The outbreak of a novel coronavirus (2019-nCoV) has prompted many scientists to share their findings through unconventional means such as social media, blogs and impromptu email threads. Recently, a post on Twitter identified more than 300 2019-nCoV-related papers on bioRxiv and requested support from the scientific community in vetting these preprints. Among the questions asked was a direct appeal to our lab to determine whether the MAFFT sequence alignment software was being used appropriately. In addition to attempting to respond to this specific question, we would like to add several general points as follows:
1. MAFFT is frequently used in MSA analyses of 2019-nCoV. For example, in the published literature:
It’s not easy for us to reproduce every MSA by collecting the same input sequences. Therefore, in order to both validate MSA methods and make these analyses more smooth, we propose to accept sequence data from anyone working on 2019-nCoV and, as long as we have time and our computational resources allow, appropriately apply MAFFT to prepare MSAs and/or trees.
2. In addition to carrying out analysis of virus sequences, it may be possible to obtain valuable information pertaining to the immune responses to 2019-nCoV by sequencing the B and T cell receptors of infected individuals. We can also accept such BCR or TCR repertoire data, and use our own in-house tools or third-party tools to identify likely 2019-nCoV-responsive BCRs or TCRs.
If you wish to have your sequence data analyzed in this fashion, please contact us using one of the forms below:
Do not include the data itself (or a link to the data) in this request. After receiving your inquiry we will ask for access to the data and further details.