Brain Pathology in COVID-19: Clinical Manifestations and Potential Mechanisms

Abstract

Neurological manifestations of coronavirus disease 2019 (COVID-19) are less noticeable than the respiratory symptoms, but they may be associated with disability and mortality in COVID-19. Even though Omicron caused less severe disease than Delta, the incidence of neurological manifestations is similar. More than 30% of patients experienced “brain fog”, delirium, stroke, and cognitive impairment, and over half of these patients presented abnormal neuroimaging outcomes. In this review, we summarize current advances in the clinical findings of neurological manifestations in COVID-19 patients and compare them with those in patients with influenza infection. We also illustrate the structure and cellular invasion mechanisms of SARS-CoV-2 and describe the pathway for central SARS-CoV-2 invasion. In addition, we discuss direct damage and other pathological conditions caused by SARS-CoV-2, such as an aberrant interferon response, cytokine storm, lymphopenia, and hypercoagulation, to provide treatment ideas. This review may offer new insights into preventing or treating brain damage in COVID-19.

Introduction

As of Jan 5, 2023, the global pandemic coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 600 million confirmed cases and 6 million deaths (https://covid19.who.int/). The majority of COVID-19 patients initially suffer respiratory symptoms, which can progress to severe substantial pulmonary diseases, such as pneumonia or acute respiratory distress syndrome (ARDS) [1]. With increasing clinical evidence, researchers have discovered that SARS-CoV-2 causes neurological manifestations in ~30% of patients who recovered from COVID-19. The most common neurological manifestations include cognitive impairment, depression, and psychosis [2, 3]. Further investigations have revealed brain pathology in COVID-19 patients with neurological manifestations [4]. Although Omicron causes less severe disease than Delta, it still leads to brain pathology in many patients. However, the mechanisms of brain disease in COVID-19 continue to be a mystery because of the complexity of brain structure and function, the uncertain course of central SARS-CoV-2 invasion, and the diverse responses to the virus. In this review, we summarize the clinical manifestations and brain pathological features of COVID-19 and discuss the mechanisms of brain damage caused by SARS-CoV-2.

Clinical Neurological Manifestations in COVID-19 Patients

Neurological manifestations have been reported in COVID-19 patients of all ages. For instance, in a study conducted in Wuhan, China, more than a third of COVID-19 patients developed new neurological symptoms after being infected, as shown in Table 1 [5]. Another retrospective cohort study that included 236,379 patients also found a similar rate (33.62%) of patients with neurological manifestations [6]. During the acute phase of infection, patients most frequently experience headache, anosmia, and stroke [7], while "brain fog", headache, anxiety, anosmia, ageusia, and cognitive impairment are common post-acute neurological sequelae of SARS-CoV-2 infection [8]. Many patients had anosmia, and further investigations showed that their nasal components [9] and olfactory gyrus [10] had been damaged. A recent study suggested that sensory and neurological disorders are more evident in younger patients, whereas mental health, musculoskeletal, and episodic disorders are more noticeable in older patients [11]. While most of these symptoms gradually disappear within a few months after COVID-19 recovery, more research is required to confirm the duration of these symptoms and subsequent changes.

Table 1.

Brain Pathology or Manifestations in COVID-19

Author and Area	Date	Population Characteristics	Key Findings
Ruz-Caracuel et al. [32], Sudan, Khartoum	September to December 2021	35 patients who developed cognitive impairment after COVID-19 infection; mean age, 66.7 years	Patients showed deficits in memory recall (22%), memory recognition (23%), memory encoding (24%), processing speed (16%), executive functioning (19%), phonemic fluency (17%), and category fluency (17%).
Cho et al. [33] 1507 sites worldwide	January 30, 2020, to May 25, 2021	161,239 patients (158,267 adults and 2,972 children) with COVID-19; median age, 69 years	The most frequent neurological manifestations at admission were fatigue (adults: 37.4%; children: 20.4%), altered consciousness (20.9%; 6.8%), myalgia (16.9%; 7.6%), dysgeusia (7.4%; 1.9%), anosmia (6.0%; 2.2%), and seizures (1.1%; 5.2%).
Pun et al. [34] multicenter cohort study across 14 countries	January 20 to April 28, 2020	2,088 consecutive patients with COVID-19; median age. 64 years	1,704 (81.6%) of 2,088 patients were comatose for a median of 10.0 days, and 1,147 (54.9%) were delirious for a median of 3.0 days in the 21-day study period.
Taquet et al. [6], retrospective cohort study in 62 healthcare organizations using electronic health records	January 20 to December 13, 2020	236,379 patients diagnosed with COVID-19; median age, 46 years	The neurological or psychiatric diagnosis incidence in the following 6 months was 33.62%. 0.56% of patients had intracranial hemorrhage, 2.10% had ischemic stroke, 0.11% had PD, 0.67% had dementia, 6,229 of 236,379 patients had encephalopathy (2.64%).
Mao et al. [5], Wuhan, China	January 16 to February 19, 2020	214 individuals with COVID-19; median age, 52.7 years	Neurological symptoms were seen in 78 patients (36.4%), and 53 had central nervous system (CNS) manifestations (24.8%). The most frequent CNS symptoms were dizziness (36, 16.8%) and headache (28, 13.1%).
Frontera et al. [35], New York, USA	March 10 to May 20, 2020	4,491 patients with COVID-19 were hospitalized during the study time frame; median age of 606 patients with neurologic disorder was 71 years; median age of 3885 patients without neurologic disorder was 63 years	606 (13.5%) patients had a new neurologic disorder, among which 309 (6.8%) had toxic/metabolic encephalopathy, 84 (1.9%) had a stroke (ischemic/transient ischemic attack, intracerebral/intraventricular hemorrhage, spontaneous subarachnoid hemorrhage). In 65 (1.4%) individuals, hypoxic/ischemic brain damage was noted.
Vanichkachorn et al. [36], Mayo Clinic, USA	June 1 to December 31, 2020	100 patients with post-COVID-19 syndrome; median age, 45.4 years	Neurological complaints, including headache, dizziness, paresthesia, and labile vital signs, were seen in 59 patients (59%). Cognitive impairment occurred in 45 patients (45%).
Meppiel et al. [37], France	March to April 2020	222 hospitalized COVID-19 patients with neurologic manifestations; median age, 65 years	43 patients (8.8%) with neurologic manifestations were reported from 490 hospitalized with COVID-19 in one center. 189 (85.1%) had CNS manifestations, including encephalopathy (85, 38.3%), stroke (63, 28.4%), and encephalitis (21, 9.5%).
Mendez et al. [38], Valencia, Spain	March 8 to July 24, 2020	179 patients completed the test battery; median age, 57 years	Neurocognitive impairment (58.7%), immediate verbal memory/learning (38%), delayed verbal memory (11.8%), semantic verbal fluency (34.6%), and executive function (6.1%) were seen in a mild-to-severe group of patients.
Garcez et al. [39], Brazil	March 30 to May 18, 2020	707 patients with COVID admitted to hospital consecutively; median age, 66 years	Delirium was identified in 234 (33%) patients.
Forget et al. [40], Quebec, Canada	April 20 to May 17, 2020	127 patients with COVID-19; median age, 82 years	In 14 (11.0%) patients, COVID-19 symptoms were mostly neurological, and in 13 (93%, a total of 10.2%) of them, delirium, confusion, or impaired consciousness was present. Delirium was reported in 62 patients (48.8%), among which 9 (14.5%, a total of 7.1%) were reported after admission.
Ray et al. [41], UK	April 2, 2020, to February 1, 2021	Of 52 patients, 27 (52%) were assigned to the COVID-19 neurology group; median age, 9 years	In the neurology group, there were 7 cases of status epilepticus (25.9%), 5 of encephalitis (18.5%), 2 of psychosis (7.4%), 2 of isolated encephalopathy (7.4%), and 1 of transient ischemic stroke (3.7%).

Search strategy: search "(brain) AND (COVID-19) AND (cohort)" in PUBMED and filter articles with specific neurological manifestations. Notably, the study should have explicit inclusion criteria and an experimental process to ensure the validity of the results.

Compared to the patients infected by influenza, COVID-19 patients with neurological manifestations are older and exhibit a higher incidence of altered mental status, headache, anosmia, dysgeusia, and ischemic stroke [12, 13]. In addition, COVID-19 patients develop symptoms more quickly. As shown in Tables 3 and 5, flu patients may suffer from influenza-associated encephalitis/encephalopathy (IAE) with symptoms such as altered consciousness and seizures. Flu patients may also experience post-influenza encephalitis, Guillain-Barre syndrome (GBS), Reye's syndrome, and Parkinsonian symptoms (PD) [14].

Table 3.

Brain Pathology or Manifestations in influenza infection

Author and Area	Date	Population Characteristics	Key Findings
Zayet et al. [12], France	February 26 to March 14, 2020	54 patients with confirmed influenza; mean age, 61.3 years	5/54 (9.3%) patients had a frontal headache, and 2/54 (3.7%) reported a retro-orbital or temporal headache. Dysgeusia occurred in 11/54 (20.4%) patients, while anosmia occurred in 9/54 (16.7%).
Okuno et al. [48], Japan	2010 to 2015	385 IAE cases reported through the National Epidemiological Surveillance of Infectious Diseases database; median age at diagnosis, 7 years	Between children and adults, the mean seasonal incidence of IAE cases was 2.83 and 0.19, respectively, per 1,000,000 people. IAE frequency was highest in school-aged (5-12 years) children (38%), followed by children aged 2-4 years (21%) and adults aged 18-49 years (11%). The proportion of cases with seizures was higher in children.
Mastrolia et al. [49], Italy	October 2017 to April 2019	15 children (13.1% of those with influenza infection in the study period) had influenza-associated CNS manifestations; median age, 27 months	8 patients (53.3%) were diagnosed with influenza encephalitis and 7 (46.7%) with influenza encephalopathy. In children <2 years of age (40% of all cases), altered consciousness was the most frequent neurological manifestation.
Muhammad et al. [50], Malaysia	June to November 30, 2009	1244 patients with influenza A H1N1; mean age, 4.2 years	69 (66.9%) cases were diagnosed as febrile seizures, 16 (15.5%) as breakthrough seizures with underlying epilepsy, 14 (13.6%) as IAE, and 4 (3.9%) as ANE of childhood.
Jantarabenjakul et al. [51], Bangkok	2013 to 2018	397 hospitalized children diagnosed with influenza; median age, 3.7 years	16.9% of patients had neurological problems, such as seizures or acute encephalopathy. Among the 39 (58.2%) acute symptomatic seizure cases, 25 (37.3%) had simple febrile seizures, 7 (10.4%) had repetitive seizures, and 7 (10.4%) had provoked seizures with pre-existing epilepsy. In 28 (41.8%) of encephalopathy cases, the clinical courses were benign in 20 (29.9%) cases and severe in 8 (11.9%).

Search strategy: search "(brain) AND (influenza)" in PUBMED and filter articles with specific neurological manifestations. Notably, the study should have explicit inclusion criteria and an experimental process to ensure the validity of the results.

Table 5.

COVID-19 versus influenza virus

	COVID-19	Influenza virus
Manifestations	COVID-19 patients with neurological manifestations were older, exhibited a higher incidence of altered mental status, headache, anosmia, dysgeusia, and ischemic stroke [12, 13], and developed symptoms more quickly.	Flu patients displayed IAE including consciousness and seizure activity, as well as post-influenza encephalitis, GBS, Reye's syndrome, and PD. Flu patients had neurological manifestations later and experienced a lower incidence of altered mental status [14].
Brain pathology	The most common neuroimaging features of COVID-19 patients include ischemic infarcts, intracerebral hemorrhages, perfusion abnormalities, and leptomeningeal enhancement.	Flu patients with IAE might show neuroimaging features, including brain lesions, edema, rapid and fulminant demyelination, and inflammation, typically in the cortex, white matter, or brainstem. Glial activation, metabolic disorders, and genetic factors are involved [18, 19].
Central invasion	SARS-CoV-2 might enter the brain through the BBB, CSF, and retrograde nerve transmission. No direct evidence of neuronal invasion.	Influenza virus might enter the CNS from peripheral nerves, and the olfactory system might be a major route to forebrain invasion. Like SARS-CoV-2, viral invasion of the CNS lacks direct evidence [58].
Neural mechanisms	SARS-CoV-2 has a small probability of causing brain damage through direct invasion of the brain and a large probability of causing indirect damage by causing abnormal states such as cytokine storms.	Nerve damage is mainly caused by metabolic dysregulation and an aberrant immune response. Brain invasion of the influenza virus can infect vascular endothelial cells, astrocytes, and neurons and induce their apoptosis [59].
Population susceptibility	People with older age and pre-existing neurological disorders are inclined to neuropathy.	Neurological complications of the influenza virus mainly occur in children [57].

Neuroimaging Findings of COVID-19 Patients

Neuroimaging applies quantitative techniques to visualize the brain's structure and function. As listed in Table 2, medical imaging examinations, particularly magnetic resonance imaging (MRI) and positron emission computed tomography (PET) reveal the brain structure and function of patients with neurological manifestations [15]. The most frequent imaging features (affecting >60% of patients) include ischemic infarcts, intracerebral hemorrhages, perfusion abnormalities, and leptomeningeal enhancement. Hypometabolism in the pons, cerebellum, bilateral insula, bilateral medial lobes, and prefrontal cortex indicates brain function dysregulation in COVID patients. The high incidence of cerebrovascular events such as ischemic stroke and intracerebral hemorrhage, indicates potential endothelial injury and coagulation dysfunction. Other investigations have also reported hypoxic alterations in the cerebellum and cerebrum, metabolic alterations of astrocytes, microglial activation [16], neuro-axonal damage, and neuronal loss [17], which provide additional evidence for brain damage in COVID patients.

Table 2.

Neuroimaging findings of COVID-19 patients

Author and Area	Date	Population Characteristics	Key Findings	Imaging Test
Kremer et al. [42], France	March 23 to April 27, 2020	37 patients with neurological manifestations and abnormal MRI related to COVID-19; mean age, 61 years	16/37 patients (43.2%) had signal abnormalities in the medial temporal lobe. 11/37 patients (29.7%) had non-confluent multifocal white matter hyperintense lesions on FLAIR and diffusion sequences, with variable enhancement, with associated hemorrhagic lesions. 9/37 patients (24.3%) had extensive and isolated white matter microhemorrhages. A majority of patients (20/37, 54%) had intracerebral hemorrhagic lesions with a more severe clinical presentation.	MRI
Chougar et al. [4], Parisian, France	March 23 to May 7, 2020	73 COVID-19 patients with acute neurological manifestations; mean age, 58.5 years	43 had pathological MRI findings (58.9%), including 17 with acute ischemic infarcts (23.3%), 1 with a deep venous thrombosis (1.4%), 8 with multiple microhemorrhages (11.3%), 22 with perfusion abnormalities (47.7%).	MRI
Lambrecq et al. [43], Paris, France	March 30 to June 11, 2020	78 hospitalized adults with COVID-19; mean age, 61 years	Of 78 patients who underwent electroencephalogram (EEG), 69 showed pathologic EEG findings (88.5%), including metabolic-toxic encephalopathy features, frontal abnormalities, periodic discharges, and epileptic activity. Of 57 patients who underwent MRI, 41 had abnormalities (71.9%), including acute ischemic lesions (13), white matter–enhancing lesions (5), basal ganglia abnormalities (4), and metabolic lesions (3). 20 patients had perfusion abnormalities (35.1%), almost entirely hypoperfusion (19).	MRI
Morand et al. [10], Marseille, France	August 20 to November 17, 2020	7 children with COVID-19; mean age, 12 years	Children with long COVID exhibited hypometabolism in bilateral medial lobes, the pons, the cerebellum, and the olfactory gyrus.	PET
Helms et al. [44], Strasbourg, France	March 3 to May 5, 2020	28 individuals who received MRI after being referred for ARDS since they were diagnosed with SARS-CoV-2	Brain MRI in 28 patients demonstrated enhancement of subarachnoid spaces in 17/28 patients (60.7%), intraparenchymal, predominantly white matter abnormalities in 8, and perfusion abnormalities in 17/26 (65.4%). The EEG mostly revealed unspecific abnormalities or diffusion, especially bifrontal, slow activity.	MRI
Helms et al. [45], Strasbourg, France	March 3 to April 3, 2020	13 patients had a brain MRI; median age, 63 years	8 patients (61.5%) were had leptomeningeal enhancement. 11 (84.6%) showed perfusion abnormalities. 3 with ischemic stroke (23.1%) had increased diffusion-weighted imaging signals.	MRI
Lu et al. [46], Anhui, China	March 3 to April 3, 2020	60 COVID-19 patients; mean age, 44.10 years	In addition to a general drop in mean, axial, and radial diffusivity in white matter, patients were more likely to have enlarged olfactory cortices, hippocampi, insulas, Heschl's gyrus, Rolandic operculum, and cingulate gyrus.	MRI
Kas et al. [47], Paris, France	March to June 2020	7 consecutive cases of COVID-19-related encephalopathy hospitalized in the neurology or psychiatry wards; median age, 63 years	one patient presented with typical white matter-enhanced lesions. Arterial spin-labeling perfusion imaging revealed frontal hypoperfusion and cerebellar hyperperfusion in 2/7 and 1/7 patients, respectively. In the whole group of patients vs controls, prominent hypometabolism occurred at the prefrontal cortex prevailing on the right side, bilateral insula, anterior cingulate, and caudate nucleus.	18F-FDG-PET/CT

Search strategy: search "(brain) AND (COVID-19) AND ((MRI) OR (PET))" in PUBMED and filter articles with detailed and concrete radiographic outcomes. Notably, the study should have explicit inclusion criteria and an experimental process to ensure the validity of the results.

As for flu patients, the most prevalent imaging features include brain lesions, edema, rapid and fulminant demyelination, and inflammation. These abnormalities are mainly in the cortex, white matter, or brainstem (Tables 4 and 5). In addition, glial activation, metabolic disorders, and genetic factors may be involved [18, 19].

Table 4.

Neuroimaging findings in influenza patients

Author and area	Date	Population characteristics	Key findings	Imaging test
Zeng et al. [53], China	September 2009 to December 2011	17 patients with severe neurological complications after H1N1 infection (6 children died, 11 recovered); mean age, 6.7 years	Their manifestations of H1N1 were meningitis (3), encephalitis (1), and influenza encephalopathy (7). MRI features of acute necrotizing encephalopathy (ANE) included multiple symmetrical brain lesions demonstrating prolonged T1 and T2 signals in the thalami, internal capsule, lenticular nucleus, and pontine tegmentum. Postmortem MRI in two children with ANE showed diffuse prolonged T1 and T2 signals in the bilateral thalami, brainstem deformation, and tonsillar herniation.	MRI
Thabet et al. [53], Japan	2002 to 2004	14 children diagnosed with influenza infection with neurological complications	EEG showed a focal slowing in 4/9 patients with delirium and 4/5 with febrile seizures. Generalized slowing occurred in 1 patient with delirium.	EEG
Britton et al. [54], Australia	May 2013 to December 2015	13 cases of IAE; median age, 3.7 years	MRI showed typical bilateral, symmetrical thalamic lesions with varying degrees of basal ganglia, brainstem, and cerebellar involvement in the 4 children with ANE.	MRI
Dadak et al. [55], Germany	January 2012 to December 2017	6 children with influenza encephalopathy following influenza A infection, 5 underwent MRI and 1 CT; aged between 10 months to 14 years	Impaired consciousness followed by epileptic seizures was the most common CNS symptom. The MRI findings of 1 child were concordant with mild encephalopathy with a reversible splenial lesion (MERS); this patient recovered but remained aphasic. In 2 cases, MRI showed typical bilateral thalamic lesions as a feature of ANE. In 3 patients, the common finding was multiple intracerebral hemorrhages without thalamic and pontotegmental involvement.	MRI and CT
Li et al. [56], Guangzhou, China	January to February 2019	4 patients with H1N1 influenza A-associated MERS; mean age, 4.9 years	Brain MRI revealed similar ovoid lesions in the corpus callosum, mainly in the splenium and, in 1 case, in the splenium and genu of the corpus callosum. Only 1 patient had an abnormal EEG outcome.	MRI and EEG
Meijer et al. [57], Data for the case review were identified by searching Medline	November 2013 to May 2016	44 patients with influenza virus infection at the onset of neurological symptoms	Confusion and seizures were the most prevalent neurological symptoms in 12 (27 %) and 10 (23 %) patients. MRI was performed in 21 cases. It was abnormal in 13 cases, including multiple lesions in 10 cases and a single lesion in 3 cases. Brain edema was observed in 5 cases. EEG was performed in 25 cases. It was abnormal in 15 cases (60 %), mostly described as generalized or diffuse slowing (9 cases) or consistent with encephalitis (4 cases).	MRI, CT, and EEG

Search strategy: search "(brain) AND (COVID-19) AND ((MRI) OR (EEG))" in PUBMED and filter articles with detailed and concrete outcomes. Notably, the study should have explicit inclusion criteria and an experimental process to ensure the validity of the results

Variant and Neurological Complications in Patients with COVID-19

After the appearance of the Alpha variant, there was no discernible difference in the prevalence of neurological manifestations in patients with COVID. However, the risk of anxiety disorders, insomnia, cognitive deficit, and ischemic stroke were significantly higher after the appearance of the Delta variant. Patients diagnosed with COVID-19 after the emergence of the Omicron variant have a lower death rate, but their neurological outcomes still carry a similar risk to those with the Alpha variant [20]. Therefore, despite the reduced rate of severe cases of Omicron, we cannot underestimate the high incidence of neurological sequelae. It is important to note that this aspect has not been adequately studied because of the difficulty of differentiating the variants of viruses that infect patients in those published clinical studies.

Patients’ Characteristics and Brain Pathology in COVID-19

Cohort studies on the neurological manifestations of COVID-19 have shown that older age and pre-existing neurological disorders are risk factors for neuropathy and mortality [21]. It is known that aging results in immunosenescence, which is a progressive weakening of the ability to mount efficient immune responses against infections [22]. In addition, older people are more likely to have pre-existing neurodegenerative diseases, including Alzheimer’s disease (AD) and PD [23]. Previous studies have suggested that patients with AD are vulnerable to experiencing severe conditions and passing away during COVID-19 [24]. It is worth noticing that the apolipoprotein E4 (APOE4) allele, which is strongly associated with AD, is also a risk factor for severe COVID-19 [25]. Neuropathy in COVID-19 may be exacerbated by APOE4 because it can increase fibrinogenesis, blood-brain barrier (BBB) permeability, and cerebral amyloid angiopathy in the brain [26]. In contrast to female patients, aged male patients have fewer activated and differentiated T cells, as well as poorer CD8⁺ T cell activation and IFNγ production [27]. However, the incidence of COVID-19 sequelae does not differ significantly by gender or exhibits a modest overrepresentation of female patients [28]. Patients with pre-existing diseases, such as hypertension, diabetes, and cardiac diseases, are at a higher risk of infection and brain pathology [29]. Pre-existing pathological conditions, such as arteriosclerosis, contribute to acute ischemia, stroke, dementia, and other neurological manifestations [30]. Moreover, drugs used to treat pre-existing diseases must also be considered for their potential impact on the incidence and severity of infection. One study has suggested that patients treated with drugs that increase angiotensin-converting enzyme 2 (ACE2) expression may be more vulnerable to severe COVID-19 infection [31]. Therefore, patient characteristics, including age, pre-existing conditions, and medication use, should be carefully evaluated when making clinical decisions.

Evidence for Central Invasion of SARS-CoV-2

In several post-mortem studies, small amounts of SARS-CoV-2 have been detected in the brains of patients, but in almost all cases [60], the patients had at least one site in the brain with low but positive amounts of SARS-CoV-2 RNA, with the cerebellum being the most frequently affected [61]. The astrocyte has been identified to be the preferred target for SARS-CoV-2 infection and replication. However, SARS-CoV-2 is difficult to detect in microglia, although the activation of microglia is prominent in the brain of severe COVID patients and is similar to the state of human neurodegenerative disease [62]. In addition, SARS-CoV-2 has also been detected in brain capillary endothelial cells [63]. Notably, SARS-CoV-2 has been found to infect and kill neurons in human brain organoids [64]. A recent study identified virus-specific protein expression in the hypothalamus and spinal ganglia neurons by immunofluorescence. Furthermore, this study demonstrated that SARS-CoV-2 RNA persists in the brain for months, even after the virus has been eliminated from the plasma [65]. However, additional research is required to confirm the virus's capacity for replication in the brain. It should be emphasized that the existing studies are insufficient to demonstrate direct viral invasion of neurons or detect low virus levels in the brain. Currently, no conclusive information about the brain invasion of SARS-CoV-2 is available in human post-mortem studies. Besides, unlike animal studies with a good perfusion process before sampling, the SARS-CoV-2 detected in the human brain might originate in the blood. Thus, it is more likely that the virus indirectly causes damage to the brain by triggering a series of responses. The importance (even the existence) of direct viral brain invasion of SARS-CoV-2 still needs further study.

Virus Structure and Cellular Invasion Mechanisms

SARS-CoV-2, known as the main culprit of this global pandemic, possesses single-stranded positive-sense RNA (+ssRNA), four structural proteins (N, E, M, and S), and sixteen non-structural proteins (nsp1−16) [66, 67]. The spike (S) protein, which consists of S1 and S2 subunits, plays a prominent role in viral invasion and is regarded as a crucial target for antiviral treatment [68, 69] (Fig. 1). In addition, the nucleocapsid (N), envelope (E), and membrane (M) proteins are all involved in viral production and combine with host cell organelles to cause various dysregulation of physiological processes [70, 71]. ACE2 is a significant receptor for SARS-CoV-2 entering host cells [72]. After binding to ACE2 via the S1 unit, SARS-CoV-2 can initiate membrane fusion depending on a furin-like cleavage site on the S1/S2 and S2 units [73]. The S2 unit is cleaved by the endosomal proteases cathepsin B and L (CatB/L) [74], or the transmembrane protease serine 2 (TMPRSS2) [75], to form a fusion pore, which allows the viral genome to enter cells [76]. The replication and transcription complex discontinuously processes the viral RNA, mainly formed by nsp12 cooperating with nsp7 and nsp8 [77]. Viral transcription, replication, and translation depend on host cell organelles, including the endoplasmic reticulum and Golgi [78]. It is worth noting that the S protein of Omicron has a higher ACE2 binding affinity than the S protein of other variants, which might explain the higher infection of Omicron [79]. In addition, since different receptors are highly expressed on different types of cells, it is important to consider the impact of additional receptors, such as neuropilin-1, in bringing about pathological changes.

Fig. 1.

The structure of SARS-CoV-2. SARS-CoV-2 consists of 4 structural proteins (S, M, E, and N) and 16 non-structural proteins (nsp1−16). After the S1 component binds to ACE2, the S1/S2 cleavage primes the fusion and creates extra cell surface receptors, like NRP1. Then, SARS-CoV-2 starts entry by CatB/L and TMPRSS2. The viral RNA is released after the entry and translated into corresponding viral structures. The open reading frame 1a (ORF1a) and ORF1b of RNA are translated into polyprotein 1a (pp1a) and pp1ab, further being translated into nsp1−11 and nsp12−16. Host cell organelles, such as the Golgi, are involved in virus replication. SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; ACE2: angiotensin-converting enzyme 2; NRP-1: neuropilin-1; TMPRSS2: transmembrane protease serine 2.

As SARS-CoV-2 has been shown to cause damage and dysregulation in other systems [80], its detection in the brain by polymerase chain reaction [81] and immunohistochemistry [82] suggests that it may also harm brain cells and tissues. Typically, the virus causes damage through two mechanisms: (1) replication in cells to produce daughter viruses and breaking the cell to release more viruses to invade other cells [83]; (2) the body’s response against the virus inevitably results in cell destruction. Thus, SARS-CoV-2 might also enter the brain and directly or indirectly damage brain cells. In direct damage, while the daughter virus is released by secretory vesicles and causes light damage to cell structure, interference by viral protein in the cell cycle can result in severe cell damage and death [84]. The nonstructural proteins (nsps) of SARS-CoV-2 disturb host DNA replication, protein synthesis, and transport [85], leading to some pathological brain changes. Besides, the virus can directly kill cells by inducing apoptosis, necroptosis, and autophagy in infected cells [86].

Possible Brain Entry Mechanisms of SARS-CoV-2

Via the BBB

The BBB typically serves as a barrier and a transporter. It transports ions, macromolecules, nutrients, and toxins into or out of the brain [87]. The BBB is mostly composed of vascular endothelial cells, pericytes, and astrocytes. The tight junctions (Tjs) and adhesion junctions between endothelial cells act as significant parts of the barrier [88]. Pericytes, embedded in the basement membrane of microvessels, regulate BBB formation and permeability and serve in CNS immune surveillance, such as the leukocyte migration across endothelial cells [89]. Astrocytes exhibit a strong link with BBB formation and dominantly enhance the frequency, length, and complexity of Tjs [90, 91].

As remarked above, ACE2 is the main receptor of SARS-CoV-2 and has been detected in several tissues, especially in arterial and venous endothelial cells [92]. In the human brain, the substantial nigra, paraventricular nuclei of the thalamus, raphe nuclei, tuberomammillary nucleus, central glial substance (an area of gray matter surrounding the central canal), and choroid plexus (ChP) of the lateral ventricle may have high ACE2 expression [93]. SARS-CoV-2 might infect brain microvascular endothelial cells through ACE2 and replicate in them [94]. However, entry through endothelial cells may be limited, because numerous studies have not yet demonstrated that infection and replication can occur there effectively. Besides, the basement membrane disruption of the BBB induced by SARS-CoV-2 through matrix metalloproteinase-9 is considered a significant factor for virus entry [95]. Indeed, BBB disruption and leakage have also been reported in COVID-19 patients with neurological manifestations [96].

The SRAS-CoV-2 may also use host cells to convey traffic across the BBB [97]. The virus is believed to preferentially invade lipid-secreting cells and use lipid metabolism for replication and spread [98]. A study has also shown replication of SRAS-CoV-2 in infected monocytes and macrophages [99]. Since the immune cells can enter the brain through the BBB and the ChP, SARS-CoV-2 may get a ride and get out after brain entry [100, 101]. However, it is not yet known whether viral replication in monocytes produces infectious viruses [102]. Further research is needed to investigate this mechanism

Via the CSF

As some cases have reported the presence of SARS-CoV-2 in cerebrospinal fluid (CSF), it is worth discussing the possibility of the CSF route [103]. The blood-cerebrospinal fluid barrier (BCSFB) is one of the selectively permeable barriers which regulates the transportation of substances between the blood and CSF. The BCSFB is formed by epithelial cells of the ChP, which separate the fenestrated capillaries from the CSF [104] (Fig. 2A and B). Similar to the BBB, The Tjs between ChP endothelial cells function as the barrier [105]. The ChP also secretes pro-inflammatory cytokines and provides space for transporting immune cells into the stroma [106]. ACE2 and its co-receptors TMPRSS2 and TMPRSS4 are highly expressed in the ChP, through which SARS-CoV-2 destroys the structure and function of the BCSFB in organoids [107, 108]. The circumventricular organs (CVOs) are located in the third and fourth ventricles and have continually fenestrated and highly permeable vessels. ACE2 has been detected at a high level in CVOs, which provide a facility for virus entry [109, 110]. However, due to the limited detection of SARS-CoV-2 in CSF, the efficiency of virus entry through this route must be further studied.

Fig. 2.

The CSF and retrograde nerve transmission pathways for virus entry. A, B The CSF pathway. SARS-CoV-2 traverses the permeable vessels of the choroid plexus (ChP) to reach the stroma. In the stroma, it binds to ACE2 and TMPRSS2/4 to enter endothelial cells and then be released into the CSF. C The retrograde nerve transmission pathway. The virus invades the olfactory sensory nerves (OSNs), moves retrogradely along nerves, and finally enters the neurons of the CNS. Besides, the virus can invade nervous terminal neurons that contact Bowman’s gland through cathepsin B/L (CatB/L). Tj, tight junction; ACE2, angiotensin-converting enzyme 2; TMPRSS2, transmembrane protease serine 2; OB, olfactory bulb.

Via Retrograde Nerve Transmission

Olfactory dysfunction has been frequently reported in COVID-19 patients [111] and may be correlated with the invasion of olfactory cells by viruses (leading to the downregulation of odor detection pathways) [112]. Olfactory mucosa is in contact with droplets by ciliated cells and perceives them through the olfactory sensory nerves (OSNs) in the basal cells, which are supported and nourished by sustentacular cells. Signals are then transferred to the olfactory bulb (OB) where they reach the mitral cells. The virus might invade the peripheral nerves, move retrogradely along them, and finally enter the CNS [113]. Given that many viruses enter the brain in this way, it might also be a possible route for SARS-CoV-2 to invade the brain [114] (Fig. 2C). Meinhardt et al. analyzed regional mapping of the consecutive olfactory nervous tracts and defined CNS regions in 33 individuals, suggesting that neuroinvasion can occur by transmucosal entry via regional nervous structures [115]. Besides, the invasion of OSNs by SARS-CoV and SARS-CoV-2 has also been revealed in hamsters [116]. However, many other studies conversely showed a low possibility of the OB route in humans. Based on 88 post-mortem cases of COVID-19 patients, Khan et al. found that SARS-CoV-2 infects ciliated cells, sustentacular cells, and even leptomeningeal layers surrounding the OB, while the OSNs and OB are uninfected [117]. Another post-mortem research also obtained the same result and suggested that inflammation might cause axon and vascular injury [118]. Butowt et al. pointed out that a lack of quantitative analysis and false positives might explain the contradictory reports on OSN infection [119]. In addition to the OSNs, Bowman's gland, a branching tubular gland in the olfactory mucosa, has been found to show both CatB/L and furin expression [120]. Thus, the nerve terminals of neurons might receive SARS-CoV-2 from the infected Bowman's gland. Overall, retrograde nerve transmission at least is a theoretically possible means of SARS-CoV-2 invasion but needs further determination. Besides, retrograde nerve transmission is also being considered in the infection of the eye, intestine, and lung through the vagus nerve [121] or optic nerve [122].

Other Mechanisms for Brain Pathology in COVID-19

Apart from the direct damage caused by the cellular invasion, several pathological conditions, such as an aberrant IFN response, cytokine storm, lymphopenia, and hypercoagulation in the brain, may result in more severe and widespread damage to the brain. In this section, we elucidate the periphery-related potential mechanisms of central pathological conditions (Fig. 3).

Fig. 3.

Pathological conditions in the brain. SARS-CoV-2 may cause several pathological conditions, including an aberrant IFN response, cytokine storm, lymphopenia, and hypercoagulation, resulting in pathological brain changes. NETs, neutrophil extracellular traps.

Aberrant IFN Response

The innate immune system plays a significant role in defending against infection and determining the disease severity [123]. Dysregulation of type I and II IFN is the main cause of the insufficient innate immune response. In the early stages of infection, a large amount of type I IFN may be present in the patient’s body to fight the virus, and the ChP is the most vulnerable area to infection in the brain. A study by Suzzi et al. has demonstrated that the increased IFN response may disrupt the ChP and be involved in the process of brain damage [124]. After a peak of type I IFN in the early stage of infection, a delayed aberrant IFN response has been reported in most severe cases [125]. For example, in the later period of COVID-19, a decrease of IFN occurs in the CSF of severe patients with neurological manifestations, and this may be related to the deficient innate immune response [126]. SARS-CoV-2 interferes the IFN production and activation in two ways: (1) the nsp1 of SARS-CoV-2 inhibits the gene expression and translation of IFN, and (2) pattern-recognition receptor (PRR)-mediated signaling pathways are suppressed to downregulate the IFN signaling. PRRs, including membrane-bound C-type lectin receptors, NOD-like receptors (NLRs), retinoic acid-inducible gene I (RIG-I)-like receptors, and Toll-like receptors (TLRs), are commonly expressed on sensory neurons, astrocytes, and microglia [127, 128]. SARS-CoV-2 RNA and M proteins can bind to RIG-I and melanoma differentiation-associated gene 5, blocking the activation of interferon regulatory factor 3 and the type I IFN signaling [129]. In addition, it has been demonstrated that several SARS-CoV-2 components, including nsp6, nsp13, and open reading frame 3a, inhibit the type I IFN response in vitro [130]. As the balance of the innate immune response is closely related to the disease severity of COVID-19 patients with neurological manifestations, the potential strategy to rectify the IFN response is worth discussing.

Cytokine Storm

The cytokine storm is a dangerous sharp increase of cytokines in body fluid that is also a concern in COVID-19 patients, especially in severe cases. As inflammation has been considered to be involved in several CNS diseases such as AD and PD, the elevated cytokines induced by SARS-CoV-2, including IL-6, TNF-α, IL-1, and IL-10 [131], might also be related to the pathological brain changes in COVID-19. It is worth mentioning that the increase of cytokines not only occurs in the acute phase but also may persist in patients for 3 months after recovery from COVID-19. Low-grade chronic inflammation may be associated with brain injury and vascular injury-related stroke in patients [132].

The generation of inflammation in the brain may be closely relevant to the brain barriers. SRAS-CoV-2 can infect components of barriers such as endothelial cells and astrocytes to process pro-inflammatory cytokines [133] and influence BBB permeability [134]. The neurofilament light chain protein and glial fibrillary acidic protein are at high levels in both the plasma serum and CSF of COVID-19 patients, indicating that astrocytic and neuronal injury indeed occurs in these patients [135]. Notably, C-C motif chemokine ligand 11, which can specifically cause hippocampal microglial reactivity and impaired neurogenesis, has been found to be elevated in CSF only in COVID-19 patients with cognitive syndrome [136]. In addition to elevated CSF cytokines [137], the choroid-to-cortex network across inflammatory pathways also increases in COVID-19 patients. This indicates that the inflammatory signals are sent from the choroid plexus into the brain more effectively to activate the glia. Microglia, the innate immune cells in the CNS, respond to the virus and form clusters with infiltrating T cells, which are associated with the brain and perivascular inflammation [138]. Elevated complements like C1q and C3, combined with microglia, are linked to the synaptic loss and toxicity of soluble β-amyloid (Aβ) oligomers [139]. Moreover, the mast cells, as innate immune cells participating in the adaptive immune response, can be activated by SARS-CoV-2 and release pro-inflammatory cytokines, including IL-1β, C-C motif chemokine ligand 2, IL-6, granulocyte-macrophage colony-stimulating factor, and TNF-α, which makes them significant components in neuroinflammation [140, 141].

SARS-CoV-2 may bind to receptors on host cells, including ACE2 and PRRs, to promote inflammation. ACE2 plays a key part in the renin-angiotensin system (RAS) [142]. As SARS-CoV-2 interacts with ACE2 and influences its catalytic activity, it can further regulate the RAS and contribute to the cytokine storm [143]. Besides, the reduction of ACE2 leads to an increase of serum Ang II, which activates the production of reactive oxygen species (ROS) and nuclear factor-kappa B pathways. These activations accordingly promote the expression of pro-inflammatory cytokines and inactive NOD-like receptor family pyrin domain containing 3 (NLRP3) [144, 145]. Excessive ROS can trigger apoptosis through the mitochondria, which causes morphological and functional changes in the host cell [146]. ROS also leads to the overactivation of the immune response and other pathological reactions [147]. NLRP3 inflammasomes, activated by ROS production and mitochondrial dysfunction, show a high correlation with apoptosis, dysregulation of tau protein phosphorylation, and neurofibrillary tangles [148]. Uncontrolled activation of NLRP3 has also been found in endothelial progenitor cells of COVID-19 patients [149, 150].

As discussed above, PRRs, including TLRs, NLRs, and RIG-I, participate in the signaling pathways of IFN. PRRs in the CNS, especially TLRs, are also involved in the production and release of several cytokines including IL-1, IL-6, and TNF-α [151]. The S protein of SARS-CoV-2 can bind to TLR2 and TLR4 and activate the myeloid differentiation factor 88 signaling pathway to promote the cytokine storm [152]. Besides, TLR4-mediated inflammatory cytokines are reported to be upregulated in peripheral blood mononuclear cells and CSF [153].

Lymphopenia

Lymphopenia has been found in severe COVID-19 patients, and several factors may account for this phenomenon [154, 155]. Firstly, ACE2 has remarkable expression in lymphocyte cells, through which the SARS-CoV-2 can directly destroy them. SRAS-CoV-2 RNA has also been detected in macrophages, neutrophils, B cells, T cells, and natural killer cells [156]. Secondly, the elevated cytokines, especially TNF and IFNγ, can contribute to apoptosis and pyroptosis, which leads to the death of lymphocytes and atrophy of the spleen [157, 158]. The systemic reduction of lymphocytes also results in lymphopenia in the brain [60], which directly decreases the body’s defense against viruses and leads to pathological changes. Several studies have suggested that changes in immune cells might induce neural and neuroendocrine dysregulation, such as anxiety [159], depression [160], and neurodegenerative diseases [161]. Meanwhile, these psychiatric sequelae have been reported in COVID-19 patients with an aberrant immune system and include significant post-traumatic stress disorder [162]. In addition, lymphopenia is also considered a hallmark of poor prognosis in COVID-19 patients, further highlighting the importance of lymphopenia [163, 164].

Hypercoagulation

Hypercoagulation-related neurological manifestations, such as ischemic stroke, have been reported in COVID-19 patients [165]. In addition, risk factors of coagulation are also considerably elevated in COVID-19 patients, including D-dimer, von Willebrand Factor (vWF), vWF antigen, and FVIII [1, 166]. Both white and red thrombi have been observed in microvascular, macrovascular, and venous systems [167]. Affected individuals may experience neuropsychiatric diseases, neurocognitive (dementia-like) syndrome, and altered mental status as a result of the thrombi in the cerebrovascular, system; they obstruct the bloodstream and kill endothelial cells [21]. The term "coagulation cascade" refers to the sequence of events that leads to the formation of clots during the coagulation process.

The coagulation process includes the extrinsic, intrinsic, and complement pathways. (1) The extrinsic pathway starts with tissue factor, which is expressed on neutrophils and monocytes and can be activated by cytokines and neutrophil extracellular traps (NETs) [168]. NETs consist of cytosolic and granule proteins and mitochondrial DNA. Triggered by ROS against infection, NETs regulate the activation of the extrinsic pathway [169]. An elevated number of neutrophils and myeloperoxidase /DNA complexes, a well-defined marker of NETosis, indicates a high incidence of NET formation in COVID-19 patients [170]. (2) The intrinsic pathway begins with factor 12 and ultimately participates in fibrin formation. The intrinsic pathway is triggered by an endothelial injury, which can be caused by infection with SRAS-CoV-2. Factor 8 and vWF, a carrier of factor 8, and fibrinogen are highly expressed in COVID-19 patients [171]. In addition, patients with COVID-19 have remarkably elevated levels of the plasminogen activator inhibitor-1 (PAI-1), which downregulates the plasminogen activation to plasmin by inhibiting tissue-type plasminogen activator (tPA). Contradictory opinions have been generated by the fact that some other COVID-19 patients have elevated tPA. That is, the PAI-1 could counteract the local tPA effect to create a net prothrombotic hypofibrinolytic state, while the fibrinolysis led by tPA is predominant [172, 173]. Furthermore, despite the decrease or maintenance of platelet numbers in COVID-19 patients, the plasma thrombopoietin levels, platelet surface P-selectin expression (a marker of platelet activation), and circulating platelet-leukocyte aggregations are prominently high. These results may partly apply to the hypercoagulation state in COVID-19 patients and also suggest that the JAK3-MAPK pathway is involved in the process [174, 175]. The platelet-to-lymphocyte ratio level is significantly higher in severe patients than in non-severe patients with COVID-19 and shows a correlation with the cytokine storm [176]. The D-dimer, a protein produced when clots dissolve, is elevated in COVID-19 patients, which also suggests a serious hypercoagulation syndrome [177]. (3) The complement pathway is a cascade of events that leads to hemostasis. It has been found that the N protein of SARS-CoV-2 can cause abnormal complement activation [178]. Indeed, complements such as C5, C6, C5a, and C8 also increase in severe COVID-19 patients [179]. The complement dysregulation might impel thrombosis and endothelial injury, ultimately leading to brain damage. In summary, the “coagulation cascade” might be started by SARS-CoV-2 and result in a pathological hypercoagulation state, which induces endothelial injury and subsequently causes pathological brain changes.

Other Potential Mechanisms

Several studies have detected anti-neuronal and anti-glial autoantibodies in the serum or CSF of COVID-19 patients with neurological symptoms, suggesting that autoantibodies may be involved in the brain injury of COVID-19 [180, 181]. Autoantibodies may directly damage neurons and can also lead to immune abnormalities. In addition, Franke et al. found that autoantibodies have undetermined antigenic epitopes, which may be related to the molecular mimicry of the SARS-CoV-2 virus [182].

Hypoxia due to pulmonary fibrosis can cause multi-organ damage, which is more prominent in patients with severe disease [183]. Hypoxia in COVID-19 may be correlated with the expression of ACE2 and TMPRSS2 as well as Aβ deposits in the neocortex [184, 185]. Zilberman-Itskovich et al. found a lower incidence of neurological manifestations in COVID-19 patients subjected to hyperbaric oxygen therapy, suggesting that improving hypoxia may reduce neurological pathology by improving brain perfusion and neuroplasticity [186].

Conclusion

COVID-19 is still a problem that affects the entire world and interferes with people's daily lives. Approximately 30% of COVID-19 patients experience new neurological manifestations or exhibit pathological brain changes. However, the current treatments have hitherto been insufficient. In this review, we emphasize the need for clinical practice to consider patient features, such as pre-existing diseases, when treating COVID-19 patients with neurological symptoms. As for the mechanisms, in this review, we indicate that SARS-CoV-2 can infect host cells through ACE2 (accompanied by TMPRSS2 or CatB/L) and may further enter the brain through the BBB, CSF, and retrograde nerve transmission. SARS-CoV-2 may cause cell and tissue damage once it has entered the brain by preventing replication and promoting apoptosis. Apart from these direct effects, several systemic or peripheral pathological conditions, including an aberrant IFN response, cytokine storm, and hypercoagulation, may also contribute to brain pathology. The aberrant IFN response can result in a delayed innate immune response, rendering the viral defense ineffective. The cytokine storm produces excessive tissue damage and cell death, even in the brain, despite its original function as a defense mechanism against the virus. Besides, severe COVID-19 patients exhibit remarkable lymphopenia, indicating a high risk of neurological pathology. Hypercoagulation may be related to endothelial injuries, infarcts, and hemorrhages in the brain. Thus, in addition to host receptors (such as ACE2 and TMPRSS2) and virus structures (such as the S protein and nsps) as potential targets, we suggest that protecting the brain barrier, regulating immune responses, and ameliorating the hypercoagulation state via specific targets also potentially prevent or suggest treatment strategies for pathological brain changes in patients with COVID-19.

Conflict of interest

Zhong Chen is an Editorial Board member of Neuroscience Bulletin and a co-author of this article. To minimize bias, he was excluded from all editorial decision-making related to the acceptance of this article for publication.