Covid-19: what we know so far

13 min readMay 21, 2020

The quarantine is about to complete 3 months worldwide, and still, we have no effective drug, vaccine or antibody to fight it. After about 100 days of worldwide concern towards the virus (although the epidemic started in China more than 5 months ago), we only have unfolded the Pandora Box of SARS-CoV 2, which is its genome, but have not found one specific substance of bioagent that can brake it effectively and safely.

Firstly, chloroquine, an antiparasite drug, was considered the Holy Grail of novel coronavirus, along with herbs and some practices of the Tradicional Chinese Medicine, since the epidemic started in Hubei, China. After several weeks of extensive research over chloroquine, scientists found only a mild, controversial action against the virus, with severe adverse reactions (such as retinopathy and hepatic and renal toxicity).

Other drugs — like oseltamivir, lopinavir, favipiravir, dexamethasone and even ivermectine, another antiparasite drug — were candidates to treat covid-19, but none of them are promising enough, even only to treat the virus, since no drug will stop the coronavirus epidemic.

To understand why only a vaccine — and no molecule, new or old, even if it is an artificial antibody targeted against the viral proteins — is going to finish the pandemic, first, we need to understand the virus itself and the course of an epidemic.

Coronavirus-related severe acute respiratory stress syndrome — SARS-CoV 2

Etiology and virology

The coronavirus-related disease of 2019 (or covid-19) is an infectocontagious disease, caused by a new, wild viral agent, the novel coronavirus, which allegedly emerged from a fishmarket in Wuhan, China, after humans ate bats and other animals that serve as this virus natural reservoir. By the process of adaptation, the virus migrated from another species to the human, becoming a zoonosis.

The novel coronavirus is a positive-sense, single-stranded RNA (+ssRNA), enveloped virus, which explains some of its virulence. Like other coronaviruses, it is composed by 4 proteins, the S, E, M and N proteins. The S (spike)protein, also called haemaglutinin, is the structure that makes possible for the virus to bind to the host cells; the E (envelope) protein is responsible for, besides forming the envelope itself, targeting the to-be-infected cell; M (membrane) protein plays a role at defining the virus format, and coordinates structural protein activity, by interating with all other viral structural proteins; and N (nucleocapsid) protein, besides forming the nucleocapsid itself, regulates some of its genectic activity, orchestrating the virus life cycle. It is hypothesized its proteins react with angiotensin-converting enzyme 2 (ACE-2) receptor, present in lungs, heart, kidneys and blood vessels, explaining the virus pathology. It is 50nm long, thousand times smaller than an animal cell.

It has 7 non-structural proteins, each with a different role in viral infectivity, synthesis and survival. ORF1ab, the largest, produces a series of endonucleases, exoribonucleases RNApolymerases and other molecular instruments to guarantee virus replication; ORF3a, which activates the inflammosome and drives host-cell to apoptosis; ORF6, a virulence fator, probably mediates immune avoidance of the virus; ORF8, a candidate for the interespecies mechanism of transmission; ORF10, which is hypothetical (it is present on the genome, but it is not expressed). ORF7a is of obscure function, but, in experimental models, it binds to heme porphyrin.

Genomic organisation of SARS-CoV 2. The ruler shows where in its genome (pair of bases) its proteins are synthesized. Proteins S, M and E are structural; ORF1a, 1b, 3a, 6, 7a, 8 and 10 are non-structural.

Pathophysiology

After entering the body via transmucosa, which usually happens via upper airways or ocular mucosa, but can potentially occur via other mucosas, such as rectal, the virus spreads hematogenically and, once in the bloodstream, it can reach any part of the body, including brains and male genital tract.

The most accepted theory of novel coronavirus cell entry is via angiotensin-converting enzyme 2 receptor, the ACE2 receptor. SARS-CoV 1 uses receptor binding domain (RBD) to enter cells, with which it has high affinity. SARS-CoV 2, differently, uses its spike protein (S), binding more intensely to ACE2 receptors, whereas paradoxically it can either enable receptor-binding or make it down, explaining the rich clinical presentation variations of the disease. Nonetheless, the supressed RBD can evade immune response, leading to undercovered infection and insufficient leukocyte mobilisation.

Summary of cell entry mechanisms of SARS-CoV-2. Available: https://tinyurl.com/ycelhw2u

ACE2 is a type I transmembrane metallocarboxypeptidase homologous to ACE1, a very understood enzyme of the renin-angiotensin system. It cleaves both angiotensin I and II, and it is better expressed through the cardiovascular apparel (i.e. heart and vasculature) and in the urogenital tract. It lowers blood pressure, by catalysing the angiotensin-converting enzyme, antagonising ACE 1. The distributive shock sometimes seen in covid-19+ patients might be due its superexpression and other mechanisms, expained in the next section.

Gene expression pattern of the ACE2 gene. Note it has a higher expression in testis, testis germ cell, testis interstitial cells, leydig cells and seminiferous tubule. It is also expressed on heart, lungs, vessels, pancreas, intestines, brain and promielocytes, in a way coronavirus could, hypothetically, trigger oncohaematological diseases. Available: https://tinyurl.com/yaphbeg3

Hence novel coronavirus uses ACE2 receptors to bond, some of its manifestations can be explained according to this theory. Upper respiratory tract symptoms, pneumonia, heart failure, distributive shock, pancreatitis, diarrhea, encephalopathy and infertility were already reported in literature since november outbreak.

In the respiratory tract, mainly lungs, covid-19 causes direct alveolar damage, promoting its necrosis; in the interstitium, there is diffuse infiltration and a degree of microangiopathy of unknown cause, resulting in the typical radiological findings at CT scan “ground glass” and hyaline membrane disease, conducting to respiratory failure.

Heart showed various degrees of focal edema, interstitial fibrosis, and myocardial hypertrophy, along with atrophy of myocites. Those findings are likely worse in cardiovascular-related disease patients.

The cardinal change in the hematological system is lymphopenia. There is also hypercoagulopathy associated, with elevation of D-dimer. PT and PTTa prolongation has also been reported, and disseminated intravascular coagulation is not uncommon. In macrophages, ORF8b strongly activates NLRP3 inflammasome, which can induce to cell death. Hyperactivation of lysossomal machinery leads to inflammatory stress and disrupts autophagy/apoptotic homeostasis.

In the urogenital tract, there is testis germ cell apoptosis, death of leydig cells and acute tubular necrosis in various degrees. There is evidence of diffuse tubular damage and hyalinization of arterioles and spread vacuoles. It may be prerenal or renal acute kidney injury depending on the patient clinical state.

Acute kidney injury in COVID-19. Self-explanatory. Available: https://tinyurl.com/ybatw2cx

There is edema and cell death in the brain. Glial cells and neurons have been noticed involved in the infection, as well in the cerebrospinal fluid. Those changed are still obscure and poorly understand, as a major group in University of Campinas, Brazil, is researching it.

There was no revelevant studies about changes in the feminine genital tract so far.

SARS-CoV 1 anatomo-histological features. Self-explanative table. Available: https://tinyurl.com/t8e5bfc

The role of the cytokine storm

After activation of leukocytes via INF-gamma and TLR, the main release of IL-6 along with other immunokines such as IL-10 and TNF-alpha triggers the cytokine release syndrome (CRS) in covid-19.

The infection of monocytes, macrophages, and dendritic cells results in synthesis of IL-6, the main pyrogenic cytokine (responsible for fever) and other inflammatory cytokines. IL-6, consequentially, has three main pathways of releasing cytokines: cis, trans and via liver.

The cis pathway in lymphocyte leads to pro-inflammatory differentiation of Th17 cells via JAK-STAT and general activation of innate response. There is also recruitment of TCD8 and B lymphocytes.

The trans pathway in endothelial cells leads to augmentation of VEGF, which enhances vascular permeability; and MCP-1, IL-8 and 6, which recruits monocytes and neutrophils.

The liver pathway activates complement, acute phase proteins (C-reactive protein, hepcidin and fibrinogen) and lowers albumin.

Altogether, those inflammatory alterations generate CRS and all of its consequences: low sp02, liver failure, diminshed heart output, azotemia, hyperbilirubinemia and, ultimately, shock and death. This might be the main cause of organic deterioration, lung damage and poor prognosis in coronavirus infection.

SARS-CoV 2 cytokine release pathaway and the proposed target of siltuximab. Self-explanatory. Available: https://tinyurl.com/ybc68p2w

Coagulopathy

There is a strong hypothesis on Covid-19 being an haematological disease with systemic repercussions and tissue-specific pathological changes, as shown above.

Still poorly understood, the thrombosis mechanism in covid-19+ patients might be due to changes in the coagulation homeostasis and the production of antiphospholipid antibodies, as already reported. As similar in antiphospholipid antibody syndrome, AA+ patients may have lowered protein C and S action and increased clevage from prothrombin to thrombin. This also suggests an autoimmune, crossed reaction between viral and host proteins.

The sensitive elevation of D-dimer in the early stage of the disease, the consumption of fibrinogen and the fatal evolution to DIC and shock sustain this hypothesis. No strong association between low platelets and covid-19 has been reported, and no major bleeding episodes, even in patients with DIC, is seen in the latest literature. Micro and macrovascular damage has been noticed as well, with the inflammatory cause being the best candidate to its etiology.

Autopsies, however, show a high incidence of venous thrombosis and venous thromboembolic episodes in deceased patients. Massive pulmonary embolism was the cause of death in one third of the cases in a certain cohort. The mechanism is still to be found, though a combination of endotelial damage, free radicals, cytokines, vasospasm, excessive coagulant factors in blood and direct virus deleterious activity could contribute together to coagulopathy in new coronavirus infection.

Signs and Symptoms

According to Guan et al, 88.7% of the patients presentes fever and 67.8% had cough, making it the two main clinical features of covid-19. Also, coronavirus infection can present sputum (33%), dyspnoea (18%, mainly on advanced disease), myalgia (14%) and headache (13%). Gastrointestintal symptons are relatively uncommon. Sore throat is seen in around 12% of the patients.

Although rare, symptomatic infection on infants presents cough as the most common symptom (48%), followed by pharyngeal erythema (46.2%) and fever (41.5%).

Manifestations of COVID-19 and other viral and bacterial pneumonia. Extracted from Saxena K. COVID-19 handbook, p. 67.

The infection in pregnant women is treated equally as non-pregnant woman. In utero transmission was reported, but this only happened casuistically. It is uncertain if transmission occurs via mother’s milk, but aerosol and droplet precautions are necesary when lactating.

Most common complications are ARDS (3,4%), septic shock (1.1%), AKI (0.5%) and coagulopathy (0.1%). More than 90% of the patients present clinical pneumonia.

The only two proven comorbities related to covid-19 are hypertension and cardiovascular disease. Although diabetes, COPD and cancer may fragilise the covid-19 patient, those did not have sufficient level of evidence to relate to a poorer prognosis.

Main laboratory finding is low albumin (75.8%). High C-RP and LDH are found in around 58% of the patients. Lymphopenia is ascertained in a little less than half patients. Abnormal liver enzymes affect a third of patients. Less common findings (<10%) include high bilirubin and creatinine.

Radiologically, the main finding is bilateral pulmonary compromise (>72% of patients). Ground-glass opacity on chest X-ray is accountable for 68.5% of findings.

Diagnosis

Some guidelines proposed three criteria to diagnose covid-19, which included clinical features of cough and fever, positive history of contact with known covid-19+ patients or recent trip to areas with high prevalence of the disease, and ground-glass findings at thorax CT-scan.

Albeit the positive predictive value of that routine is high, its specificity is pretty low, so as the virus spread and our knowledge of it started to increase, labs have started nasopharingeal swab culture to confirm the diagnosis, but with a poor sensivity and somewhat high specificity. The culture is also too slow to be time-effective and save a life.

After the unveiling of the viral RNA, genetic tests became a very precise diagnosing method, but it is not available in all medical services. As of today, the most used test is enzyme-linked immunosorbent assay (ELISA) IgG and IgM for novel coronavirus, with a reliability of over 90%. PCR is required only in cases of indefinition (IgG+ and IgM- symptomatic individuals or such).

Viral culture with direct cytopathic efect on cells is the gold-standard still.

Treatment

There is no randomised, placebo-controlled, test-effective, clinical-tried drug for novel coronavirus so far. To give the theoretical counterproof on why chloroquine, ivermectin, azithromicin or such known drugs are useless against SARS-CoV 2 infection is not the escope of this article. Nevertheless, we will adopt Siddiqi and Mehra proposed therapeutical strategy, along with well-consolidated advanced life support on acute respiratory distress syndrome, distrbutive/cardiogenic shock, acute kidney injury and disseminated intravascular coagulation.

Classification of COVID-19 disease states and potential therapeutic targets. The figure illustrates 3 escalating phases of COVID-19 disease progression, with associated signs, symptoms, and potential phase-specific therapies. Available: https://tinyurl.com/y7f52j4c

Stage I: mild to moderate disease
Disease limits itself to this phase in most patients (~80%). When symptomatic, coronavirus infection may be presented with fever, cough and general malaise. Patients require only painkillers, if pain, and social isolation with in-house isolation from relatives as well. World Health Organisation suggests home-care for those patients, in order not to overwhelm the health system and prevent the positive patient from spreading the infection in intra or extra hospitalar environment.

Stage II: “pulmonary” phase
The remaining 20% of patients will evolve to this phase, of which 8% become critical. In this stage, there is frank pneumonia along hypoxia. Some patients will require mechanical ventilation (i.e. PaO2/FiO2 < 300 mmHg) and intensive care.

Some antiviral drugs, as remdesivir, favipiravir and kaletra may be introduced, if available. Convalescent plasma transfusion is, so far, the only undoubted therapy for covid-19. When available, a cautious, cost-benefit analysis for every patient should be done, evaluating the scarcity of this resource and the chances of survival.

According to brazilian societies of pneumology, infectology and intensive medicine, there is a recommendation of anticoagulation therapy with heparin in order to prevent disseminated cardiovascular events at the third and last phase, which may be initiated in the second stage yet.

Stage III: inflammatory/shock phase
Added to the previous therapeutics, patients at the last phase of coronavirus infection may require advanced, multiorgan life support in ICU environment. Patients present prerenal AKI, probably due to cardiac failure caused by pulmonary hypertension and hypovolemia; or direct kidney damage due to nephrotoxins or cytopathic viral activity. Indications for dialysis include oliguria with refractory hypervolemia, severe acidosis and azothemia.
Follow-up with a nephrologist after the AKI diagnosis is recommended.

The use of corticosteroids may be considered when synergic with cytokine inhibitors such as tocilizumab or anakinra to get around the cytokine storm.

Multiorgan disfunctions, such as myocarditis, secondary hemophagocytic lymphohistiocytosis, AKI, hepatic failure, cardiorenal syndrome, pulmonary hypertension and immune disorders impoverish the prognosis of these patients. The physician must evaluate the opening of palliative care protocol of the referred institution when necessary.

Prognosis

Some patients presented end-stage kidney disease and male infertility after recovery. Most sequels to coronavirus infection cannot be appointed to be o direct responsibility of disease or mere aggravation of chronic diseases. Apparently there is no cronification of the infection. Endocrinopathies, cardiopathies and other organ-related syndromes might be seen in recovered patients due to necroscopy studies that showed damage to such tissues. Late complications are still to be discovered.

Epidemiology

As of today, May 20, 2020, covid-19 reached 5 million cases and 330,000 deaths, with a 6.6% lethality worldwide. In China, the lethality was of 3.5%, probably due to a younger population, whereas in Italy were of 11.2%, due to an older population.

Transmission routes include droplet and airborne vias. Virus can also enter by direct contact with nasal, oropharingeal and conjunctival mucosa, mainly by contact. Therefore, three-level precaution (aerosol, droplet and contact) is required.

Novel coronavirus transmission rate (R0) relies on the population it is infecting, but it is average 2.7. Since it is >1, the infection may persist among communities and eventually become endemic in the lack of a vaccine. Death toll is directly proportional to age, even though the biggest number of infected persons are young adults. Death toll is also higher on those above 60 (~45% of lethality rate and 80% of deaths). Healthcare professionals are commonly infected in their workplace.

Supercommunicators can infect up to 100 people. Asymptomatic individuals may be responsible to most transmissions.

Since the pandemic is still at large, those numbers may change and increase for several months yet.

Vaccine

Over a hundred research groups are developing anti-covid vaccines worldwide. Multiple kinds of vaccines are under develpoment: nucleic acid-based vaccines, innactivated/recombinant vaccines and viral-vector vaccines.

Since main form of cell entry is via ACE2 receptor, which binds to protein S, the ideal target for induced immunity is that protein, triggering host response antibodies to virus binding, fusion and neutralisation.

Alternative targets, such as ORF1ab, 6 and 8 are also being studied and important candidates for subunit vaccines. Native danger signalling in those experimental models is the limiting factor.

Subunit vaccines, based chimeric virus vaccines, and virus-like replicon particle vaccines have successfuly been tested in animal models to prevent MERS and SARS-CoV 1.

There is also evidence that BCG vaccination protects against covid-19 due to IL-1β induction in those individuals, which points to an innate response against the virus, that could be better than an adaptive-inducing response vaccine.

It is believed that a combined or serial vaccination scheme may be more effective against n-CoV. However, the lack of information about the immunopathology of the disease and the induction of memory T-lymphocytes puts in check the very existence of a vaccine.

DISCLAIMER
This is an informal review. It should not replace any guideline or consecrated literature published by scientific maganizes.

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