ATCC Genome Portal Update: SARS-CoV-2 Genomes and New Support for the ATCC Virus Collection

As the world works together to end the COVID-19 pandemic, ATCC is continuing its mission to provide the highest-quality material and data to the scientific community. We’re responding to the global health crisis by providing SARS-CoV-2 reference materials, synthetic molecular standards, specific cell lines for virus propagation, and many other materials (you can find out more about ATCC’s SARS-CoV-2 materials here).

For the ATCC Genome Portal, we’re excited to announce the launch of Coronavirus genome sequences, give you the first preview of new genome pages built to support even more genomes from the ATCC virology collection, and tease some new UI changes that will make finding the reference genome you need even easier.

ATCC SARS-CoV-2 Genome Sequences Available Now

Clinically relevant reference material and data are the essential backbone of basic research and the development of novel diagnostics, vaccines, and therapeutics. Since the COVID-19 outbreak began, ATCC has been prioritizing the production of genomic RNA from SARS-CoV-2 strains originating from clinical sources. The first SARS-CoV-2 genomic material launched (ATCC® VR-1986D™) was derived from the 2019-nCoV/USA-WA1/2020 clinical isolate, which was the first COVID-19 case in Washington state and serves as the reference strain for the United States (check out its whole-genome sequence here). Soon after, we launched genomic material (ATCC® VR-1991D™) derived from the Hong Kong/VM20001061/2020 clinical isolate, which was from a COVID-19 case in Hong Kong (check out its whole genome sequence here).

Because of ATCC’s ongoing enhanced authentication initiative, sequencing and accurately reporting the genome of these isolates to researchers was of utmost importance during production. Genomic RNA from these isolates were sequenced on the Illumina platform, then mapped against both the Wuhan-Hu-1 reference genome for SARS-CoV-2 and the sequence for their respective clinical isolates. These efforts once again demonstrated why whole-genome sequencing of ATCC material is so essential as we discovered a rare deletion in the ORF6 region of VR-1991D that may have strong implications in the resultant protein’s function; this deletion was not present in the original clinical material.

In the last few days, we’ve be made even more Coronavirus genomes available, starting with genomes for the endemic Coronavirus strains 229E (ATCC® VR-740™) and OC43 (ATCC® VR-1558™), followed by the genome sequence of an Italian SARS-CoV-2 isolate (ATCC® VR-1992™).

ATCC Virology Collection: Coming Soon to the Genome Portal

When the COVID-19 pandemic began, we knew we needed to re-evaluate our priorities for expanding the ATCC Genome Portal. Although we’re currently 670 ATCC bacterial genomes strong (and growing every month!), the need for high-quality, reference-grade virus genomes tied to authenticated material has never been more obvious.

So, we went back to the drawing board and began envisioning what genomic data would be essential to the virology community members that rely on ATCC materials. Although the new Coronavirus genome pages were essential to make available as fast as possible, they represent just the start of what we have planned for our virology collection. Here’s what’s coming up later this year:

• A new section dedicated specifically to DNA and RNA viral genomes, enabling the rapid exploration using search terms and taxonomy unique to viruses.
• Lot-to-lot viral genomes.
• Within-lot minor variant reporting from Illumina deep sequencing.

Live Chat, Enhanced Search Capabilities, and Forward to Fungi

Finally, we wanted to share some non-virus-related news and teasers. First, we’ve made it easier to find answers to all your questions about the genome portal! Available now, just click on the chat icon in the bottom right corner of any genome portal page, and you’ll be connected to a wonderful One Codex team member who will be able to respond to your question in real time. If you have any ATCC product-specific questions, One Codex will put you in touch with the experts at ATCC Technical Support right away.

While you’re there, you can also explore in depth documentation for how to use the ATCC Genome Portal, and how we generate our reference-quality genomes. If you’re more up for exploring and discovering the genome portal on your own, you can also access all our newly centralized documentation from the top menu bar.

Second, in our ongoing quest to keep making the ATCC Genome Portal as user-friendly as possible, we’re overhauling our search bar to incorporate some of the same look-and-feel as our genome tags. Soon you’ll be able to more intuitively filter the genome collection of your choice by adding and subtracting search tokens of your key criteria. No more typing!

Lastly, we’re now in the development phase of yet another major ATCC collection: the ATCC mycology collection. Leveraging the power of long-read sequencing technology, we’re again altering the landscape of reference-quality genomes by providing fungal genomes derived from authenticated and traceable ATCC material than public genome portals.

Look for these features and the start of the ATCC fungal genome collection at the end of 2020.