Question: My husband has COVID.  He was pretty sick with it, but is finally on the rebound (thankfully).  I’ve been so curious to know whether he was infected with the B.1.1.7 variant.  Is there a way to find out?  For reference– we live in Virginia and I think he got it from our neighbor who tested positive shortly after returning from Texas.

Answer: I’m so sorry that your husband has been sick and I’m sending well wishes his way.  When it comes to knowing whether he was infected with the B.1.1.7 variant (UK variant), there are two ways to find out:  

1. Make assumptions based on what’s known about viral transmission in your community: CDC’s COVID Data Tracker includes data on variant proportions across the US and by state (FIgure 1).  The data are collected through CDC’s national genomic surveillance, include >40,000 sequences collected since late December, and are grouped in 2-week intervals.  According to CDC’s genomic surveillance data, over the last month, B.1.1.7 has been the most common variant circulating in Virginia (53.3%), and it’s been even more common in Texas (59.2%).  For readers in Tennessee– B.1.1.7 circulation is the highest in Tennessee as compared with all other states (72.3%).  Based on these data, the odds favor that your husband was infected with B.1.1.7. Of course this really is just a guess. If you really wanted a definitive answer, you should opt for path 2:
2. Ask that he be given a PCR test that can detect the variant:  Some background here– RT-PCR tests are highly sensitive and specific (see Q&A of 11/6),  and RT-PCR tests that use multiple genetic targets (e.g. those that look for multiple markers of a virus) are more accurate than RT-PCR tests that look for only one genetic target, particularly in the context of multiple circulating variants (see FDA note).  When it comes to B.1.1.7, it has a mutation on the S gene, which also happens to be a common testing target.  Basically, RT-PCR tests that look for multiple genetic targets oftentimes include S as one of those targets.  When these tests are analyzing a sample from someone infected with B.1.1.7, they will return positive results for other gene targets (e.g. N, ORF1ab), alongside a negative result for the S target.  Though these tests were not designed to test for the B.1.1.7 variant, they can ultimately be used as a proxy thanks to the way they were designed and the way SARS-CoV-2 has mutated..  But– not every PCR test is designed this way!  So if you were to ask that your husband be tested for the B.1.1.7 variant, you’d need to be sure that the RT-PCR test included multiple genetic targets, one of which being the S-target. Given how decentralized testing is in the US, it might be a challenge to find the right testing provider.     

Figure 1. Proportions of SARS-CoV-2 by Variant over Time, USA (from CDC)