Severe Acute Respiratory Syndrome Coronavirus–2 (SARS-CoV-2), a member of the Coronaviridae family, emerged in Wuhan, China in late 2019 and has since infected over 750 million individuals globally and has resulted in almost 7 million deaths according to the World Health Organization (https://covid19.who.int). The WHO declared SARS-CoV-2 a global pandemic from March 11, 2020, to May 5, 2023. Like other coronaviruses, SARS-CoV-2 has four key protein subunits. The spike protein (S), membrane protein (M), envelope protein (E), and the nucleocapsid protein (N). Of these proteins, the S protein is critical for attachment, initiating infection by S protein binding to angiotensin converting enzyme 2 (ACE-2) which is the main receptor for viral entry. Genetic variants that have generally shown reduced virulence and increased transmissibility relative to the original USA/WA-1/2020 isolate [1], have established additional host cell receptor tropisms including interactions with host proteins Basigin (CD147), Neuropilin-1 (NRP), and Dipeptidyl peptidase 4 (DPP-4) [2]. Unlike ACE-2, CD147 is highly expressed in neural and brain cells [2], [3]. Infection also requires the Transmembrane Serine Protease 2 (TMPRSS2) for cell entry [2], [3].

The SARS-CoV-2 pandemic began with wild type strains exemplified by isolate USA/WA-1/2020 [1]. Those viral strains tended to infect the lower respiratory tract after initial replication in the upper respiratory tract. Common symptoms of WA-1 included fever, cough, shortness of breath, diarrhea, ageusia, and anosmia. Over time, the original viral strains evolved, spawning multiple variants distinguished by genomic markers. As of September 2023, the Omicron cluster remains the dominant worldwide circulating variant group of concern (https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html). Omicron variants tend to infect and remain associated with the upper respiratory system producing headache, runny nose, and sore throat as the dominant symptoms. On average, Omicron variants generally lead to less serious illness compared to prior strains [4].

SARS-CoV-2 utilizes two S protein subunits, S1 and S2, to infect host cells. The S1 subunit attaches to the ACE-2 receptor and the S2 subunit elicits fusion with the host cell membrane through endocytosis. These viral particles then infect surrounding alveolar epithelial cells or other ACE2+ cell types spreading to other organs or moving to other hosts [5], [6]. Importantly, recent variants of SARS-CoV-2 are capable of infecting, replicating, and persisting in respiratory and non-respiratory tissues in the human body.

Viral RNA has been detected in the respiratory tract, heart, lymph nodes, gastrointestinal tract, adrenal gland, eye, and the CNS, including the brain based on analysis of autopsy tissues [7]. Not surprisingly this study confirmed the highest concentrations of SARS-CoV-2 RNA (as much as 100-fold higher titers) were found in respiratory tissues [7]. In the CNS, SARS-CoV-2 RNA has been found in the hypothalamus, cerebellum, cervical spinal cord, and the basal ganglia [7]. Detection of sub-genomic RNA in at least one organ was an indication that the virus persisted in the non-respiratory tissues for months after contracting the original infection [7]. By this assessment, SARS-CoV-2 RNA was detected in the respiratory tract, myocardium, lymph nodes, sciatic nerve, ocular tissue, and all regions of the brain except for the dura mater. Interestingly, evaluation of RNA loads supports the conclusion that viral clearance is slower in non-respiratory tissue than respiratory tissue [7].

The primary area of infection and entry into the human body is the respiratory system. After infection, the virus can spread to other organs in the body through direct cell-cell transfer or hematological transit through systemic spaces that can lead to endothelial cell damage and thromboinflammation, immune system dysregulation, and renin-angiotensin-aldosterone system (RAAS) dysregulation [8]. SARS-CoV-2 tropism creates an affinity for infection and damage of organs with significant ACE-2 receptor expression, but recent variants may be changing this outcome. Extrapulmonary manifestations of SARS-CoV-2 are briefly summarized below [8], [9], [10] and depicted in Fig. 1.

The gastrointestinal system is affected almost immediately after viral infection due to the abundance of ACE-2 receptors in the epithelial cells of the gastrointestinal (GI) tract. Patients with GI tract manifestations are more likely to have a more severe course of the disease with a higher incidence of hepatic manifestations and acute respiratory distress syndrome (ARDS) than those without GI tract manifestations [10]. These impacts have been associated with substantial shifts in the GI microbiome that include reduced abundance of anti-inflammatory bacteria that likely create broad short- and long-term effects that are still being studied [11], [12], [13], [14], [15], [16]. Interestingly, there are a growing number of reports that the GI microbiota predicts disease severity and fatality, amplifying the importance of infection of the GI tract [14], [16], [17], [18].

SARS-CoV-2 manifests in the central nervous system (CNS) with symptoms that include headache, dizziness, anosmia, ageusia, and fatigue [8]. CNS manifestations are associated with more severe presentations of the disease that result in either venous or arterial ischemia, and encephalopathy, encephalitis, and cerebral or acute necrotizing encephalopathy related hemorrhages have been reported [9]. Some of the CNS injury may be related to ischemic events caused by circulating microclots associated with the viral S protein as noted above. It also appears that the spike protein leads to microclot formation, direct damage of the endothelium, and accumulates in the CNS which may be associated with long term sequelae in some patients [19], [20], [21], [22]. Additionally, circulating inflammatory and other damage response proteins have been hypothesized to add to neurologic manifestations including a recent report of the reelin protein associated with inflammatory cell migration and thrombosis [23].

Although SARS-CoV-2 is mainly a respiratory infection, there is growing evidence that the virus infects and replicates in the CNS [24], [25], [26], [27]. SARS-CoV-2 viral products have been identified in the hypothalamus and the CSF of patients [28], [29], [30] indicating that the virus can infect CNS regions where ACE2 expression is detected [3], [24], [31]. In addition to infecting and damaging neurons in the brain, the S protein can also impact glial cells including microglia and activates CNS mast cells triggering release of proinflammatory cytokines and subsequent neuroinflammation [31], [32]. Furthermore, CNS infection by SARS-CoV-2 decreases release of growth hormone (GH) and other metabolic hormones which may, in turn, impact disease severity [28], [33], [34], [35], [36].

Neuroinvasion from the upper respiratory infection site to the CNS may involve direct crossing of the blood brain barrier (BBB) from the bloodstream. Viral capsids from the blood infect BMECs in the BBB and increase permeability of the BBB by altering tight junction (TJ) proteins. This was confirmed experimentally in vitro with detection of high levels of viral RNA in infected BMECs 24-72 hours after infection [25], [37]. Increased BBB permeability and the presence of viral products also led to elevated inflammatory cytokines around the infected BMECs and signaling for immune cell migration into the CNS [25]. A second neuroinvasion route may be direct transit through the olfactory bulb [28], [30], [38]. SARS-CoV-2 infects nasal epithelial cells producing virion loads as much as 124% higher than in the lower respiratory system [39].

A third route by which SARS-CoV-2 may reach the CNS involves infection of the GI tract where ACE-2 is highly expressed in mucosal epithelial cells [15] where the virus can replicate to high titers [7], [10]. As noted above, the virus damages epithelial cells that create the intestinal mucosa which subsequently impacts the microflora that provide nutrients to the intestinal mucosa and helps maintain intestinal mucosa integrity [15], [40], [41]. Disruption of the homeostatic balance also disrupts the gut-brain-axis which impacts vagal nerve activity. Additionally, there is evidence of SARS-CoV-2 infection of ACE-2+ cells in the dorsal vagal nerve complex [38], [42], [43], [44]. This provides a direct conduit to CNS regions where the virus may cause additional damage. The gut-brain axis infection also releases inflammatory signals such as IL-1, IL-6, and TNF- α leading to increased permeability of the intestinal mucosa allowing leakage of virus and pro-inflammatory cytokines into the circulatory system [17], [41].

The pituitary gland contains ACE-2-expressing cells, although ACE-2 mRNAs and proteins are not highly expressed [28], [45]. Analysis of fatal SARS-CoV-2 infections have shown the presence of virus along with decreased numbers of somatotropic, thyrotropic and corticotropic cells with associated lower levels of GH, TSH, and ACTH [45], [46]. However, the pituitary gland has a significant vascular network and the endothelial cells in the vascular system are susceptible to the hypercoagulability exhibited by SARS-CoV-2 patients together with thrombocytopenia, high fibrinogen, and D-dimer levels that can lead to adrenal insufficiency, hypopituitarism, hypophysitis, and pituitary apoplexy [45], [47], [48].

Impact to pituitary function also may be via the hypothalamic-pituitary-adrenal (HPA) axis or damage to other endocrine tissues due to immune regulated responses [28], [31], [48], [49]. In patients who have recovered from infection, an alternate hypothesis for adrenal insufficiency is reversible hypopituitarism or direct damage to the hypothalamus from antiviral antibodies that destroy ACTH and reduce sensitivity of the cortisol stress response [50]. In this situation, adrenal insufficiency reverses itself in around a year [50]. However, based on prior research with coronaviruses in general, it can be assumed that patients with current or prior SARS-COV-2 infection may present with adrenal insufficiency [27], [51]. All these actions can potentially contribute to altered GH levels in COVID-19 patients.

Infection of the GI tract and the systemic impacts of SARS-CoV-2 infection are now clearly related to significant changes in the GI microbiome [13], [14], [15], [16], [17], [18], [41], [52], [53] that in turn may lead to additional impacts on the nervous system and the HPA axis. The GI microbial community has potent effects on the nervous system through metabolism of vitamins, neurotransmitters and neuroactive microbial metabolites including short chain fatty acids (SCFAs) that utilize both systemic and vagus nerve transit pathways [54], [55]. Studies have shown that a patient’s GI microbiome at the onset of infection affects the individual’s response to COVID-19 disease, disease severity, and development of PASC symptoms. Specific microbes were associated with anti-inflammatory states and milder COVID-19 presentation while pathobiont species were associated with more severe symptomatology [14], [52].

In other works, composition of the GI microbiome in hospitalized patients accurately predicted severity of COVID-19 disease [17]. The observed GI microbiome dysbiosis may also contribute to the hormonal impacts and development of PASC but additional work to establish causation is needed. Importantly, the GI microbiome of COVID-19 patients can be destabilized for months after even mild infection [11], [52]. Bacterial metabolite differences have been reported across the COVID-19 disease spectrum suggesting direct impacts of high concentrations of SCFA-producing bacteria (e.g. Alistipes Onderdonkii, Bacteriodes stercoris, and Parabacteriodes merdaii) and others that moderate plasma concentrations of inflammatory cytokines and CRP were highly correlated with patients that experienced low COVID-19 severity [14], [52]. Preclinical work in a mouse model confirmed a protective role for some of these same bacterial metabolites [56].

To directly illustrate that SARS-CoV-2 infection altered GI microbial composition, Sokol et al. infected rhesus and cynomolgus macaques observing community changes from baseline to 10 days post-infection [57]. Like other clinical studies, Sokol et al. found that the concentration of opportunistic bacteria, such as Proteobacteria increased and the concentration of beneficial bacteria such as Firmicutes decreased [57]. This implies that SARS-CoV-2 infection may cause an inflammatory immune response that alters gut microbiome composition which leads to a different expression of metabolites directly impacting ACE-2 transcription [15], [56], and immunologic and neurologic functions. Additional studies including fecal transplant of COVID-19-influenced GI microbiota in germ-free mice are needed to fully understand the role of this community to COVID-19 outcomes.

COVID-19 progression can be broadly classified into four phases: Asymptomatic, spread of infection in the upper respiratory tract, lower respiratory tract infection, and finally post-acute sequelae of COVID-19 (PASC).