Primer dropout with a suspected XBB.1.1 sequence

[iahdb]

Hi, I am trying to find out which MRT001 primer scheme version I have in my kit - it doesn't say on the product page. I want to confirm XBB.1.1. lineage of a virus stock I want to use for an experiment. the pipeline assigns it at BA.2.10, however there appears to be 3 amplicon drop outs (see attached image). Barcode01 is my XBB.1.1. stock and Barcode02 is a positive control which is B.1.617.2. I ordered the MRT001 kit on 06/09/2022.

[mattdmem]

Hello @iahdb,

Could you please provide more information from the label from your kit box? A photo would be great. I’ll consult with my colleagues.

We did change primers for Omicron details here: https://labs.epi2me.io/ont-midnight-scheme-update/

Thanks

Matt

[iahdb]

Hello @mattdmem thanks for your quick response. Here's the kit box.

thanks, I'ah

[mattdmem]

@iahdb - this is version 3 of the kit (the 30 in MRT001.30.0006 tells us this). I don't think we've had reports of XBB.1.1 causing significant issues with drop-out.

The latest version of the workflow updates pangolin at run time by default, I'm just wondering which version you're running? Is it possible it's not a typical XBB.1.1 sequence?

[iahdb]

Ah ok, I thought it would be V3 since we bought the kit after the update, good to confirm. It could be an atypical XBB.1.1. sequence, but we received the isolate from a trusted source who said they confirmed it was XBB.1.1, although i'm not sure if they used midnight to do so. The report says it used pangolin 4.1.1. The workflow runs automatically on our GridION, could that be a reason it hasn't auto-updated (latest version is 4.3.1)? I'll try running pangolin separately using the fasta generated by the workflow and see if that gives me anything different

[iahdb]

@mattdmem Ok, I ran with pangolin 4.3.1 and that's returned XBB.1.1. Thanks for your help!