Apart from straight file downloads COVID-19 PubSeq allows for exporting forms and data for other services.

First of all, PubSeq exports a SPARQL endpoint here that allows you do do any query on the data. See this document for examples.

In addition to above flexible SPARQL endpoint - which is essentially is a query REST API - PubSeq exports its own REST API.

Uploading data to EBI/ENA with PubSeq is described here.

To export, first search for an uploaded entry through its identifier: