Query about M2-2 gene annotation discrepancy in Nextstrain RSV-A module

General
1

Dear Nextstrain Team,

I hope this message finds you well. I am writing to seek clarification regarding the annotation of the M2-2 gene in the RSV-A module on Nextstrain.

I noticed a discrepancy between the M2-2 gene coordinates in Nextstrain and those in the NCBI reference sequence (PP109421.1):

  • Nextstrain annotation: M2-2 = 8193–8465 (+)
  • NCBI (PP109421.1): M2-2 = 8199–8465 (+)

This 6-nucleotide difference at the start of the gene results in a translation discrepancy:

  • Nextstrain translation: TTMPKIMILPDKYPCSINSILITSNYRVTMYNQKNTLYINQNNQNSHIYPPDQPFNEIHWTSQDLIDATQNFLQHLGITDDIYTIYILVS*
  • NCBI translation: MPKIMILPDKYPCSINSILITSNYRVTMYNQKNTLYINQNNQNSHIYPPDQPFNEIHWTSQDLIDATQNFLQHLGITDDIYTIYILVS* (lacking the initial “TT”).

Could you kindly clarify:

  1. What is the basis for the 8193 start position in Nextstrain (e.g., experimental evidence, historical annotation, or alignment-based inference)?
  2. How should this discrepancy be resolved for downstream analyses? Is there a recommended canonical annotation for RSV-A M2-2?

Thank you for your time and expertise. I greatly appreciate your work in maintaining this invaluable resource.

Best regards,
Jingqi Yang

2

Dear Jingqi Yang,

thank you for bringing this to our attention. The underlying reason is that we used to use to annotation of a related strain LR699737 which (for reasons unclear to me) has added the six nucleotides coding for TT to the M2-2 protein. I will review this and correct as necessary.

thanks again,
richard

3

thanks again. I have fixed the annotations. The changes should be live soon.

4

Thank you very much for fixing the annotations - I really appreciate your corrections and the work you put into making those updates.