This is a brief update to the previous menB analysis we’d posted here.

UKHSA have released a technical briefing and further data which includes four further isolates from the outbreak, and a high quality hybrid assembly of the first isolates.

I repeated our analysis from before mapping everything to this new reference, and including the new genomes. In summary:

• Certainly looks like a very closely related outbreak, there is only a single likely SNP separating the isolates.
• There are no recombination events found within the outbreak.
• As before, pilus and PorB recombinations would be what I’d investigate further, but I still think it will be hard to distinguish between diversifying selection and more invasive.
• The alignment had 196083 as ancestral to the other samples, but when doing stricter filtering on the SNPs this went away. Ideally I’d want the reads to confirm this, and to ultimately match with any contact tracing data.

We did also look at the pangenome, but didn’t find any gene level differences either.

We’ve done a quick analysis on the meningitis outbreak genome to try and answer whether there is anything obviously genetically unusual about the publicly available outbreak strain.

We aimed for three things:

• To see if the outbreak genome is on an unusually long branch, or otherwise different phylogenetically from its neighbours.
• Look for where mutation/recombination has occurred on the branch leading to the outbreak.
• Look for any effect of phase variable loci in the outbreak.

The final one of these didn’t work reliably without a close high-quality reference and/or more careful analysis time.

This blog post summarises some checks and comprobations done while developing Sparrowhawk after we discovered an unsettling surprise. The first two sections explain quickly what a genomic assembler is and the issue we found during the development (bad performance when assembling at large k values), and why it prompted us to study hash collisions as a potential cause for this. If you are here only for the hashes and the collisions, jump directly to the third section (ntHash and collisions).