David Winter

Haven't really moved to bluesky,but had to jump on to highlight this cool result from Joanne's team . We have been watching BA.3.2, a highly divergent COVID linage, closely. Wastewater was the first to find it in NZ, with enough resolution to know where it fits among lineages from Australia.

There will be a wee break, partly because we want the ppl at the treatment sites taking the samples to have a clean break. Diagnostic labs are holding samples, so clinical genomics will be able to cover continuously

You are too kind, but I hope to do some good!

Finally, a little news from me. 2023 is my last year as Technical Lead Pathogen genomcs @ ESR. Next year I'll be back as Science Leader Genomics with less focus on the day-to-day and more on how we can best use genomics to support public health now and in the future.

There are a huge number of dedicated people underneath all those headline statistics, so a massive thanks to everyone collecting samples, growing bugs, running the sequencers and analysing and interpreting the results.

This year, we moved Shigella, Vibrio, Yersinia Strep and Legeionlla to genome sequencing. All told we processed 4,361 bacterial genomes gathering information about antimicrobial susceptibility, disease severity, vaccine coverage, outbreak detection, and a lot more.

ESR does a lot more than COVID-19. Genomics is increasingly how we support our national reference laboratories to track diseases in the community.

`23 was also the year we brought COVID-19 wastewater sequencing in-house. Been great to work with
@joannehewittnz.bsky.social 's team and bring results and expertise from the two threads of SARS-Cov-2 surveillance much closer together. Check out poops.co.nz and closer collab in `24

In summer 22/23 the "variant soup" meant sequencing was called on to match treatments to genomes, with a tonne of patient-level reports going out for the first time. Later we had XBB sweep through and 'old' lineages like CH.1.1 and XBC stick around locally for a long time. Now our focus is on JN.1

And epidemological curve of COVID-19 cases in NZ, shaded estimated numbers of cases caused by each variant.

Last sequencing run of 2023 about to go on here @ ESR
, time for a little review of what we achieved this year before we get stuck into analysing them...

First a whole year of COVID genomics:

4.5 yo's most endearing trait right now is point blank rejecting any time I say I'm doing a bad job.

-do we have any snacks?
-no sorry, didn't put them in the swim bag: bad Dadding there
-No. You're a good Dad. It's OK!

Weekly social media log in.... It's a shield bug, but sure which but not the bad one www.mpi.govt.nz/biosecurity/.... Cute !

(also, author limits at the journal means this paper sees the birth of the "ESR Genomics Consortium" to capture the folks that worked on this... possibly the smallest consortium to publish a genomic paper)

This paper describes how to fit that workflow into a busy diagnostic lab. Now e have @rhystwhite.bsky.social as our embeded ESR scientist working with Max I expect some really interesting results to come from routine sequencing of common hospital pathogens

First little output from a very cool project with Max Bloomfield @ Wellington Hospital.

Max is using Nanopore sequencing to help Infection Control teams spot transmission on or between wards. Max does the bulk of the work, and ESR is ready for any tricky bionfo problems: doi.org/10.1016/j.pa...

Think you already got there, but looks like a tunnel web. A live one fell out of my jersey the other morning jsut before I put it on... testing my archnophillia to its limit....

gotta send a (whatever a tweet is here) about any other topic!

still can't edit 'huh.

I meant to say ''their advantage is _not very large_' 😑

Wastewater surveillance is updated too, till the only way we have found the highly-divergetnt BA.2.86 in NZ: poops.nz

We try to stay ahead of the variant name game, and look for what might be able to replace our tracked variants in future. HK.3 and FL.2 are contentders, but their advantage is now very larger (1-2% per day)

I guess our public covid report is going to be the thing that makes me finally send a message here...

www.esr.cri.nz/our-expertis...

This month has seen the kākāpō palette really come together as EG.5 became our most common variant. NZ and Aus remain really unusual in having room for XBC...