Discussion
This study shows the importance of WGS-based analysis to correctly understand COVID-19 recurrences and, additionally, the true links within nosocomial transmission events. This technique provided key data to describe a COVID-19 reactivation, which was subsequently responsible for another two nosocomial cases.
The similarities between the strains infecting Case R in the July and September episodes may be explained by either a persistent infection or a reactivation. Persistence was ruled out because the patient fully recovered from mild clinical symptoms experienced during his first episode. Furthermore, X-rays at admission did not show abnormal SARS-CoV-2-related findings and two sequential negative PCRs just before being diagnosed again in September (at admission and 14 days later) were obtained. Finally, during the 23 days of hospital stay before reactivation, the patient had close contact with four roommates, none of which had a COVID-19 diagnosis. All these findings rule out a hypothesis of persistence.
An alternative explanation for the high sequence similarities between the specimens collected during the two episodes experienced by Case R would be reactivation. The subtle differences (two different SNPs and 16 identical SNPs) found for this case are similar to those described in a reactivation reported elsewhere (Yadav et al., 2021). Reservoirs for SARS-CoV-2 after the resolution of a COVID-19 episode have not been defined yet. The involvement of extra-pulmonary tissues (eyes, gastrointestinal tract, liver, and brain) has been reported (Meinhardt et al., 2020; Paizis et al., 2005; Wang et al., 2020), due to the ubiquity of the ACE2 receptors. Moreover, SARS-CoV-2 RNA has been detected in anal swabs for 42 days in an asymptomatic carrier, while nasopharyngeal swabs were negative (Jiang et al., 2020). The presence of SARS-CoV-2 in non-respiratory tissues suggests that further studies are needed to identify other viral reservoirs (Kalkeri, Goebel, & Sharma, 2020).
If the reservoir hypothesis were correct, we would expect reactivations to be mainly associated to immunosuppression, which would trigger the replication of the latent strain. Few studies have proposed reactivation as the explanation for COVID-19 recurrence (Coppola et al., 2020; Lancman, Mascarenhas, & Bar-Natan, 2020), some involving immunosuppression. However, only two were supported with viral genome analyses (Molina et al., 2020) (Yadav et al., 2021). Several factors suggest the presence of immunosuppression in Case R. Firstly, he had stayed hospitalized 23 days suffering of severe conditions before his first positive RT-PCR. Acute care settings is a risk factor of malnutrition. Before the diagnosis of COVID-19, Case R had lymphopenia for 12 days; this may impair immunity, a factor associated to increased morbidity and mortality (Liu Y, 2020; Ziadi A, 2020). Secondly, the patient suffered of severe gastrointestinal conditions (acute cholangitis, post-ERCP acute pancreatitis, and gastrointestinal bleeding requiring blood transfusion) that could have worsened his immune system. Finally, he presented two infections (cholangitis and a catheter-related infection) and acute kidney injury that might have further worsened his already weakened immune system.
A relevant retrospective finding in Case R is the positive SARS-CoV-2 RT-PCR in three sera specimens taken the same day he had his first diagnostic SARS-CoV-2 RT-PCR, and four and six days later. SARS-CoV-2 may be detected in plasma samples from patients with respiratory disease and this may have value to predict the severity of the disease (Veyer et al., 2020). However, this has not been found close to diagnosis, even in cases with pneumonia (Nijhuis et al., 2020). Therefore, the presence of SARS-CoV-2 in plasma in the second episode experienced by Case R, would suggest that we are not facing a new infection but a likely longer-term disease, which may support the reactivation scenario .
In summary, we report genomic viral analysis allowed to identify a reactivation case with major consequences, leading to a more severe second episode with fatal resolution and subsequent nosocomial transmission of the same strain with an additional COVID-19-related death.