about Serine, though, is that it is one of the few amino acids which appears on opposite sides of a Translation wheel (see picture).  So it is encoded quite different nucleotide triplets – for example AGT (on the left) and by TCT (on the right), which is kind of weird.  (“T” is actually “U” in this wheel, of course).

The effect of this weird encoding is that if one has a 50:50 mixture of AGT and TCT (two different S282S HCV variants which are susceptible to sofosbuvir) and perform Sanger Sequencing (or NGS sequencing and create an amino acid consensus sequence), the result is “WST”.    This will be naively translated to S282C/S/T.  One would interpret that the S282T is present and that the virus is sofosbuvir resistant, but this is not the case – we just made that up!.

The good news is that this artefact must be pretty rare, or everyone would be reporting detecting the S282T all the time!   S282T is pretty rare.  But this is definitely something to look out for.