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Check D1 and D2 serogroup predictions being accurate #49

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kbessonov1984 opened this issue Aug 10, 2021 · 0 comments
Open

Check D1 and D2 serogroup predictions being accurate #49

kbessonov1984 opened this issue Aug 10, 2021 · 0 comments

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@kbessonov1984
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In the next SISTR release check serogroup predictions. In version 1.1.1 the predicted O9,46 antigen was reported as D1 serogroup instead of expected D2 for PulseNet sampleID 21-01676. Not critical, but need to check the cause of this serogroup misassignment.

Useful reference:
As per Structural diversity in Salmonella O antigens and its genetic basis publication https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106985/

The Salmonella O antigens belonging to serogroups O2 (A), O4 (B), O8 (C2–C3), O9 (D1), O9,46 (D2), O9,46,27 (D3), O3,10 (E1–E3), and O1,3,19 (E4) form a distinct set that is characterized by having a Gal residue as the first sugar of the O unit and a wbaP gene in the O-antigen gene cluster

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