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.