New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic

2.1. SARS-CoV-2 and its infection cycle

SARS-CoV-2 has a single-stranded positive-sense RNA genome (ssRNA+) with an approximate size of 29,891 nucleotides (~30 kb), containing 15 ORFs ( Figure 1 ). During the infection process, replication, and virulence of SARS-CoV-2, different viral proteins intervene, such as structural proteins (SP) and non-structural proteins (NSP). Both kinds of proteins play multiple roles and functions, which are shown in the Table 2 and Figures 1 – 3 (163, 164).

SARS-CoV-2 SPs participate in the pathogenicity of the virus, which includes receptor recognition, replication process, viral resistance, and others (165). On the other hand, NSPs of this virus are involved in genome replication and regulation of the early stages of transcription (166). Additionally, the different SARS-CoV-2 proteins exhibit participation as virulence factors that are resistant to the immune response, among others (167–169). These biological traits of SARS-CoV-2 allow it to infect different types of cells. The virus first enters the upper respiratory tract through respiratory droplets or viral particles and then progresses to the lungs. Within the lung, the virus prefers to infect the surface of alveolar epithelial cells and cells expressing ACE2 and possessing coreceptors such as TMPRSS2 and neuropilin-1 (NRP1), among others (170). These proteins are not exclusive to the lung but are expressed on the surface of various cells in different tissues, including the ciliated epithelium, nasopharyngeal tract, upper respiratory tract, bronchial epithelium, type II pneumocytes, alveolar monocytes, macrophages, liver, kidneys, among others (171–174). This widespread expression pattern has been postulated as a potential explanation for the diverse multisystem damages observed in COVID-19 (175–178).

In the lung, the virus enters the cell through the Spike protein (Protein S), which is composed of 2 subunits (S1 and S2). The initial step of infection involves the binding of S1 to the host RBD. Subsequently, TMPRSS2 cleaves the S1/S2 region, inducing fusion of the virus with the membrane through the S2 domain (although other proteases such as endosomal cysteine proteases, cathepsin B and L, furin, basin, and neuropilin-1 are relevant, TMPRSS2 has been proved to be essential for SARS-CoV-2 pathogenesis) (179). The virus’ entry mechanism into the cell depends on multiple factors, such as cell-type physiological conditions. SARS-CoV-2 entry into the cell can be through membrane fusion or endocytic pathways ( Figure 2 ) (165, 175, 180). Upon completion of viral entry, the ACE2 receptor detaches from the cell membrane, increasing serum concentrations of angiotensin II and causing vasoconstriction, inflammation, and thrombosis, as explained below in the section “Complications of organs and body systems after SARS-CoV-2 infection” (178, 180).

2.2. Viral progression: recognition of SARS-CoV-2 by the immune system and pathophysiology of COVID-19

After membrane fusion, the viral nucleocapsid of SARS-CoV-2 is removed, and the viral genome is released into the host cell’s cytoplasm. Viral infection generates Pathogen-Associated Molecular Patterns (PAMPS) and Damage-Associated Molecular Patterns (DAMPS), which are detected by different Pattern Recognition Receptors (PRRs) ( Figure 3 ). Activation of these PRR receptors leads to activation of downstream transcription factors, such as Interferon Regulatory Factor (IRF) 3 and Kappa Light Chains of Activated B-cell Nuclear Enhancer Factor (NF-κB), which express type I and III Interferons (IFNs), along with pro-inflammatory agents, cytokines, Tumor Necrosis Factor α (TNF-α), Transforming Growth Factor β (TGF-β), Interleukin (IL)-1β, IL-6, IL-8, IL-12, IL-18 and chemokines such as Chemokine Ligand (CCL) CCL2, CCL3, CCL5, and Chemokine Ligand Motif C-X-C (CXCL) 8, CXCL9 and CXCL10 (181–183). The secreted IFNs bind to the cell surface receptor on neighboring cells to increase the expression of IFN-Stimulated Genes (ISGs) via the Signal Transducer and Activator of Transcription (STAT) 1/2/IRF9 complex, driving an antiviral state (184).

The release of these pro-inflammatory substances induces the recruitment of monocytes, neutrophils, and macrophages into the infected tissue, which in turn secrete IL-6, IL-1β, IL-8, TNF-α (181, 185), generating a concentrated medium of Reactive Oxygen Substances (ROS), which contribute to viral pathogenesis and by producing damage in the tissue surrounding the infection (185). This leads to an inflammatory feedback loop so that the more cytokines and chemokines are released, the greater the recruitment of immune cells, and with it, the greater the number of cytokines and chemokines, favoring tissue damage and increasing the severity of SARS-CoV-2 infection (186–189). As the infection progresses and innate and adaptive immune responses are intensified, highly glycosylated viral S protein with L-fucose and D-mannose-rich residues activates the complement system via the lectin pathway along with the major complement opsonin H regulatory factor (C3b) (190–192). Moreover, although complement activation is essential in the initial immune response, its sustained activity contributes to viral pathogenesis, leading to plasma clotting and tissue damage.

Thus, SARS-CoV-2 drives an exacerbated immune response, influencing the activity of natural killer (NK) cells, macrophages, and neutrophils, among other cells. So, all this immune response dysfunction continuously increases TGF-β concentrations, resulting in sustained damage to surrounding tissue and nerves in the affected area. As the damage proceeds, the cells affected by the harm release substances that further alter the affected area, compromising the permeability of the tissues and allowing the invasion of more immune cells into the tissues and organs. This sustained infiltration of immune cells, such as neutrophils, leads to the formation of Neutrophil Extracellular Traps (NETs), which increases tissue damage by forming a feedback loop (193–196).

CoVs employ diverse strategies to evade the immune response, primarily by interfering with IFN signaling, production, and resistance. The virus subsequently conceals itself within various types of cells to evade immune recognition, thus subverting the initial stages of immune defense. Furthermore, congenital defects in the host’s immune response have been linked to increased severity of COVID-19.

An early response by the host to the cytokine storm is relevant to reducing the replication and severity of SARS-CoV-2 infection, thus enabling it to promptly prepare an adaptive response. The damage generated by SARS-CoV-2 in tissues may be due to the destruction of infected cells by CD8+ T cells and the production of pro-inflammatory cytokines by other immune cells, which can produce collateral damage to tissues when fighting the viral infection (197). Some reports of this self-tolerance and cross-reactivity effect have shown that they are due to antiphospholipid antibodies, antitype I interferon, and antinuclear polymorphs, among others (198–200). This, in turn, increases the risk of contracting autoimmune diseases such as Guillain-Barré syndrome and systemic lupus erythematosus. Furthermore, according to some reports, the fact that the immune system attacks the organism simultaneously while it defends itself from the invading agent is due to the imitation or similarity of epitopes between the pathogen and parts of the organism. This could be one of the possible reasons for the severity of COVID-19 upon infections by SARS-CoV-2 (201).

Thus, considering the systemic effects of viral recognition by the immune system, long-term consequences of SARS-CoV-2 infection have been postulated to occur by viral persistence, which produces damage by viral replication products and tissue damage by chronic inflammation, where the dysregulated activation of proinflammatory pathways, lead to multiple organ system conditions (202). Some of these physiological alterations will be discussed further below.

It has been proposed that more than one of these mechanisms leads to diverse clinical manifestations. However, the greatest damage and consequences reported in Long-COVID-19 are due to indirect damage caused by the cytokine storm. In that regard, key cytokines implicated in the onset of disease severity include TNF-α, IFN-γ, IL-6, IL-1β, granulocyte-macrophage colony-stimulating factor (GM-CSF), G-CSF, and TSLP (1, 136, 203–207). To ameliorate this cytokine storm, the use of specific monoclonal antibodies for cytokines antagonistic to the JAK-STAT pathway inhibitory receptors, plasmapheresis, and the use of mesenchymal stem cells has been proposed (206, 208, 209).

2.3. Viral evasion and immune response to SARS-CoV-2 infection

The virus, at the beginning of the infection, hides in various types of cells to avoid immune recognition, counteracting the initial stages of immune defense, to subsequently interfere with the signaling pathways for the production and secretion of antiviral proteins, providing to SARS-CoV-2 a resistance to the IFN systems. In addition, congenital defects in the host’s immune response are associated with greater severity of COVID-19 (134, 198). The non-structural proteins Nsp1, Nsp5, Nsp13, Nsp14, and structural proteins ORF6, and ORF7 of SARS CoV-2 counteract antiviral immune response both prior to and following assembly. Moreover, as described above, SARS-CoV-2 affects the antiviral immune response by interfering with the type I IFN induction pathway and the production of other proinflammatory cytokines ( Figure 3 and Table 2 ) (133, 134, 185).

SARS-CoV-2 promotes a T helper (Th) 1 cell response and an early CD8+ T cell response, which initially helps eliminate the virus. However, in the long run, it can produce a cytokine storm (210–212). The CD4+ T cell type 1 (Th1) phenotype has been associated with promoting a state of viral control, favoring an antiviral response. In contrast, the type 2 phenotype (Th2) is associated with a greater severity of infection (213). On the other hand, circulating T follicular helper cells (cTfh) contribute to the development of neutralizing antibodies, and they have been associated with a reduction in COVID-19 severity. In addition, there are notable differences between asymptomatic and symptomatic COVID-19 patients regarding cytokine profile. Indeed, asymptomatic individuals have been shown to have a “coordinated” secretion of pro-inflammatory and regulatory cytokines, while symptomatic patients present with a polarized inflammatory reaction and a pro-inflammatory cytokine storm (214, 215).

SARS-CoV-2 has been described as using cell-to-cell transmission to spread, so the cellular response plays a role in viral control when antibody neutralization is impaired (216). On the other hand, host factors can affect the adaptive immune response. For example, it is recognized that naïve T cells are reduced in older people, which is associated with worse outcomes during infection (217). The humoral adaptive response is also relevant for controlling viral load, disease severity, and reinfection (213, 218).

When the responses of surviving and deceased patients were compared, a delay in the production of neutralizing antibodies was observed in patients with worse post-disease outcomes, which is associated with a higher viral load. The lifespan of the protective immune response produced by natural infection and vaccination is still under study and depends on multiple factors, such as the type of vaccine for the SARS-CoV-2 strain. Likewise, reports demonstrate that the immune response persists for at least 10 months up to one year upon SARS-CoV-2 infection (213, 219). Moreover, immunological memory after SARS-CoV-2 infection is observed at multiple sites, preferably in the lungs and associated lymphoid nodes (220).

In addition, studies have suggested the relationship between autoantibody levels and COVID-19 severity, so it has been proposed that self-tolerance may be affected in SARS-CoV-2 infection, leading to reactivity against host cells. Several autoantibodies have been found in patients with COVID-19, including antiphospholipid, anti- type I interferons, anti-nuclear polymorph anti-antibodies, and anti-neutrophil cytoplasmic antibodies (200, 221). In turn, some autoantibodies have been linked to a potential risk of autoimmune diseases, such as Guillain-Barré syndrome, systemic lupus erythematosus, Kawasaki disease, and autoimmune hemolytic anemia, among others (201). Although the exact mechanism underlying the development of these complications remains a topic of debate, it is hypothesized that they may result from hyperstimulation of the immune system and viral molecular mimicry. In a controlled immune response, specific T cells and neutralizing antibodies limit infection, and apoptotic cells die by phagocytosis, preventing lung damage. Conversely, a dysregulated immune response leads to an overproduction of pro-inflammatory cytokines known as cytokine storm, which directly, indirectly, or synergistically can lead to lung injury, acute respiratory distress syndrome (ARDS), and multi-organ damage in COVID-19 patients (222, 223).

In the context of SARS-CoV-2 infection, it has been postulated that T cells might have a pivotal role in the severity of clinical outcomes. Less severe disease has been observed when a prompt T cell response occurs, but this correlation is still debated (224). During natural infection by SARS-CoV-2, the whole viral particle is recognized, inducing T cell responses to several epitopes that might persist for up to 6–8 months (225). In that regard, epitope studies have identified the structural proteins ORF3, ORF8, and non-structural proteins nsp3, 4, 6, 7, 12, and 13 as dominant targets of CD4+ and CD8+ SARS-CoV-2 T cell responses (226). Likewise, T cell responses induced by vaccines have been demonstrated to have different ranges of protection. In that regard, mRNA vaccines (mRNA-1273 and BNT162b2), protein recombinant vaccine Novavax (NVX-CoV2373), or Janssen vector vaccine (Ad26.COV2.S) have been shown to induce CD4+ and CD8+ T cells that recognize a median of 11 CD4+ and 10 CD8+ SARS-CoV-2 Spike protein epitopes. Similar results have been described for inactivated vaccines, which induce T cells responses against epitopes of the Spike proteins, as well as other SARS-CoV-2 proteins included in the inactivated viral particle, both in adults and children (227–231). Particularly, the consequent T cell response against the Omicron variant persisted after 6 months: 84% for CD4+T cells and 85% for CD8+ T cells, determined by activation-induced markers (232–234). Consistently, activation of specific CD4+ T cells was detected in individuals vaccinated with Coronavac^® for 4 weeks after the second booster, and these cells demonstrated to be responsive against the SARS-CoV-2 Wild type and Omicron variants. Furthermore, cell-mediated immunity was shown to be more perdurable than the humoral immunity (228). Thus, considering the emergence of viral variants that evade neutralizing immunity, T-cell responses have gained importance in understanding protective immunity in SARS-CoV-2 infection (143). Observations of recovered COVID-19 patients, vaccinated and exposed individuals, support the role of memory T cells in reducing viral loads, in the prevention of SARS-CoV-2 infections and reinfections, and early presentation of multiple viral epitopes, avoiding viral escape by variants (233).

In that regard, it has been studied that the population has developed immunity through infection or vaccination after four years of spreading the SARS-CoV-2 virus worldwide. It has previously been discussed that heterogeneous immune imprinting repertoires would depend on several factors, including whether the population was vaccinated before infection, the type of vaccine, the infectious strain, and the particular conditions of the host (235, 236). Despite the above, epidemiological studies have shown that antibody levels gradually decrease over time, so they do not offer long-lasting protection against SARS-CoV-2 infection (233, 237). Moreover, considering the above, the emergence of viral variants with a repertoire of mutations in the Spike protein and the receptor binding domain (RBD) allows the virus to evade the binding and neutralization of antibodies, leading to outbreaks of reinfection around the world (237). In this context, considering the emergence of the Omicron lineage ( Table 1 ), bivalent mRNA booster vaccines were developed and implemented in 2022. Booster with bivalent vaccines has demonstrated greater vaccine efficacy than monovalent vaccines against the Omicron subvariants in all age groups, especially against severe clinical outcomes (238, 239). A systematic evidence synthesis and meta-analysis, conducted up to December 2022, summarize the evidence regarding the long-term effectiveness of COVID-19 vaccines in preventing infections, hospitalizations, and mortality (240). The WHO defined adequate levels of protection of vaccines against COVID-19 for infection. In the first series of primary pandemic vaccines, protection against infection was 83% and 62% after 42 days and 139 days post-immunization, respectively. This study revealed that the baseline levels of effectiveness of the vaccine against the Omicron variant were 70% against infection, and these decreased to 43%. Of note, protection levels against hospitalization also decreased from 89% at baseline to 71%, and there was insufficient evidence on effectiveness against Omicron wave mortality (240). Therefore, it is necessary to address new COVID-19 vaccination strategies to improve protection levels among the population.

3.1. Renal complications

The kidneys express a high concentration of ACE2, TMPRSS2, and furins. At the same time, the kidneys play an important role in controlling blood pressure through different mechanisms, such as the Renin Angiotensin Aldosterone System (RAAS). SARS-CoV-2 can be distributed throughout the body through the blood, infecting organs and tissues susceptible to the presence or absence of the receptors necessary for viral entry (279–281). Kidney damage is not only produced by the direct action of the virus by destroying tissues, but it can also result from an overactivation of the immune system (281).

SARS-CoV-2 damages renal tubules by inducing the infiltration of macrophages and complement proteins such as C3a and C5b-9, leading to tissue fibrosis (282). This damage causes waste to accumulate in the kidney, producing different multisystem effects. Additionally, damage to the kidney generates an imbalance of the ACE 2/Ang 1–7/MasR axis, which leads to an imbalance of the RAAS (281, 282). If kidney damage occurs together with lung damage, hypercapnic acidosis occurs, which contributes to aggravating multisystem damage. By lowering the price and not being able to activate the RAAS adequately, it causes kidney and heart damage, generating a hypovolemic state, which in turn produces vasoconstriction, leading to a procoagulant state, injuring small-caliber arteries and ducts (282–284).

The cumulative damage caused by SARS-CoV-2 results in toxins and organic waste accumulation. As it destroys tissues, the waste products enter the bloodstream, accumulating in the kidneys already compromised by the viral infection and the hyperactivated immune system. This exacerbates a detrimental loop, reaching a critical juncture where the abundance of toxins and waste in the organism compromises additional tissues, ultimately culminating in renal and/or hepatic failure (285–287).

3.2. Cardiovascular complications

When SARS-CoV-2 reaches the heart, it causes heart damage, myocardial injury, arrhythmias, and heart failure. This damage to the heart can be generated directly by the virus or by the exacerbated immune response. As SARS-CoV-2 enters and destroys cells, their functions are altered, leading to cardiac arrhythmias, deep vein thrombosis, pulmonary embolisms, and decreased lung volume (288). People with heart disease before infection tend to have more severe symptoms or develop complications during and after COVID-19, including the development of hypoxemia, coagulopathies, cardiac arrest, and damage (289). During infection, cardiac cells release troponin, and troponin concentrations have been reported to correlate with disease severity and can be considered a biomarker (284, 290–293). Synergistically, due to cardiac damage, a decrease in blood pressure occurs, leading to the activation of the RAAS system, which in turn triggers vasoconstriction, vascular inflammation, and an increase in Angiotensin 2 levels, contributing to the pathogenesis and cardiovascular complications of the infected individual. In addition, it has been shown that SARS-CoV-2 causes coagulation disorders, producing hyper coagulopathies and forming thrombi, which can trigger embolisms in different organs, causing the death of tissues or cells that release toxins and subsequently travel through the blood. These cellular wastes accumulate in the kidneys, which will hinder their functions. Likewise, the released toxins accumulate in the blood, potentially causing peritonitis (294–297).

3.3. Metabolic complications

SARS-CoV-2 can induce widespread metabolic effects, including insulin resistance, dyslipidemia, diabetes, and systemic inflammation. In particular, alterations in the pancreas and liver of individuals infected by SARS-CoV-2 can lead to a state of hyperglycemia due to metabolic stress, leading to the development of “New Onset Diabetes (NOD). This condition can significantly impact the course of the infection. However, the precise mechanisms underlying the emergence of these complications and new pathologies have not been fully elucidated (298–300).

One explanation for this is that SARS-CoV-2 infection in adipose cells can cause a decrease in insulin sensitivity, which can lead to hyperglycemia, leading to an increase in lipids in the body, which can lead to dyslipidemia (301), this affects the pancreas and liver, causing a deterioration in the function of these organs. Furthermore, since SARS-CoV-2 can infect the CNS and the Peripheral Nervous System (PNS), it has been reported that damage to either of these two systems, either at the nervous level or at the functional level, produces a cascade effect altering normal metabolism (302, 303).

3.4. Pulmonary complications

Pulmonary complications are prevalent conditions during and after SARS-CoV-2 infection. Common complications include pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. The damage to the pulmonary epithelium is due to either a direct action of the virus or the effects of the immune system in a small space. This damage and effects lead to pulmonary fibrosis, making breathing difficult. Moreover, immune cells are recruited, which release TNF-α, IL-1β, IFN-γ, and GM-CSF (304, 305). Additionally, as immune cell recruitment occurs at the site of injury, these cells also secrete Proteolytic Enzymes such as Matrix Metalloproteinase (MMP) that degrade the extracellular matrix, producing the release of cytokines, TGF-β and Chemoattractant Protein (MCP) 1, which in turn induces the detachment of fibroblasts, collagen, and cellular matrix components, aggravating pulmonary fibrosis (268, 306–308).

3.5. Gastrointestinal complications

COVID-19 has been reported to produce gastrointestinal complications due to damage to gut epithelial cells, which activates the innate immune response. Indeed, activated dendritic cells, macrophages, and NK cells target the site of infection and secrete IL-1β, IL-6, and TNF-α, while activated CD4+ T and CD8+ T cells produce IFN-γ among other inflammatory cytokines that aggravate tissue damage (309, 310). As damage increases in the intestine, cell death, cellular alterations, and pathological complications increase, hindering the absorption of nutrients, increasing intestinal permeability that induces a greater filtration of immune cells, repeating the cycle and damaging the gastrointestinal mucosal barriers. This, in turn, leads to less water reabsorption in the kidneys and intestines, which could explain the persistent diarrhea and increased nutritional disorders that occur in COVID-19 patients. Moreover, intestinal damage impairs gastrointestinal motility, fluid, and electrolyte secretion, contributing to nausea, vomiting, and abdominal discomfort (311, 312). Gastrointestinal damage drives macrophages and T lymphocytes to the injury site, secreting IL-1β, IL-6, IL-8, IFN-γ and CCL2, CCL5, and CXCL8, which can act synergistically to recruit more inflammatory cells, thus aggravating intestinal inflammation (313–315).

3.6. Hematological complications

The most common hematologic complications caused by SARS-CoV-2 are thrombocytopenia, thrombosis, disseminated intravascular coagulation (DIC), and platelet dysfunction. While these disorders have been seen in repeated cases of COVID-19, the underlying causes of these abnormalities have not been fully elucidated. Some hypotheses suggest that these effects result from the destruction of platelets in the circulation due to an antibody cross-reaction resulting from mimicry of viral epitopes with those of platelets. This hypothesis is based on the fact that the antibodies generated to fight the virus attack the platelets by mistake, or the latter is in the “crossfire” of the immune system against the virus (316–318).

On the other hand, other hypotheses suggest that this effect is because the virus could infect platelet precursor cells in the bone marrow, which would alter their function (317). Furthermore, it is known that proinflammatory cytokines such as TNF-α, IL-1β, and IL-6 can alter the coagulation factor system by increasing the production of fibrinogen, Von Willebrand Factor (vWF), Factor VIII, and Factor XII, which increase the risk of coagulopathies (319–321).

3.7. Neurological complications

It has been postulated that SARS-CoV-2 could infect CNS cells, which explains the cognitive and sensory symptoms patients experience. It has also been proposed that the virus could cross the blood-brain barrier, affecting the recognition of signals traveling from the PNS to the CNS (302). Alternatively, based on cerebral Positron Emission Tomography (PET), it has been proposed that patients with prolonged COVID-19 who change their brain metabolism have a functional alteration of cells, which do not process or transmit information properly. This effect is greater in the bilateral brainstem, which causes hyposmia, anosmia, memory impairment, cognitive impairment, and pain (303). Other hypotheses have proposed that the virus, by damaging nerves and receptors for olfactory and gustatory signals, causes ageusia and anosmia. This damage to the receptors could be due to the direct action of the virus or collateral damage from the overreactive immune system in the nervous tissue environment (322–325). Other complications observed in the brain are encephalopathy, confusion, dizziness and alterations in memory or perceptions, Cerebrovascular Accidents (CVA), transverse myelitis, memory loss, decreased reflexes, neuropathies, myopathies or Guillain-Barré syndrome (322–325).

3.8. Post COVID-19 condition

It has been described that the risk of long-term sequelae after the resolution of COVID-19 is proportional to the age and health status of the patient. Similarly, patients with a more severe infection during COVID-19 tended to have a higher probability of developing sequelae of varying severity and durability (326–328). The post-COVID-19 sequelae can be generated by various factors, such as the fact that SARS-CoV-2 uses some cells as a reservoir, entering a latency period and affecting cell function while waiting for regrowth or activation (183, 328). Other theories suggest that these sequelae are generated by damage to nerves and cells due to a direct action of the virus on nerve cells and receptors or by indirect damage produced by an exacerbated immune system that, in its function of counteracting the infection, can cause collateral diseases, affecting nerve cells and receptors (1, 183). The most common complications are chronic fatigue syndrome, sleep disorders, breathing problems or asthma, heart problems, neurological or psychological problems, anosmia, and ageusia (329, 330). Finally, other theories point out that due to SARS-CoV2 infection, the cellular and organic metabolism is altered. Specifically, the body and systems try to readapt to these new conditions, and it is during this readjustment that some functions are partially or permanently changed, thus generating a loss of tastes, sensations, and confusion of tastes or smells (330–332). In the latter hypothesis, the receptors and nerve cells remain intact. However, they can no longer process information as before SARS-CoV-2 infection (333, 334).

It is known that, in order of frequency, the symptoms of COVID-19 are fever (98%), cough (82%), and, in a lower percentage of cases, difficulty breathing (to be determined). On the contrary, the severity and symptoms of Long-COVID-19 are diverse, and their frequency is highly variable. Particularly, it is challenging to elucidate the frequency of long-term COVID-19 symptoms. However, it has been proposed, based on the number of cases, that the frequency of these, from highest to lowest, would-be cardiovascular conditions, thrombotic conditions, cerebrovascular conditions, diabetes, encephalomyelitis, dysautonomia and metabolic alterations, myalgic encephalomyelitis (ME) and chronic fatigue syndrome (CFS), which is the least common (335–341). It is important to note that ME and CFS, along with postural orthostatic tachycardia syndrome (POTS), can be lifelong (342). It has been reported that between 2 to 14% of patients who had COVID-19 present with conditions similar to or compatible with POTS during Long-COVID-19. These conditions include tachycardia, orthostatic intolerance, fatigue, cognitive and muscular impairment from 6 to 10 months (343, 344). Moreover, it has been postulated that these symptoms develop due to autoimmune disorders, autonomic dysfunction, direct damage from SARS-CoV-2 infection to nerve cells, and invasion of the virus into the CNS (343–346). At the same time, due to the different mechanisms that SARS-CoV-2 has to induce damage in the body, as well as affect the bioavailability of ACE2 and its presence in the various organ systems, other conditions can develop, such as metabolic diseases and those that affect the thyroid, kidney, and liver (347).

In addition, it has been reported that Graves’ disease and Hashimoto’s thyroiditis are among the thyroid conditions of long-term COVID-19. These conditions are thought to be induced by the cytokine storm during COVID-19 and by the molecular mimicry of components resulting from the viral infection with those of the host (347–351). Other conditions that have been reported are lymphopenia, neutropenia, and oxidative damage. However, these sequelae do not have a high frequency, so they have not been directly attributed to a Long-COVID-19 pathology but rather to late COVID-19 symptomatology due to SARS-CoV-2 viremia disseminated (352, 353).

Despite the consequences of Long-COVID-19, there is not enough information to estimate the frequency and severity of each pathology present in this disease. To overcome these limitations, studies with a larger number of patients are needed to assess the frequency, and exhaustive studies of each clinical manifestation are required to estimate severity.

3.9. Viral factors

The susceptibility to SARS-CoV-2 infection and the severity of COVID-19 are contingent upon various variables and diverse factors pertaining to both the host and the virus. Essential factors encompass viral load, replication rate, immune evasion capacity, and the pathogen’s virulence. Concurrently, host-related factors, including age, sex, immune status, comorbidities, smoking habits, and genetics, among others, play crucial roles in determining the infection’s outcome and the disease’s progression.

At the beginning of the pandemic, SARS-CoV-2 had high fidelity in the replication of its genome, but as it spread, it interacted with many other hosts, which caused this virus to mutate and generate new high-impact variants (354–358). In this sense, the reproduction number (R0) value for the first variants was ~2.9, but as it spread and generated new variants, the R0 increased, becoming more significant than 7.0 in the later variants.

SARS-CoV-2 variants tend to have different distinctive features, such as better affinity with ACE2, more resistance to the environment, and greater ability to evade the immune response, among other effects. There is still the possibility of mutations that alter the course of infection, leading to lower efficacy of current vaccines and prophylactic measures, which may ultimately lead to a new variant not affected by current vaccines ( Table 1 ) (359–361). It has been described that the Alpha variant contains mutations in sub-genomic RNA, improving efficiency and immune evasion. Other mutations, such as those associated with ORF 3a, ORF 6, and ORF 7a, provide a better ability to evade the immune response, highlighting the need to keep this viral agent under continuous investigation (362, 363).

Although SARS-CoV-2 encodes an RdRp complex and additional non-structural protein complexes that provide corrective activities, increasing the fidelity of viral replication, this fidelity does not always fulfill its corrective function by producing mutations in the genome and generating new variants with different capabilities (354–358). In the Delta and Omicron variants, the R0 was ~2.79 and ~7.0, respectively, suggesting that each variant’s mutation rate is increasing (357, 364). Other factors that modulate circulation and the appearance of variants include immunocompromised people and the implementation of COVID-19 vaccination.

4.1. Gender

It is known that there are immunological differences between men and women in susceptibility to certain infections due to, among other factors, anatomic characteristics of each gender (such as the width of the respiratory tract), metabolism, etc. (366). Although SARS-CoV-2 has been reported to affect men and women equally, more severe cases of COVID-19 occur in men more frequently compared to women, possibly due to the anatomy and physiology of each gender (367). Genetics may also be involved in the pathological differences and their respective severities. It is known that the X chromosome encodes genes related to innate and adaptive immune responses, since the genes for chemokine receptors (CXCR) 3, Toll-like receptors (TLR) 7 and CD40 ligand (CD40L) are expressed in it (368, 369). On the other hand, unlike women, a generalized inflammatory response can occur in men, probably due to immune plasticity associated with patterns of expression of genes encoded on the X chromosome (370, 371). These differences are also reflected at the level of hormones, where androgens, mostly produced in men, can increase the expression of ACE2 and TMPRSS2 in lung epithelial cells. Moreover, testosterone has been shown to decrease the immune response (370–372). On the contrary, estrogen, considered one of the female sex hormones, has anti-inflammatory properties that lead to a higher degree of immune modulation and induces a downregulation of ACE2 expression on type 2 pneumocytes, endothelial cells and kidney cells, among others (372–375). Immunological differences between men and women have been shown to affect susceptibility to infectious diseases, the immune response produced against pathogens and the effectiveness that certain vaccines can provide (366–369). In conclusion, the role of gender in the severity of COVID-19 is still unclear, so it is essential to continue studying it.

4.2. Obesity

It is important to consider that the underlying characteristics of individuals will dictate the physiological response to infection. Clinical evidence has shown that obesity is a factor to consider when defining the susceptibility and severity of COVID-19. Specifically, there is a Body Mass Index (BMI) scale, in which individuals with: a BMI of 18.5 to 24.9 kg/m2 are not obese; a BMI of 25 to 29.9 kg/m2 are overweight; a BMI of 30 to 34.9 kg/m2 have a type I obesity; a BMI of 35 to 34.9 kg/m2 have a type II obesity; and a BMI ≥ 40 kg/m2 have a grade III obesity. Likewise, degrees of obesity have been related to a less favorable prognosis during COVID-19 compared to those individuals with a BMI less than 29.9 kg/m2. Moreover, patients with a BMI ≥ 30 kg/m2 have shown greater admission rates to the Intensive Care Unit (ICU) compared to those with a lower BMI (376, 377).

Indeed, a high BMI has been correlated with complications such as increased respiratory symptoms, kidney damage, coagulopathies, thromboembolisms, and increased mortality in patients with COVID-19. Furthermore, obesity is commonly associated with metabolic alterations such as insulin resistance, alteration of serum glucose levels, dyslipidemia, etc. These health alterations, combined with the stress caused by the SARS-CoV-2 infection itself, can lead to a worsening of comorbidities or the appearance of new pathologies, such as NOD (376–378).

Furthermore, obesity is also characterized by a dysfunction of the immune system. In fact, it has been reported that patients with a high BMI have been correlated with a higher frequency of the anti-inflammatory CD4+ T cell subsets Th2 and regulatory T cells that can make it difficult to resolve a viral infection, such as that caused by SARS-CoV-2 (376, 378). Moreover, SARS-CoV-2-specific IgG antibodies have been reported to be negatively associated with BMI in COVID-19 patients. Likewise, there has also been shown a positive correlation between serum C-reactive protein (CRP), serum amyloid protein, and ferritin levels with BMI, which could be used as predictive biomarkers for dysfunctional immunity and severity of COVID-19 (378, 379). Besides that, the excess of adipose tissue has been defined as a chronic state of inflammation or “low-grade inflammation”, where proinflammatory cells (macrophages, dendritic cells, cytotoxic T cells, and Th1 cells) accumulate in it, particularly in visceral fat. Therefore, this pro-inflammatory environment in patients with higher BMI favors the amplification of the COVID-19 cytokine storm and, in turn, the exacerbation of the severity of the disease (379–381). Specifically, secretion of IL-6 and high levels of leptin, TNF-α, CXCL-10 have been observed in obese patients with a severe COVID-19 disease.

In addition, ACE-2 is highly expressed in visceral fat, suggesting an important role of adipose tissue in the severity of COVID-19. However, studies on the effect of overexpression of ACE2 in this type of tissue are still inconclusive (381). Nevertheless, it has been suggested that due to ACE-2 expression, adipocytes act as a reservoir of SARS-CoV-2, making more difficult viral clearance.

Furthermore, adipocytes can secrete TNF-α, CXCL10 and leptin. The latter is an immunoregulatory protein since several immune cells express the receptor for this protein. Leptin, when is activated, produces the induction of different downstream signaling pathways such as: the Janus Kinase (JAK) signal transducer and the STAT pathway; the phosphatidylinositol-3-kinase (PI3K) pathway; and the Mitogen-Activated Kinase (MAPK) pathway. As a result, an inflammatory phenotype is induced, including the secretion of IL-6, IL-12, and TNF-α by monocytes and ROS production by neutrophils, which stimulates activators of CD4+ T and CD8+ T cells. Additionally, adiponectin decreases in obesity, favoring a dysregulation of endothelial homeostasis and an exaggerated inflammatory response. On the other hand, weight gain could lead to leptin resistance, which, in turn, increases the frequency of Treg cells in tissues, leading to an immunosuppressive phenotype. Consequently, the effective elimination of SARS-CoV-2 infection is affected, increasing the severity of the disease (382, 383). Therefore, adipokine dynamics in obese individuals contribute to an immunological imbalance, which is relevant to the outcome of COVID-19 patients with this condition. Taken together, ACE2 overexpression in visceral fat, metabolic alterations, and immune imbalance may contribute to a poor prognosis during and after SARS-CoV-2 infection in obese COVID-19 patients (377, 383, 384).

4.3. Age

Some reports suggest that the severity of COVID-19 varies with age, with older adults facing an increased risk and severity of the disease, as well as a higher likelihood of experiencing sequelae and death compared to children and young adults. However, it is worth noting that the impact of COVID-19 on children remains a topic of debate and ongoing research (377, 384, 385). It has been postulated that the variation in the severity of COVID-19, between different age groups, could be attributed to immune immaturity in children and immune senescence in older adults (386, 387). Interestingly, although both age groups receive similar viral loads after SARS-CoV-2 infection, children tend to be asymptomatic or present mild symptoms (unless they develop a pathology known as Chronic Multisystem Inflammatory Syndrome, which is associated with unfavorable outcomes in children under 5 years of age) (388). In patients under 20 years of age, increased levels of CXCL10 and GM-CSF, together with T and B cells in the blood, produce a hyperreactive immune response, causing damage to different tissues (386).

4.4. Diabetes

It has been reported that high blood glucose levels impair the immune response. Therefore, diabetes favors infectious diseases, which are directly related to an increase in the severity and mortality of COVID-19 patients (389). In fact, patients with abnormal blood glucose levels tend to have coagulation imbalance, endothelial dysfunction, and alveolar and extrapulmonary macroangiopathy (390–392). In patients with type 2 diabetes, neutrophils, macrophages, monocytes and NK cells have altered function, decreasing the release of cytokines and IFN-α necessary to eliminate viral infections (393–396). Furthermore, metabolic alteration of glucose and lipids leads to a pro-inflammatory state by altering the synthesis of pro-inflammatory cytokines of immune cells (396, 397). Particularly, it has been postulated that diabetes affects antibodies at the glycosylation level of immunoglobulins, which increases the action of the Major Histocompatibility Complex (MHC) Class I on myeloid cells, contributing to the development of a hyperreactive immune response (24, 398, 399). Although the evidence on whether glucose levels increase susceptibility to SARS-CoV-2 infection is inconclusive, greater severity of COVID-19 has been reported in hyperglycemic patients (390). A possibility for this increase in disease severity may be that these patients have hypercoagulopathies, leukocytosis, and neutrophilia, among others (25, 26). In addition, patients with hyperglycemia increase the expression of ACE2 in the pulmonary, renal, and cardiac systems (391, 392). Of particular interest is NOD, which, as mentioned above, has been associated with SARS-CoV-2. Although the exact mechanisms by which it develops are not entirely clear, the main theories point to undiagnosed (latent) diabetes that worsens after COVID-19. Other theories point to hyperglycemia due to metabolic stress and damage to the β cells of the pancreas due to the direct action of the virus or the indirect action of the immune system (298, 392). While scientific evidence is inconclusive on susceptibility to SARS-CoV-2 infection in diabetic patients, there is a correlation between the severity of COVID-19 disease and blood glucose and insulin levels (27, 400). In addition, insulin affects blood pressure, which in turn causes activation of the RAAS, further increasing this multisystem effect and ACE2 concentrations in the body.

4.5. Nephropathy

Patients with kidney problems have been observed to present significant clinical manifestations during COVID-19, often resulting in complications such as acute kidney injury (AKI). This nephrological complication is characterized by altered values of the estimated Glomerular Filtration Rate (eGFR), serum creatinine, proteinuria, hematuria, and abnormal blood urea (BUN) levels. In particular, people with AKI are more likely to require ICU admission and tend to experience less favorable outcomes after SARS-CoV-2 infection (28, 392). One hypothesis explaining this phenomenon suggests that as the virus infects various cells and tissues, subsequent cell death releases waste materials, further contributing to the overactive immune response. These waste products and substances reach the kidney, causing this organ to function at an accelerated rate. Likewise, since the virus can still infect kidney cells and compromise their normal function, the organ becomes stressed and eventually develops AKI (28, 30, 401). Clinical management is crucial to mitigate the severity of kidney injury, which requires careful monitoring of kidney function in patients with COVID-19. Reports indicate patients may continue to shed viral loads for prolonged periods after COVID-19. This persistence could result from a dysfunctional immune response during SARS-CoV-2 infection. Alternatively, the virus may remain dormant in the system or adopt a latent form in airway epithelial cells, which could explain the epithelial damage and rearrangement observed in the post-COVID-19 period. Another possibility is that the virus persists in the cells of the nervous system, which could explain the consequences and damage observed after SARS-CoV-2 infection in sensory functions of the body, such as taste or smell (31, 32). Patients with acute renal failure (ARF) have also been reported to have a higher rate of SARS-CoV-2 infection than those without ARF. In addition, patients undergoing ARF, or chronic kidney disease (CKD) are reported to have a higher frequency of ICU admission and death (33, 36).

4.6. Cardiovascular disease

SARS-CoV-2 has the potential to directly and indirectly affect the cardiovascular system. On the one hand, direct effects include the destruction of cells of the cardiovascular system that express ACE2 and TMPRRS2. On the other hand, the virus indirectly affects the circulatory system. As the infection of SARS-CoV-2 progresses, there is an increased risk of cardiovascular complications, such as elevated coagulopathies due to alterations in the coagulation cascade and an elevated likelihood of inflammation in various tissues, particularly in the endothelial and vascular systems. This heightened inflammation contributes to cardiovascular events, including myocardial infarction, venous thrombosis, and coronary damage. Individuals with pre-existing cardiovascular conditions during COVID-19 have been reported to exhibit altered levels of biomarkers such as C-reactive protein (CRP), D-dimer (DD), tissue factor (TF), and Von Willebrand factor (VWF). These changes in biomarker levels indicate the potential impact of SARS-CoV-2 on the cardiovascular system, emphasizing the need for comprehensive monitoring and treatment in individuals with cardiovascular conditions (34, 402, 403).

It has been shown that people with pre-existing conditions such as coronary heart disease, high blood pressure, history of cardiovascular disease, or coronary heart disease are more likely to develop post-COVID-19 sequelae (43–45). As previously discussed, in the renal section, cell death results in the release of potassium into the bloodstream. Under normal circumstances, the kidneys filter potassium. However, when the kidneys are overloaded, their functioning is impaired. The increased potassium levels in the blood activate voltage-gated potassium channels (KV), inducing an altered electrical response in muscle fibers. This alteration affects blood pressure by causing a decrease in adenosine triphosphate (ATP), subsequently activating ATP-dependent potassium channels (KATP). Activation of KATP leads to a reduction in heart muscle contractions, which contributes to a decrease in blood pressure. This decrease in blood pressure activates the RAAS system, causing the synthesis of ACE2. When SARS-CoV-2 induces the activation of the RAAS system, it triggers the depletion of ACE2 on the cell surface, increasing angiotensin I in the blood, which could contribute to the development of atherosclerosis (43–45).

Atherosclerosis can manifest itself through several mechanisms: a) First, ACE2, by converting angiotensin I to angiotensin II, helps raise blood pressure. However, if there are low levels of ACE2, angiotensin II is not produced, consequently angiotensin I levels will increase; b) Secondly, ACE2 is an enzyme that facilitates the removal of cholesterol from the arteries. In the absence or reduction of ACE2, cholesterol can accumulate in the arteries, leading to plaque formation; and c) Third, ACE2 functions as an enzyme that plays a protective role for endothelial cells, which line the inside of arteries. Therefore, when ACE2 is deficient or decreased, endothelial cells may become more vulnerable to injury, contributing to plaque formation. The reduction in ACE2 expression induced by the virus may thus contribute to the onset of atherosclerosis through multiple pathways, further complicating the symptomatology of COVID-19 (34, 35, 46).

4.7. Immunocompromised conditions

Immunocompromised individuals who may have this condition due to a genetic disorder or having an underlying pathology, such as one caused by a pathogen or having received a transplant, constitute a group of particular interest. This is attributed to the alteration observed in immune responses within this population, which subsequently influences the clinical course of various pathologies.

• a) Immune disorders due to congenital problems: More than 95 inborn errors of immunity, also called primary immunodeficiency syndromes, have been reported (47). These genetic disorders are a group of conditions that impact the immune system from birth. These disorders compromise the immune system’s ability to effectively fight pathogens, making people more susceptible to recurrent infections and, in some cases, ending up with autoimmune conditions. In the context of COVID-19, people with these genetic disorders have been reported to experience prolonged durations of SARS-CoV-2 infection. Prolonged virus shedding times after infection cause a higher likelihood of severe illness, less favorable prognoses for resolution of infection, and a higher risk of developing serious complications after COVID-19, including pneumonia and sepsis, among others (49, 50, 404).

• b) Immune disorders due to infectious agents: Certain infectious agents, such as the human immunodeficiency virus (HIV) or bacteria such as Streptococcus pneumoniae, can weaken the immune system, either by suppressing or altering the body’s immune response. Theoretically, it has been postulated that individuals in this group may experience greater severity of COVID-19, due to the combined impact of the damage caused by their existing pathogens, the effects of the virus itself, and the compromised immune system. Additionally, other opportunistic infectious agents may take advantage of this depressed immune state. This complex condition poses challenges for healthcare, as treatments must target not only the SARS-CoV-2 infection, but also the coexisting pathogens that contribute to comorbidities in these patients (49–52, 404).

• c) Immunological disorders due to immunosuppressants: Patients who undergo organ or cell transplants, such as hematopoietic cells (HTC), or solid transplants (SOT), have a higher rate of admission to the ICU and a greater severity of COVID-19 (50). It is thought that in these patients, SARS-CoV-2 has a longer viral replication time and, therefore, a greater viral load is produced, leading to more significant and sustained pathology (49). However, the results of this type of research that have been carried out so far remain ambiguous. For example, other studies have reported low rates of SARS-CoV-2 infection among transplant patients. Although, this can be attributed to the strict health measures implemented for these patients (53).

Therefore, more extensive investigations are required to elucidate the mechanisms behind the pathogenesis of SARS-CoV-2 infection in immunocompromised patients.

4.8. Microbiota

It is well known that several microorganisms live in a symbiotic relationship in the human body, called Microbiota. These microorganisms produce molecules and vitamins, such as vitamin K, which are used by the human body and, in turn, provide nutrients and protection to these microorganisms (54). The Microbiota is characteristic and specific to everyone. This microbiota aids digestion and protects the host from possible pathogenic microorganisms (55). It has been reported that the microbiota has immunoregulatory functions. In fact, changes in this microbiota induce a dysbiosis that affects the host by exposing it to opportunistic pathogens, or triggering altered immune responses such as allergies or inflammatory bowel disease (IBD), which increases the probability of secondary diseases, such as obesity and diabetes (54–56).

During SARS-CoV-2 infection, bacterial co-infections or dysbiosis may occur, contributing to increased mortality and morbidity in individuals. This effect has been previously reported in CoVs such as SARS-CoV and MERS-CoV, with co-infections of each of the respective viruses together with respiratory tract pathogenic bacteria such as Streptococcus pneumoniae and Staphylococcus aureus (57). Concentrations and types of microbial populations vary upon a viral infection. Specifically, it has been shown that 3 days after SARS-CoV-2 infection, Fusobacterium periodonticum in the oral cavity decreased significantly (58). It has also been reported that Faecalibacterium prausnitzii, a vital bacterium involved in anti-inflammatory processes, is negatively altered as the severity of COVID-19 increases (58, 59). Additionally, a reduction in host-typical commensal bacteria, along with increased presence of pathogens, has been correlated with increased severity of COVID-19. This association may be related to the role of commensal bacteria in shaping the immune system response, influencing the outcome of viral infections. However, the specific association between the upper respiratory tract Microbiota and the severity of COVID-19 remains to be elucidated. Therefore, further studies in this field are warranted to provide a comprehensive understanding of these relationships (58–60, 62, 405).