Viral reactivations and co-infections in COVID-19 patients: a systematic review

Viral reactivation is associated with different types of stimuli including physiologic and physical changes, and in particular, immunosuppression [1‐3]. Viral reactivation consists of two cycles, including lytic and latent phases. Within lytic cycle, replication and expression of a viral genome and release of virions result in the lysis of host cells whereas during latency, some human viruses may remain dormant within host cells and establish persistent infection with limited or no production of viral particles [1‐3]. The pathogens may switch between the latent and lytic cycles, and a process in which a latent virus enters the lytic stage is known as reactivation [1‐3].

Patients with severe COVID-19 have been characterized by impaired immunity, hyperinflammation, lymphopenia, and cytokine storms [4]. Decline in a number of CD4+ and CD8+ T cells due to either direct attack from SARS-CoV-2 through the spike (S) protein binding with a receptor on T cell [4‐7] or induced cellular apoptosis and the subsequent decline in the type I interferons, especially interferon-gamma (IFN-γ) [4, 8, 9], as well as the T cell exhaustion marked by the increased expression of programmed death 1 (PD-1) indicate the state of immunosuppression in COVID-19 patients [4, 10]. Moreover, elevated levels of IL-2 and TNF-α can mediate T cell apoptosis by promoting Fas signaling and exacerbate lymphopenia in COVID-19 patients [4, 11‐13]. An impaired host immune system without a normal suppression of virus replication, consequently, may induce the reactivation of latent viruses in host, which could contribute to some of the neurologic, dermatologic, and hematologic manifestations among others in COVID-19 patients [14‐24].

Adverse clinical outcomes from the interplays between SARS-CoV-2 and other respiratory and systemic viruses have also become evident from their synergistic impact on further increase of the inflammatory cells to the site of infection and elevation of proinflammatory cytokines [25‐27]. For example, patients with SARS-CoV-2 and influenza virus coinfections were found to develop hyperinflammation, ARDS, myocarditis, acute kidney injury, and other disorders due to more frequent activation of the cytokine cascade by flu infection [28‐32]. A retrospective study by Yue et al. revealed that compared to patients with COVID-19 alone, those coinfected with SARS-CoV-2 and Influenza B virus (IBV) were more likely to have poorer prognosis marked by the fatigue, abnormalities in chest computed tomography (CT), and decreased lymphocytes and eosinophils, however these findings were not consistent in patients with Influenza A Virus (IAV) [33]. Primary infection by a different virus, such as cytomegalovirus, followed by SARS-CoV-2 infection, may also predispose individuals to more severe COVID-19 by compromising immunity through disruption of T-cell differentiation and upregulation of interleukin-6 [28]. immunocompromised individuals could be more prone to viral coinfections as Lino et al. observed a higher prevalence of therapeutic immunosuppression status among HHV-6/SARS-CoV-2 coinfected patients compared to the SARS-CoV-2 patients only [34]. However, exact mechanisms by which secondary infections with viruses occur in COVID-19 patients are under investigation.

Studies have additionally reported the incidence of reactivated viruses in COVID-19 patients, mainly the Herpesviridae virus including herpes simplex type 1 and 2 (HSV-1 and HSV-2), varicella zoster virus (VZV), Epstein–Barr virus (EBV), cytomegalovirus (CMV), human herpes virus 6, 7 (HHV 6, 7) [14‐24]. In rare cases, hepatitis B virus (HBV) reactivation in chronic patients have also been observed [35, 36]. le Bal’ch et al. reviewed the virology results of 38 COVID-19 patients and found the patients with either CMV or HSV reactivation required prolonged mechanical ventilation compared to patients with no reactivated Herpesviridae virus [15]. Similarly, Simonnet et al. performed systematic testing for EBV, CMV, HHV-6 DNAemia on critically ill COVID-19 patients and observed the virus reactivations in 85% of patients, among which the patients with EBV reactivation required longer hospital length-of-stay [17]. Skin and ocular manifestations, too, including lesions in multiple regions and herpetic keratitis with risk of blindness, have been observed in patients with Herpesviridae reactivations [18, 19]. Liu et al. reported HBV reactivation in three COVID-19 patients with a history of chronic HBV infection where an increase in HBV DNA upon admission was noted, with one patient developing cirrhosis [35].

Albeit the emerging evidence present a broad spectrum of medical complications among the patients, there is lack of knowledge on latent virus reactivation in COVID-19 cases. Published studies narrowly focus on specific virus species rather than conducting an overarching investigation on all relevant latent virus activation and coinfection in patients. To increase the effectiveness of complex patient care and prevent potential deterioration of patient condition from infections during COVID-19, it is critical to establish a solid understanding of the consequences of both virus reactivation and coinfections. Thus, through the systematic review, we attempted to investigate what were the reported clinical and demographic characteristics of patients undergoing either latent virus reactivation or coinfection, what diagnostic tools were used to detect the reactivation and coinfection, and whether any COVID-19 treatment was associated with an occurrence of either reactivation or coinfection, or both.

This study was reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 statement (see Additional file 1 for the checklist) [37]. A predetermined study protocol of data sources, search strategies, inclusion criteria, and data extraction method was registered on the International Prospective Register of Systematic Reviews (PROSPERO, registration number: CRD42022340897) available at https://​www.​crd.​york.​ac.​uk/​prospero/​display_​record.​php?​ID=​CRD42022340897.

Overall, our review identified 53 full text articles from the literature search, of which 40 studies reported viral reactivations, 8 studies reported viral coinfections during COVID-19 infection, and 5 studies reported viral infections which were not distinguished as either reactivation or coinfection. Case reports and cohort studies consisted over 50% of the included studies. Among the patients reported, those admitted to the inpatient units including ICU were most common next to the patients receiving the ambulatory care. Risk of bias assessments revealed 13 high and 8 moderate quality cohort studies, 2 high quality cross-sectional studies, and 11 case reports and 3 case series satisfying 70% or more of the CARE checklist items. We did not include any study with prevalence rates available only as one of the primary objectives of this study was to present summary of clinical characteristics of patients. In total, we were able to extract data for 12 viruses including the IAV, IBV, EBV, CMV, VZV, HHV-1, HHV-2, HHV-6, HHV-7, HHV-8, HBV, and Parvovirus B19. Upon summarizing the clinical findings for each infection category, EBV, HHV-1, and CMV were most frequently observed within the reactivation cohort, IAV and EBV within the coinfection cohort, and EBV within the indistinguishable infection cohort. In both reactivation and coinfection groups, patients were commonly reported to have cardiovascular disease, diabetes, and immunosuppression as comorbidities, cough, fever, and myalgia as symptoms, acute kidney injury as complication, and lymphopenia and elevated D-dimer and CRP levels from blood tests. Common pharmaceutical interventions in both groups were steroids including dexamethasone and non-specified steroids, as well as antivirals including acyclovir, ganciclovir, remdesivir, and otherwise non-specified antivirals.

We provide two possible hypotheses for the latent virus reactivation and coinfection mechanisms. First, viral reactivation and coinfection may be attributed to impaired cellular immunity by the existing SARS-CoV-2 infection [75, 78, 84‐87]. From our review, we observed high frequencies of lymphopenia with 13.42% and 92.8% in reactivation and coinfection cohorts, respectively. Similarly, retrospective study in China laboratory-confirmed 24 additional respiratory pathogens among COVID-19 patients, and 94.2% of the patients were co-infected with one or more pathogens [84]. Additionally, Paolucci et al. observed a significant loss of lymphocytes in COVID-19 patients and reported an association with the reduction of natural killer (NK) cell and CD8+ T cells and presence of EBV DNA [75]. Exhaustion of functional T cells have been observed among COVID-19 patients marked by the increased expressions of the programmed cell death protein 1 (PD-1) and T cell immunoglobulin and mucin domain 3 (Tim-3), which are indicative of the loss of effector T cell function in viral clearance [78, 85, 86]. Additionally, Ouyang et al. in their 2020 reported the downregulation of the key proteins in TCR signaling and T-cell activation, including SOS1 and MAP2K7, during SARS-CoV-2 infection [87]. Although there are accumulating evidence of diminished immunity among COVID-19 patients, specific immunopathological mechanisms of COVID-19 and viral reactivations and coinfections are yet to be established.

Second, majority of patients who were critically ill from the SARS-CoV-2 infection upon admission received immunomodulatory agents. Steroidal inhibition of inflammatory proteins through gene suppression and blockade of T cell differentiation and monoclonal antibody blockade of IL-6 receptor have been proposed to be beneficial for controlling the cytokine storm and associated organ damage [88‐90], yet such immunosuppressant properties of treatment may had favored opportunistic infections or latent virus replications [91, 92]. This is supported by the evidence of infections among the patients treated with tocilizumab (TCZ), for example, where studies reported the occurrence of infections as the most common side effect in patients with rheumatoid arthritis treated with TCZ [93], as well as the occurrence of herpes infections among COVID-19 patients who received high doses of glucocorticoids after TCZ administration [94]. In our review, steroids, including non-specified steroids, dexamethasone, prednisolone, and methylprednisolone, and tocilizumab contributed 18.11% and 13.86% of the CMV cohort medications, respectively—Gatto et al. additionally reported bacterial infections among COVID-19 patients who received steroids during ICU stay, also suggesting the immunomodulatory role of medications in activating virus latency [70]. However, there are conflicting evidence to whether the pharmacologic immunosuppression directly contributes to increasing the rates of infectious disease complications as impaired host immunity from a natural course of SARS-CoV-2 infection, comorbidities prior to treatment, and most importantly, administration of varying doses at different time points should also be taken into account.

Compared to a large body of literature focusing on a specific virus, we undertook a comprehensive review of all viral infections observed in COVID-19 patients, which enabled us to collect comparative clinical findings between different viruses. Our findings indicate that EBV, CMV, and HHV-6 were most either reactivated or co-occurred upon SARS-CoV-2 infection. We’ve also distinguished observed cases by reactivation and coinfection categories based on authors’ descriptions of detection criteria, which are described in Table 2, which may provide additional clarity on the status of patient’s infectious complication. Overall, evidence collected in this review indicate a potential risk of latent virus reactivation or secondary infection among COVID-19 patients and the cautious use of immunomodulatory agents. Further, high degree of similarity in symptoms between the single SARS-CoV-2 infection and coinfections with other pathogens, especially those of IAV and IBV, might imply that timely detection of reactivated and coinfected viruses is necessary to prevent severe illness and complications. However, based on the previous evidence of viral reactivations among the patients of other critical conditions such as cancer, longer ICU stay, severe pneumonia, or sepsis, imply more of a casual than absolute association between COVID-19 and detection of latent viral DNA. Thus, it is necessary to elaborate that the COVID-19 is rather an additional mechanism to other clinical conditions that may trigger viral reactivations and co-infections [95‐98].

There were several limitations in this study associated with the availability of information from the selected articles. First, there were challenges in differentiating between the reactivation and coinfection of viruses as some of authors interchangeably used the terms to describe an infection or did not provide accurate detection criteria used in study besides describing an infection as either reactivation or coinfection within the text or title of article. Second, demographic information of patients of our interest was not available in all studies, which limited the extent of comparisons between different virus groups. Some cohort studies, for example, did not provide the sex ratio of population or provided the sex ratio of the entire cohort including the patients with and without reactivations or coinfections but not the target of our interest. Out of 50 extracted articles, only 9 studies provided ethnicity of patients (not shown). Third, considering the longevity of viral IgG presence upon infection that could range from several years to lifelong time upon infection [99‐102], diagnostic approach with IgG detection alone in some of the studies in review may had overestimated the occurrences of viral reactivation. Lastly, reference ranges for laboratory findings either varied by studies or were not available, although the thresholds for high, normal, and low levels of each biomarker overlapped.

The study showed that patients were reported to have risk factors of severe COVID-19 including cardiovascular disease, diabetes, and immunosuppression as comorbidities, as well as additionally disease aggravating conditions including acute kidney injury as complication, lymphopenia and elevated D-dimer and CRP levels from laboratory testing, and steroids and antivirals for treatment [103‐107]. Further, EBV, HHV-1, and CMV were most frequently observed within the reactivation cohort, IAV and EBV within the coinfection cohort, and EBV within the indistinguishable infection cohort. However, it is important to note that our study did not attempt to imply an increased risk of infection among individuals with latent viruses. Through this systematic review, we aimed to collect and summarize the available evidence to fulfill the literature gap on the clinical outcomes and potential risk factors of both reactivations and coinfections. Further, our review highlights a significant need for standardizing the detection criteria for reactivation and coinfection, especially within the context of comparing cases across different study sites. With the complex immune pathways triggered by SARS-CoV-2 exposing the patients to develop more adverse outcomes from other concurrent or latent infections, it is imperative that more scientific evidence become available for more efficient treatment and diagnostic measures.