A Discussion of experiments using bioinformatics to investigate antigenic drift
The aim was to successfully run Clustal alignments of different PR8 sequences, identify mutations in coding strands, differentiate between the mutations and PCR errors, and translate how the single point mutations alter the amino acid coding sequence. The strains of the 7 cities are mostly the same with occasional alterations in codons in Leeds, Newcastle and 1 mutation in London. This demonstrates antigenic shift as they are small changes in the influenza virus. Some of these alterations had been identified as PCR error rather than real mutation. The PCR error rate for Leeds results is 0.27% which is relatively similar to the quoted tag polymerase error rate (0.2%). PCR error rates are meant to be low as it is highly accurate. The PCR error rate for the Newcastle sequence is 0.8% which is significantly higher than the quoted tag polymerase error rate. This error rate could be higher due to problems with primer design or nonspecific binding to other template sequences.
Alternatively, the high error rate could be due to the fact that the sequences we looked at being rather small samples.
There only appears to be mutations across strains in the east side of the UK (in Newcastle, London and Leeds), presenting an east-west divide. Potential causes could be due to different climates on the east side or perhaps higher levels of pollutants. There is no apparent divide between the north and the south of the UK however. As there is no pattern of mutations occurring in areas closer together, this means there is no evidence to support that is antigenic shift rather than antigenic drift.
Host immune responses will be able to recognise viruses if point mutations have occurred, resulting in silent mutations and therefore carry out an immune response. Viruses that have small genetic changes, closely related to original sequences, will be illustrated nearby on a phylogenetic tree. Closely related viruses share the same antigenic properties hence why the immune system will be able to respond to them. However, more of the recorded mutations lead to a change in amino acid rather than silent mutations. This can potentially be beneficial for viruses as it is a virulence factor. If the amino acid sequence continues to change, it may not be recognised by the host’s immune system.
Results show a common mutation where changes in codons leads to lysine being the new sequenced amino acid. This had occurred in 5 mutations. However, the mutations are random, occurring at different positions on the gene and different base changes. Results demonstrate no obvious pattern of mutation, further supporting the statement that antigenic drift has happened.
One result for Leeds stood out in particular as it was thought to be a PCR error. On the codon 199 a PCR error was flagged but is actually a real mutation. This real mutation was missed because a PCR error did occur on the exact point of mutation. We originally thought it was a PCR error because the alteration was only present on one strand.
When discussing mutations, the influenza reference is believed to the correct sequence. However, in codon 176, all 7 cities differ from the HA reference. All other codons are AAT, whilst the influenza reference is AAG, encoding lysine rather than asparagine. It is highly unlikely that all 7 city strains had random mutations on the exact same position to the exact same base. A more reasonable explanation would be to suggest that since the influenza reference is rather old (from 2013), the virus has evolved over time away from the reference strand. This would also explain where in codon 169 the only strain that is the same as the HA reference is the strain from Newcastle. It is more likely that there was a mutation in the Newcastle strain which made the sequence revert back to the older sequence than for the other 6 cities to all mutate in the exact same way.