The literature search was performed through Web of Science database in order to find relevant original articles or case series concerning COVID-19 disease. In order to focus on the most important papers the additional filter, “Hot paper”, was applied in the search engine [2]. The articles have been gathered in November 2020 and the results consisted majorly of the papers published online between January and August 2020. No additional restrictions narrowing area of search were put into the search engine. Finally, the results were sorted by the number of citations, starting from the highest cited one.

First 200 papers from the results list were briefly examined at the beginning. Reviews, systematic reviews, meta-analyses, recommendations and pure mathematical models were excluded. If the article presented worthful discovery about SARS-CoV-2 pandemic, the database was additionally searched by the original article keywords to check whether any other study may expand the topic. This approach has been found to be especially relevant when treatment plans or spread prevention methods were under consideration. This arises from the dynamic changes in drug administration policies and continuing studies on COVID-19 eradication. The data regarding morbidity and mortality were taken from the most recent WHO report at the day of this paper finalization.

The abstracts and full texts of the first 200 research papers were screened independently by W.M. and M.S. —articles were in-depth analysed to evaluate their usefulness in the subject of the review. Final choice was made after discussion and consensus. This led to rebuff of 59 papers (29.5%). At this stage additional 25 papers (17.73% of the remaining) were rejected, because their scope was already fulfilled by other, already included manuscript. We have focused on papers that presented facts important for medical professionals, also these including clinical data of the patients—they were used to calculate frequencies of certain comorbidities and clinical manifestations (29 papers) as well as laboratory markers deviation (12 papers). In the end 40 articles were rejected due to their detailed aspects that cannot be summarised without a significant lose to their value.

The collected data was split and grouped to the subjects presented in this review—pathophysiology, infectivity and detectability, clinical manifestation, diagnostic and medical treatment. Qualitative data were synthetically presented preserving consistency of pathological mechanisms and aberrations resulting from them. Quantitative data of existing comorbidities and clinical manifestations were processed to obtain averaged values for samples size. For the laboratory markers data, a weighted arithmetic means of median values presented in the papers were calculated.

The key symptoms seen during the first days of a SARS-CoV-2 infection are generally related to the respiratory system, which suggests its extended tissue tropism [3]. Animal studies confirmed that the virus is excreted from type I and II pneumocytes as well as ciliated respiratory system epithelial cells [4]. Using the transgenic-mice model with expressed human angiotensin-converting enzyme 2 (ACE2) receptors, Bao et al. [5] observed high affinity of the virus for them. Their number varies depending on the tissues—the predominant sites are the small intestine, heart and kidneys whilst lungs demonstrated a comparably lower ACE2 expression profile [6–9]. However, this does not explain such things as anosmia, which is a typical COVID-19 symptom. Aside from the fact that the respiratory tract is the most accessible transmission approach, recent studies suggest that ACE2 and transmembrane serine protease 2 (TMPRSS2) must work together in the viral uncoating mechanism—they are significantly co-expressed e.g., in the nasal cavity or type II pneumocytes [7, 8, 10]. To adhere to the host’s cell, the virus uses its receptor-binding domain allocated in the S1 subunit of the trimeric spike (S) glycoprotein, expressed on the surface of the viral envelope. Upon binding with ACE2, TMPRSS2 primes the S1-S2 junction, presenting another subunit (S2) responsible for the membranes’ fusion [3, 11].

The uncontrolled viral infection leads to macrophage and lymphocyte infiltration and accumulation in the alveolar interstitium [5, 12]. The endothelium of the damaged lungs releases procoagulant factors, e.g., von Willebrand factor and Factor VIII, and pathological fibrin clot formation takes places in the alveolar spaces. This process is further amplified due to the impairment of the fibrinolytic functions caused by plasminogen activator inhibitor-1 upregulation deriving from the interference between the NSP1 and ORF6 viral proteins and the signal transducer and activator of transcription (STAT1-STAT3) cascade [13, 14]. Fibrin clots formed in alveolar capillaries by the complement system were found to cause injuries of the interalveolar septum, and consequently, diffuse alveolar damages [14, 15]. Due to the hypoxic vasoconstriction (or even complete blockage of blood vessels) and activation of hypoxia-inducible factors, blood flow becomes drastically reduced, which explains the breathing problems that are common among the hospitalised patients, as well as hypoxia being a major cause of death [14, 16, 17].

The viral sepsis mechanism is multifactorial and depends on the cytokine storm, microcirculation dysfunctions and virus dissemination. Activated immune cells excrete cytokines and inflammation mediators, mainly IL-6; the increase of its levels in the plasma results in the cytokine storm syndrome. Upon reaching other organs through the haematogenous route, cytokines induce local inflammation. Such condition—if not remedied quickly enough—may evolve into a more critical systemic inflammatory response [12, 14, 17, 18]. It is worth noting that increased interferon type I (IFN-1) concentration observed during the infections seems to upregulate the ACE2 gene expression and enable easier transmission of the virus between host cells [8, 19]. Through the damage in bronchi, the virus gains access to vascular endothelial cells and then to the bloodstream where it resides [20].

A reverse sequence takes place when other organs are infected. For example, renal tissue damage is claimed to be an outcome of three different ways of action: 1) the previously–mentioned ACE2–TMPRSS2–dependant pathway and direct cytopathic effect; 2) by interaction with immune cells and the immunological effect mechanism (immune complex, cytotoxic effect); 3) indirectly by the pathological activity of the released cytokines [20, 21]. Furthermore, hypercoagulability is inseparably associated with blood clot formation manifested by lower limb deep vein thrombosis and pulmonary embolism [22, 23]. This happens even while therapeutic anticoagulant doses are administered [14].

One of the most specific and clinically relevant SARS-CoV-2 infection symptom is sudden anosmia and hyposmia (56.97% of infected patients [24]). Their development might be linked to the viral invasion of the nasal cavity, which disrupts the functioning of the olfactory epithelium and olfactory nerve. The olfactory epithelium and olfactory nerve also seem to be the starting points of the central nervous system (CNS) infection, which are different from the hematogenous route—the virus might enter the CNS through the retrograde neuron pathway via olfactory bulb [3, 24, 25]. However, further studies are required to explain this problem.

Since the virus exhibits immunosuppressive activity, it weakens hosts’ natural defence system [26]. The antibody–dependant enhancement (ADE) mechanism was observed in patients who had previously been exposed to non-SARS-CoV-2 coronaviruses. It relies on a quick but inappropriate immune response which leads to an increase of viral load. It may results in a sustained cytokine storm and inflammation which are manifested in the clinical course among the patients [27, 28]. For these reasons, we suppose that ADE might be involved in the more severe course of the reinfections. Concluding, all mechanisms presented may together contribute to the severity and lethality of the disease course.

To et al. [29] found that the viral load correlated positively with age and Zheng [30] determined that virus duration was longer in older male patients. The basic reproduction number—expressing the expected number of new cases generated by a single case—estimated for the Diamond Princess cruise ship passengers by Zhang [31] is 2.28. In our opinion, the statistics presented are reliable because samples were taken from a large and closed group (3,711 samples), which was not affected by other factors.

The results presented by Wölfel [3] indicate that viral load was mostly found in the sputum, making it an efficient aerosol or droplets transmission carrier, e.g. though coughing or sneezing. Recently, airborne and fomite–based transmissions also suggested as well [3, 32]. These reports indicate that special attention should be paid to tracheal intubation as it increases the risk of the exposure to viral loads suspended in the air, and consequently, superinfection incidents. Aside from the respiratory tract, samples of viral mRNA were also found in the serum (16 days since the first detection [30]) and stool (22 days [30]; 11 days [33]; average = 16.5 days), indicating the virus may replicate in the gastrointestinal (GI) tract.

We divided the disease course into three general phases based on clinical manifestation — 1) asymptomatic or presymptomatic; 2) symptomatic; 3) post-symptomatic.

Phase 1) begins when the virus enters the host and starts to replicate. This phase finishes upon the first symptoms or when the virus vanishes in the case of the asymptomatic patients. The virus incubation period, estimated based on a group of 262 patients located in Beijing, was determined to be about 1 week [34]. Nonetheless, the virus can still be transmitted even if reaching the peak viral load is delayed. He et al. found that over half of the infections occurred during the presymptomatic phase [35]. Since the Diamond Princess study tells us about 17.9% of the asymptomatic patients [36], isolating persons who potentially had contact with patients who have tested positive is justified.

Phase 2) starts after the first symptoms and lasts throughout the respiratory tract symptoms and/or fever.

Phase 3) occurs directly after phase 2) when acute symptoms subside. Patients in phase 3) can still manifest symptoms—not directly linked to viral replication—and excrete enough viral load to infect others [3, 29, 36]. Figure 1 shows the common SARS–CoV–2 infection symptoms that patients complained about, along with their frequency.

An interesting observation regarding the virus activity can be made based on the studies presented [17, 37, 38]. Among the patients included in the trials, second–generation hosts were less likely to die. This would suggest that the longer the virus is present in the population, the further its mortality lowers. It may be connected with the virus evolution process—with the loss of pathogenicity, it increases its transmissibility, and consequently, the number of infected hosts.

No differences were found between pregnant and non–pregnant patients; neither foetal malformations nor birth injuries were observed [39]. The disease course in children is likely to be similar to asymptomatic patients or be accompanied by cold/flu symptoms—fever, cough, shortness of breath [40]. While occasionally present, complications are rather uncommon.

As for now, it has been observed that post–symptomatic patients suffer from long–term complications due to SARS-CoV-2 derived lungs fibrosis, i.e., persistent fatigue and decreased respiratory capacity. Further observations are required to recognise other ones.

Table 1 shows the list of all diagnostic markers. A sufficiently quick diagnosis is vital for both the patient prognosis and eradicating the epidemic. Many valuable diagnostic tools can be used for this purpose. For example, in several studies, an increased D-dimer concentration (>1.0–2.0 μg/ml) —a blood clot degradation product—was an independent predictor of death due to the SARS-CoV-2 infection [47–49].

Similarly, white cells profiles should be monitored systematically. Severe lymphopenia is also linked to the higher mortality—patients with total T cell, CD8⁺ T cells and CD4⁺ T cell counts lower than 800/μL, 300/μL and 400/μL, respectively, were more likely to die. Additionally, such CD4⁺ and CD8⁺ cells often expressed programmed cell death protein 1, which indicated their fatigue [50].

Long et al. [51] estimated that 17–19 days elapsed until the positive virus–specific IgG had reached 100%, whereas 20–22 days are required to reach a positive virus-specific IgM at the rate of 94%. The authors distinguished three seroconversion types: synchronous seroconversion of IgG and IgM; IgM seroconversion before IgG; and IgM seroconversion after IgG. Based on the real-time polymerase chain reaction from a sputum, the viral load slowly decreases after seroconversion occurs. Nonetheless, “slowly” is the keyword here because viral RNA is still detectable at least one week from the symptom onset and sometimes even longer [3, 29, 49], though the median time to the first negative test from the respiratory tract was 9.5 days [33]. The overall seroconversion rate was 96.8% in a group of 63 patients [51].

The radiological evolution of COVID-19 pneumoniae is a suitable tool for tracking the disease’s progress. Computed tomography (CT) makes it possible to observe respiratory tract injuries, which are particularly relevant in the diagnosis of asymptomatic patients with negative serum–antibodies assay. An attention should be paid to ground–glass opacities and consolidations [52]. CT scans might also make it easier to diagnose paediatric patients. The typical findings among youngsters are unilateral or bilateral subpleural ground–glass opacities and consolidations with reverse echo [40, 53]. Yet, this procedure is not advocated in the case of paediatric patients due to the possible harmful effects of X–ray radiation.

Despite the fact that it has only been one year since the outbreak, the scientific goal of eradicating the virus has resulted in hundreds of publications of all types. As a result, the biggest constraint we are aware of is the difficulty of covering them all in this paper. Even as these lines are being written, a novel and scientifically important contribution may be reviewed. Nonetheless, owing to pharmaceutical companies' engagement in vaccine research, the prospects are promising, and we expect many amazing breakthroughs in the future.