What to do next

If you identified a novel variant of SARS-CoV-2 with “interesting” genomic features, you should probably report the variant to Health authorithies in your country and to the scientific community.

Normally virological or Pango would be the right place to start to report your novel findings to the community.

If the novel candidate variant was identified by HaploCoV, HaploCoV.pl (see –varfile option) or augmentClusters.pl should/could have provided a file with the complete list of genomic variants that define your novel lineage/lineages of interest. It might be worthwile to add this/these definitions to your favourite “Genomics variant file” (see here) and use assign.pl or p_assign.pl to re-assign genomic sequences using the augmented nomenclature.

Whence the novel nomenclature is assigned, you can extract the data (and metadata) of the novel candidate lineage/variant from a HaploCoV formatted metadata table (like for example the output of assign.pl) by using the subset.pl utility included in github repo. The next section of the manual illustrates some possible applications of the tool, and explains how to use it to extract data of interest.

Finally the increase.pl utility can be used to calculate the prevalence of your novel/candidate variant/variants in space and time and derive global patterns (if any and if your novel designations were not already derived from the analysis of all the available genome sequences) and/or identify countries or places where it is prevalent.