Question: One thing that has become evident is that for omicron, it is best to swab the throat than the nose for home and other rapid and PCR tests.  Is that the current practice?

Answer: The current practice in the US is to follow the testing instructions (i.e., take/use the nasal swab).  As the FDA tweeted on January 7th, “FACT: When it comes to at-home rapid antigen #COVID19 tests, those swabs are for your nose and not your throat (1/3), The home antigen tests available today are only authorized using nasal swabs. We don’t have any data yet suggesting throat swabs are an accurate or appropriate method for at-home tests. (2/3) Use your at-home #COVID19 test exactly as directed to avoid invalid results or injuries. (3/3) “(Figure)  And as Dr. Fauci elaborated in last week’s Senate hearing, “There have been recent reports that, in fact, [there may be higher] sensitivity and ability to detect [the virus] in a swab of the throat versus the nasopharynx, at least with omicron. I think it needs to be validated and verified.”   

All this confusion has arisen because: 1) We know that the sensitivity of antigen tests has likely declined with omicron (reminder: home-based tests are usually antigen tests; sensitivity is the ability of the test to detect everyone truly infected); 2) Initial data from South Africa indicate that when using PCR tests, saliva swabs are more accurate than nasal swabs at detecting omicron (reminder: PCR are lab-based tests); and 3) Israel recently instructed its citizens to swab both the throat and nose and the UK issued an instructional video way back in July 2020 on how to take a throat and nasal swab.  

It’s exceptionally hard for science to keep pace with the quickly changing dynamics of the pandemic.  It’s very possible that the guidelines change in the future and we move from nasal to throat swabs.  In the meantime, with limited data, no news from test manufacturers, and at-home tests designed for nasal swabbing, I’d recommend sticking with current practice.  You might be wondering what the harm would be in taking both throat and nose swabs; I’d say that it’s the possibility of invalid results.  There’s also the possibility of injury, but that seems avoidable with a bit of caution.

Figure. FDA Reminds the Public to Use Nasal Swabs as Instructed (from FDA)