Where can I see Biobot's variant sequencing results?
If your organization has chosen to join the Biobot Network, you can see the sequencing results of your location’s samples on Biobot’s public data visualization at biobot.io/data. These results published on our website are aggregated by region and by county, and are updated weekly. For more information on the sequencing results reported on the data visualization, please visit FAQ - Data Visualization vs. Standard Reports.
Can I receive variant sequencing data specific to my location?
Yes! To see location-specific variant sequencing data, we can deliver our variant sequencing product directly to you. This product is an add-on to our Covid-19 reports.* If you are not already enrolled in variant sequencing but are interested in receiving this data in addition to your Covid-19 reports, please contact us at firstname.lastname@example.org.
What do the percentages of variants mean in my sequencing results?
There are always many different SARS-CoV-2 variants and sub-variants circulating at any one time but only a fraction of variants are considered clinically relevant and impact how public health officials respond. We track a subset of variants of concern designated by the CDC and WHO circulating in the US. See our release notes for the list of variants we are tracking.
What does “% other variants” mean in my sequencing results?
In our reports, we describe percent abundances of those variants that are the most common and clinically relevant. The percent abundances of less common variants are combined into “% other variants”. There are numerous named variants of SARS-CoV-2 aside from those widely in circulation (for an up to date list see cov-lineages.org) and these are the variants combined into the “other variants” category. In most, but not all cases, “other variants” will be a small percentage of the total SARS-CoV-2 abundance within a sample.
What does “Pending” mean in my sequencing results?
Results may be pending for a variety of reasons and will be included in a subsequent report. For example, sample results could be delayed if we received the sample later than was expected or if samples required reanalysis. In some rare cases, we reanalyze samples to obtain more certainty regarding the variants present (for instance, if an unusual variant was detected).
What does “Non-detect” mean in my sequencing results?
If there was no SARS-CoV-2 identified by qPCR, we do not send the sample for sequencing.
What does “Concentration too low” mean in my sequencing results?
If there is SARS-CoV-2 in the sample, but the concentration is too low (<30 copies/mL sewage) to attempt sequencing, then your report will show “Concentration too low”.
What does “Sample QC failure” mean in my sequencing results?
Samples were tested for SARS-CoV-2 via qPCR but failed quality control and were not eligible for sequencing. For example, qPCR results appear to be compromised because of the presence of inhibitory compounds within the sample or poor amplification of the molecule we use to gauge human waste abundance.
What does “Sequencing failed” mean in my sequencing results?
Your report may show “Sequencing failed” which means we were able to detect SARS-CoV-2 but the sequence data obtained from the sample did not meet our quality criteria.
What does the quality control process for sequencing entail?
As part of our bioinformatics pipeline we include numerous quality control checks. If we do not feel that the quality of sequencing data is high enough to support differentiation and relative quantification of variants we will report “sequencing failed”. We use Freyja, a tool developed by Dr. Kristian G. Andersen’s lab at the Scripps Research Institute, to identify and quantify SARS-CoV-2 variants of interest.
What can I do to improve sample quality to avoid failing?
We haven’t identified any single step customers can take that will reliably improve sequencing results from wastewater. One inherent challenge with wastewater is the fragmentation of the SARS-CoV-2 genome as well as the presence of chemicals that inhibit the sequencing reaction.
Some sampling sites may have more of these chemicals than others, which could cause consistently poor sequencing results. We are continually improving our laboratory processes in hopes that we may better address inhibition in the future.
My values have changed a lot since my previous report, what does this mean?
Similar to qPCR, if your sampling site represents a smaller population, small changes in which variants are circulating can lead to large week-to-week swings in the data. In addition, new variants can take over quickly when they begin to spread exponentially (e.g., Omicron's explosive spread in winter 2021-2022).
There can also be some variability in lab procedures that can lead to small differences from week-to-week.