What is prolonged viral shedding/excretion?

As could not be otherwise, the current pandemic of COVID-19 has brought about a number of relevant questions for research and for epidemiological and genomic surveillance itself. Since it is a virus recently introduced into the human population, it was not known – especially at the beginning of the pandemic – what the capacity of SARS-CoV-2 was to cause viral infections that lasted months in some patients, neither what the health profile of these people would be, or even the maximum duration of these persistent infections.

The virus evolution, enhanced by a scenario of high contagiousness and low population immunity, led to the emergence of variants that were not effectively recognized by the immune response acquired during the initial infection, and are therefore capable of causing reinfections. In this complex scenario a simple question arises: how to separate cases of reinfection from those where a single viral strain remains in a person’s organism for months?

Genomic surveillance – one of the pillars of the Fiocruz Genomic Network – is capable of providing answers in cases like this, as long as there are samples from the patient at both moments of infection. By comparing the samples from the initial period of onset of symptoms with those of suspected reinfection (after a few weeks or months, with or without the onset of new symptoms), it is possible to identify whether the virus from the first moment is genetically different from the one collected at the second moment.

If both samples are genetically very similar, the probability of reinfection is usually ruled out. If they are different – for example, belonging to different lineages – it can be confirmed that the case is in fact a reinfection.

Reinfection versus prolonged viral shedding

When a person has a positive RT-PCR test several weeks or months after recovering, it is difficult to confirm reinfection. That’s because it requires genetic testing of both infections to determine whether they are in fact different.