Question: Are anal swabs better at detecting COVID-19 than nasal swabs?

Answer: Anal swabs have been in the news quite a bit in the past week or so with the revelation that the Government of China subjected US diplomats to anal swab tests for COVID-19.  This news follows reporting from Fobes and Reuters from late January 2021 that China had begun to use the tests for high-risk individuals, including passengers arriving to Beijing and individuals in quarantine.  Anal swab tests include the insertion of a cotton-tipped swab 1-2 inches into the rectum to collect a sample for PCR testing.  The tests are clearly far more invasive than nasal and throat swabs.  Based on the evidence I’ve read (further described herein), unless the testing involves very young children, anal swabs are not meaningfully better at detecting active infection.

• The virus is detectable in stool for a longer period than in nasal/throat cultures, but this finding is not necessarily clinically meaningful. Evidence from a pooled analysis of 8 cohort studies indicates and a systematic review of 95 studies found that the virus is detectable for a longer period of time in stool samples compared with nasal/throat samples.  However, just because anal swabs are better able to find viral particles does not mean that they are better able to find active infections. A longer duration of viral shedding in the gastro-intestinal tract does not necessarily equate to a longer-duration of infectivity.  In fact, available data show that clinically recovered adults with prolonged viral shedding have not transmitted SARS-Cov-2 to others.  As a result, CDC does not recommend using a testing-based strategy to end isolation (except among severely immunocompromised patients) because viral shedding can last much longer than infectivity and sickness.  
• Anal swab testing may be worthwhile if a young child presents with COVID-19 symptoms/exposure, but tests negative from nasal/throat swab. Based on their experience treating an infant, the doctors who authored this case study concluded, “Physicians should be aware that asymptomatic or mildly ill children with history of exposure and negative pharyngeal/nasal swabs and positive anal swabs are potential sources of infection via fecal–oral transmission for COVID-19. In addition to nasal/pharyngeal swabs, we believe that children should be tested for SARS-CoV-2 using anal swabs.”
• Fecal/oral transmission remains a theoretical concern. Because SARS-CoV-2 can be present in stool, the role of fecal/oral transmission is a possibility.  This is yet another reason that good hand washing behavior is so important!