Category Archives: Infectious Diseases

COVID-19 Tests Explained

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There are 2 major types of COVID-19 tests: diagnostic tests for active infection, and antibody tests for past infection.
Diagnostic tests look for components of the virus in a sample taken from the nasal cavity, throat, or saliva. Sample taken from the nasopharynx, the upper part of the throat behind the nose, is preferred when higher accuracy is required.
There are 2 types of diagnostic tests: molecular tests detecting viral RNA, and antigen tests detecting viral proteins.
Antigen tests use a technology similar to that of a pregnancy test. Some are made available as at-home test kits. The test is fast and less expensive, but is less sensitive. Antigen test gives positive results only with high viral loads, when the person is near the peak of infection, so it’s more likely to miss an active infection. In other words, the rate of false negative – a test that says you don’t have the virus when you actually do, is high. Symptomatic patients who test negative with rapid antigen test must be confirmed with a more sensitive molecular test. On the other hand, positive results are highly accurate, but false positive – a test that says you have the virus when you actually don’t, can still happen, most commonly due to errors in sample handling.
Molecular tests detect viral RNA. They are also called nucleic acid amplification tests, NAAT, because they amplify viral nucleic acids until there are detectable levels. Different tests are based on different technologies, with polymerase chain reaction, PCR, being just one of them. PCR is the gold standard for diagnostic testing but it requires specific equipment and takes longer to deliver results.
Molecular tests are much more sensitive than rapid antigen tests, but they can still produce false-negative results early in the infection. On the other hand, the high sensitivity may sometimes pick up the low viral load in a patient who has recovered and is no longer contagious. Positive results are highly accurate, most false positives are due to lab contamination or other errors with sample handling.
Antibody tests, also called serology tests, detect antibodies that the body produced in response to the infection. A blood sample is taken for this test. Because antibodies can take a couple of weeks to develop and may stay in the blood for weeks or months after recovery, a positive test result only proves that the person has been exposed to the virus. It gives no indication about active infection and should not be used to diagnose COVID-19.

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Antiviral Drugs, with Animation

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Antiviral drugs are medications used to treat viral infections. Because viruses replicate entirely inside host cells using the host’s machinery, it is difficult to develop drugs that affect viruses without also harming the host. Antiviral drugs do not inactivate or kill viruses, they merely inhibit viral reproduction by interfering with a certain stage of the virus life cycle.
A virus is composed of a genome, DNA or RNA, wrapped inside a protective protein coat, called a capsid. Most animal viruses also have an additional lipid membrane, called an envelope, with protein spikes that serve to attach to host cells.
A viral life cycle typically consists of the following steps:
– attachment to host cell receptor, followed by viral entry: via endocytosis, membrane fusion, or both.
– release of viral genome, also known as uncoating,
– replication of viral genome,
– synthesis and processing of viral proteins, assembly of viral components into new viruses,
– and release of new viruses from host cell.
Antiviral strategies aim to block viral reproduction at any of these stages.
To prevent viral attachment, a drug can either bind to host cell receptor/coreceptor, or to the viral spike protein. Examples are HIV drugs – CCR5-antagonists. They bind to CCR5 coreceptor, masking its binding site for HIV.
For enveloped viruses, one strategy is to prevent fusion of viral and host cell membrane. An agent can bind directly to the viral protein that is responsible for fusion, or disrupt the condition that is required for fusion.
Several drugs have been developed to inhibit the uncoating of influenza A virus – they impair the function of the protein responsible for viral genome release from endosomes.
Viruses that use reverse transcriptase for replication are usually targeted for this enzyme. Because the process of reverse transcription, converting RNA to DNA, occurs only in these viruses and not human cells, drugs targeting reverse transcriptase are generally safe for humans. Most of these agents are nucleoside or nucleotide analogs. They compete with regular nucleotides, insert themselves into the growing chain of DNA, and stop the process prematurely. There are also non-nucleoside reverse transcriptase inhibitors, which bind non-competitively to the reverse transcriptase, impairing its function. The 2 classes of inhibitors are usually combined for maximum effects.
Retroviruses, such as HIV, use viral enzyme integrase to insert their genome into host cell DNA, a critical step for viral reproduction. Drugs that inhibit integrase have been developed to treat HIV and other retroviruses.
Viruses with large DNA genomes usually encode their own DNA polymerase for DNA replication. Viral DNA polymerases are the target of many currently available antiviral drugs. Most of these drugs are nucleoside analogs, they incorporate into the growing DNA and cause premature termination of viral DNA synthesis.
Another approach is to inhibit viral protein synthesis by antisense mechanism. Antisense antiviral drugs are short synthetic nucleic acid strands that are complementary to part of an essential viral mRNA. They bind specifically to the viral mRNA, effectively preventing it from being translated into protein.
Some viruses require activity of a specific protease to cleave precursor viral proteins into functional components for viral assembly. Several drugs have been developed to target this protease in HIV.
Influenza virus requires action of viral enzyme neuraminidase to release new viruses from host cell. Blocking neuraminidase is an effective way to treat influenza.

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Current status of possible treatments for COVID-19, with Animation, updated May 1, 2020

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Convalescent plasma, Remdesivir, Chloroquine and hydroxychloroquine: mechanisms of action, current status, effectiveness and side effects.
At this time, no specific drugs or therapies have been proven effective for prevention or treatment of COVID-19. Current disease management is supportive care, including supplemental oxygen and mechanical ventilator when indicated.
However, several possible treatment options are under intensive investigations:
Convalescent plasma: when someone is infected with SARS-CoV-2, the coronavirus that causes COVID-19, their immune system produces antibodies to fight the virus. People with healthy immune systems produce enough antibodies to fight the disease and recover, while those with compromised immune systems may struggle. Antibodies from blood plasma of recovered patients can be given to people with active illness to help neutralize the virus. This approach has been used in the past for some other diseases, with varying success. Studies are underway to determine its effectiveness in COVID-19, and if convalescent plasma is best used to prevent infections in high-risk individuals; to prevent mild infections from becoming severe; or to improve recovery in severely ill patients. The FDA has allowed emergency use of convalescent plasma in patients with serious or immediately life-threatening COVID-19 infections. While the treatment concept is simple, the process involves multiple steps, from selecting donors, to collecting, processing blood and safety screening. On average, plasma from one donor is only enough to treat 1 to 3 patients. For these reasons, convalescent plasma is considered a temporary solution while antiviral drugs and vaccines are developed.
Remdesivir is an antiviral drug originally created by Gilead Sciences to fight Ebola virus, but it was proved effective in treating SARS and MERS coronaviruses in laboratory and animal research. Recent studies show that Remdesivir inhibits SARS-CoV-2 infections in cultured cells, and efficiently prevents COVID-19 disease progression in monkeys. Remdesivir is an adenosine nucleotide analogue. During viral RNA synthesis, it incorporates into the nascent RNA and causes premature termination, thus interrupting viral RNA production. There are currently 6 ongoing clinical studies, some of which are large-scale phase 3 trials; and initial results are encouraging. However, as an experimental drug, Remdesivir is not expected to be available in large amounts very soon.
Chloroquine and its derivative hydroxychloroquine had recently made headlines thanks to early reports from China and France about its effectiveness in treating severely ill COVID-19 patients. Having been used to treat malaria and some autoimmune diseases, these drugs are readily available. In laboratory studies, the drugs have been shown to block entry of the virus by interfering with host cell receptor. In addition, they also inhibit virus/host cell fusion, preventing the release of viral nucleocapsid. However, more recent human studies suggest that these drugs may produce serious side effects that can be fatal. Specifically, they may cause QT interval prolongation, an abnormal heart rhythm that can quickly develop into lethal rhythms of ventricular tachycardia and fibrillation. The FDA now recommends against taking chloroquine or hydroxychloroquine for COVID-19 infections unless they are prescribed in hospitals under close supervision, or as part of a clinical trial.

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Antibiotic Resistance, with Animation

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Bacterial infections are treated with antibiotics. Antibiotic resistance occurs when an infection responds poorly to an antibiotic that once could treat it successfully. It’s the bacteria that have become resistant to the antibiotic, not the patient. This happens because the bacteria acquire a mutation – a change in their DNA – that gives them a new protein as a tool to fight the antibiotic. There are many mechanisms by which this tool may work. It can:

– prevent the antibiotic from entering the bacterial cell;

– pump the antibiotic out of the cell;

– destroy the antibiotic by enzymatic reaction;

– modify the antibiotic’s target so it no longer binds to the drug;

– or give the cell a way to bypass the antibiotic’s target, making the drug irrelevant.

Mutations in bacterial genome occur all the time, spontaneously, but only the ones that confer a certain advantage would persist to the next generation. Let’s consider a situation when a new mutation emerges and makes the bacteria resistant to a certain antibiotic. In the absence of the antibiotic, such mutation offers no advantage, and because mutations usually come with slower growth, the mutation would be diluted and eventually disappear in the following generations. On the other hand, in the presence of the antibiotic, only bacteria that carry such mutation would survive and they would soon take over the whole bacterial population. The use of antibiotic is therefore the factor that drives the selection of antibiotic-resistant organisms.

Mutations that confer antibiotic resistance can be transmitted not only vertically, from parent cells to offspring, but also horizontally, from one bacterial cell to another, using mobile genetic elements such as plasmids or bacteriophages. This means a bacterial strain can share their antibiotic resistance with other bacterial strains and even with distantly related bacterial species. Horizontal transfer is a major mechanism underlying the spread of antibiotic resistance among bacterial species. These antibiotic-resistant bacteria can infect humans, animals and spread between them through food and the environment.

Antibiotic resistance is one of the biggest global health concerns. Infections by antibiotic-resistant bacteria are much harder, sometimes impossible, to treat. Some bacteria, called superbugs, are resistant to most of the common antibiotics, and are especially difficult to kill. Treatments for infections caused by such bacteria are costly and toxic to the patients.

While the emergence of antibiotic resistance is inevitable, the process is greatly accelerated by misuse and overuse of antibiotics. To help control spread of antibiotic resistance, antibiotics must be taken correctly, only when prescribed by a healthcare professional, who should do so only when antibiotics are needed, according to current guidelines. Antibiotics should not be used to promote growth or prevent diseases in healthy animals. Measures that help prevent infections also help reduce antibiotic overuse.

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Antibiotics – Mechanisms of Action, with Animation

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Antibiotics are medications used to fight bacterial infections. Originally, the term “antibiotics” referred to natural compounds produced by certain microorganisms for the purpose of fending off others; for example, penicillin is produced by the fungus Penicillium. Nowadays, this term includes all antibacterial products, most of which are semi-synthetic, meaning they are modifications of natural products. Antibiotics are just one type of antimicrobials. They target bacteria, and are usually not effective against other types of organisms. Antibiotics cannot treat viral infections such as common cold or flu.
Antibiotics can be bactericidal, meaning they destroy bacterial cells; or bacteriostatic, meaning they inhibit bacterial growth.
Some antibiotics are broad-spectrum – they are effective against a wide range of bacteria, including both Gram-positive and Gram-negative; while others are narrow-spectrum – they are more specific, affecting a smaller group of bacteria.
Antibiotics can be classified by their mechanisms of action:
– Inhibitors of cell wall synthesis. Bacterial cells are surrounded by cell walls made of peptidoglycan. Antibiotics that affect bacterial cell wall act at different stages of peptidoglycan synthesis and cell wall assembly. Because mammalian cells do not have cell walls, this class of antibiotics is highly selective – they target bacteria and have minimal effects on mammalian host cells.
– Disruptors of cell membrane. Some antibiotics disrupt the integrity of cell membrane by binding to membrane phospholipids. Because cell membrane is also found in mammalian cells, these antibiotics are also toxic to host cells if administered systemically. Their clinical use is therefore limited to topical applications.
– Inhibitors of protein synthesis. Antibiotics that interfere with bacterial protein synthesis may act at different steps of this process, including: formation of the 30S initiation complex, assembly of the 50S ribosome subunit, formation of the 70S ribosome from the 30S and 50S complexes, and elongation process. Some of these antibiotics also inhibit the eukaryotic mammalian counterparts, but their effect on bacterial ribosomes is significantly greater.
– Inhibitors of nucleic acid synthesis. Some antibiotics interfere with DNA synthesis by binding to bacterial topoisomerase II – the enzyme that relaxes the supercoil DNA before its replication. Some others interfere with RNA synthesis by inhibiting RNA polymerase. Some antibiotics of this class are selective – they do not interact with mammalian counterparts of these enzymes, while others do affect mammalian host cells. The latter are used for cancer treatment instead. Because cancer cells grow faster than normal cells, they are more affected by the action of these agents.
– Inhibitors of folic acid synthesis. Bacteria synthesize their own folic acid, unlike humans who get the vitamin from food. Because of this, antibiotics that inhibit enzymes involved in folic acid synthesis only harm bacterial cells, and not human cells.

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Understanding the Virus that Causes COVID-19, with Animation

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Coronaviruses are a large family of enveloped, RNA viruses. There are 4 groups of coronaviruses: alpha and beta, originated from bats and rodents; and gamma and delta, originated from avian species. Coronaviruses are responsible for a wide range of diseases in many animals, including livestock and pets. In humans, they were thought to cause mild, self-limiting respiratory infections until 2002, when a beta-coronavirus crossed species barriers from bats to a mammalian host, before jumping to humans, causing the Severe Acute Respiratory Syndrome, SARS, epidemic. More recently, another beta-coronavirus is responsible for the serious Middle East Respiratory Syndrome, MERS, started in 2012. The novel coronavirus responsible for the Coronavirus Disease 2019 pandemic, COVID-19, is also a beta-coronavirus. The genome of the virus is fully sequenced and appears to be most similar to a strain in bats, suggesting that it also originated from bats. The virus is also very similar to the SARS-coronavirus and is therefore named SARS-coronavirus 2, SARS-CoV 2. At the moment, it’s not yet clear if the virus jumped directly from bats to humans, or if there is a mammalian intermediate host.

Coronavirus genome is a large, single-stranded, positive-sense RNA molecule that contains all information necessary for the making of viral components. The RNA is coated with structural proteins, forming a complex known as nucleocapsid. The nucleocapsid is enclosed in an envelope, which is basically a LIPID membrane with embedded proteins. From the envelope, club-like spikes emanate, giving the appearance of a crown. This is where the “corona” name came from.

The integrity of the envelope is essential for viral infection, and is the Achilles’ heel of the virus, because the lipid membrane can easily be destroyed by lipid solvents such as detergents, alcohol and some disinfectants. In fact, enveloped viruses are the easiest to inactivate when they are outside a host.

In order to infect a host cell, the spikes of the virus must BIND to a molecule on the cell surface, called a receptor. The specificity of this binding explains why viruses are usually species specific – they have receptors in certain species, and not others. Host jumping is usually triggered by mutations in spike proteins which change them in a way that they now can bind to a receptor in a new species.

The novel coronavirus appears to use the same receptor as SARS-coronavirus for entry to human cells, and that receptor is the angiotensin-converting enzyme 2, ACE2. Infection usually starts with cells of the respiratory mucosa, then spreads to epithelial cells of alveoli in the lungs.

Receptor binding is followed by fusion of the viral membrane with host cell membrane, and the release of nucleocapsid into the cell. The virus then uses the host machinery to replicate, producing viral RNAs and proteins. These are then assembled into new viral particles, called virions, by budding into intracellular membranes. The new virions are released and the host cell dies.

Uncontrolled growth of the virus destroys respiratory tissues, producing symptoms. Infection triggers the body’s inflammatory response, which brings immune cells to the site to fight the virus. While inflammation is an important defense mechanism, it may become excessive and cause damage to the body’s own tissues, contributing to the severity of the disease. In an otherwise healthy person, there is a good chance that the virus is eventually eliminated and the patient recovers, although some may require supportive treatments. On the other hand, people with weakened immune system or underlying chronic diseases may progress to severe pneumonia or acute respiratory distress syndrome, which can be fatal.

 

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HIV and AIDS infection stages, HIV life cycle, Transmission, Diagnosis and Treatment, with Animation

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HIV, for human immunodeficiency virus, is a virus that attacks the immune system, weakening the body’s ability to fight infections. Progressive destruction of the immune system eventually leads to its failures, a state known as “acquired immunodeficiency syndrome”, or AIDS, when the body is INcapable of defending itself from common infections.

HIV targets a specific group of cells called CD4+ cells. CD4 is a receptor expressed on the surface of many immune cells, including T helper cells, macrophages and dendritic cells, where it is essential for cell communication and hence normal function of the immune system. HIV hijacks this receptor to gain access to the cells. Apart from CD4 receptor, another factor, called a co-receptor, is also required for HIV entry and infection. Several co-receptors have been identified in different cell types, with CXCR4 and CCR5 being the most common. CXCR4 is expressed on many T-cells, but usually not on macrophages, and is used by T-tropic strains of HIV. CCR5 is expressed on macrophages, some T-cells, and is used by M-tropic strains. Some HIV strains use CCR5 to infect initially but evolve to use CXCR4 later during disease progression. Viruses that can use both co-receptors are call dual-tropic. Some people are born with a deletion in CCR5 and are substantially RESISTANT to HIV infection.

HIV life cycle starts with attachment of a HIV envelope protein, gp120, to CD4 receptor and co-receptor, followed by fusion of HIV with host cell. The virus then injects its content, HIV RNA and several enzymes, into the cell. One of these enzymes, known as “reverse transcriptase”, is used to convert HIV RNA into DNA, an important step that would allow the virus to integrate into host cell DNA. Once in the nucleus, HIV enzyme INTEGRASE inserts the viral DNA into the host DNA. At this point the virus may adopt either LATENT or ACTIVE infection.

In active infection, HIV uses the host machinery to produce multiple copies of its RNA and proteins, which are then assembled into new virus particles, ready to infect more CD4 cells.

In latent infection, the virus remains integrated in host DNA, and may lie dormant for years, forming a latent HIV reservoir, which can REactivate and infect again at a later time.

HIV is transmitted through infected body fluids, most commonly via sexual contacts, shared contaminated needles, and mother to child during childbirth or through breastfeeding. It is not transmitted through air or casual contacts.

Diagnosis is by detection of viral protein, RNA, proviral DNA , or antibody produced against HIV.

There are three stages of HIV infection:

The ACUTE stage generally develops within a couple of weeks after a person is infected with HIV. During this time, patients may experience flu-like symptoms. HIV multiplies RAPIDLY resulting in HIGH viral load in the blood and INcreased risks of transmission.

The CHRONIC stage, also called clinical latency, is usually Asymptomatic. HIV continues to multiply but at much SLOWER speeds. Patients may not have any symptoms, but they can still spread HIV to others. Without treatment, the disease usually progresses to AIDS within 2 to 10 years.

AIDS is the final stage of HIV infection. As the immune system is failing, the body can’t fight off common diseases, and opportunistic infections take hold. AIDS is diagnosed when CD4 cell count is LOWER than 200 per microliter, or if certain opportunistic infections are present.

There is currently no cure but treatment with anti-retroviral therapy can SLOW DOWN progression to AIDS and reduce transmission risks. Anti-retroviral drugs are classified based on their ability to interfere with certain stage of HIV life cycle. Accordingly, there are: entry and fusion inhibitors, reverse transcriptase inhibitors, integrase inhibitors, and protease inhibitors. These drugs, however, can NOT reach the LATENT virus, which hides out safely in healthy T-cells but may reactivate and infect again. This is the major reason why HIV infection is not curable with current available treatments.

 

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Zika Virus Outbreak Review and May-2016 Updates (with Video)

Feb 2016, WHO has declared the Zika virus a global public health emergency.  What you should know?
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Zika virus is a member of the Flavivirus genus which also includes viruses that cause dengue fever, yellow fever and Japanese encephalitis. The name Zika came from the Zika forest of Uganda, where the virus was first isolated in 1947.

Transmission

The virus is mainly spread through daytime active Aedes mosquitoes, but can also be transmitted by blood transfusion, via sexual contact, and from an infected mother to the fetus during pregnancy.

Zika Fever – Symptoms 

Infection with Zika virus is known as Zika fever. Most infected people, however, do not develop any symptoms. In those who do, the symptoms are usually mild and may include: fever, rash, conjunctivitis, joint pain and headache. The disease commonly clears up on its own after a week and does not require any treatment other than rest.

So why the big fuss?

Originally considered a mild disease, Zika fever has been getting a lot of attention lately due to reported connection between the virus and incidents of microcephaly in infants born from infected mothers.

Microcephaly is a serious birth defect where the brain of the newborn is underdeveloped and so smaller than usual. Depending on the extent of the defect, microcephaly may result in a number of neurological disorders, including: seizures, developmental delay, intellectual disabilities, vision and hearing loss. The problems are usually life-long and may also be life-threatening.

Several studies newly published in May 2016 showed that Zika virus in infected pregnant mice can cross the placenta to the fetuses, where it destroys neural progenitor cells. Because neural progenitors cells are fast-replicating and give rise to a large number of brain cells, even a small loss of these cells would result in missing parts of the brain.

The number of infants born with microcephaly has surged 20 folds in the affected areas of the Brazil outbreak, which started in May 2015. While the link between Zika and microcephaly has not been fully proven, the evidence has become overwhelming.

Infection in adults has also been linked to Guillain–Barré Syndrome, a rare condition characterized by a rapid onset of muscle weakness.

Where is ZIKA now?

Since the start of its outbreak in Brazil, Zika has spread rapidly to other surrounding countries. The World Health Organization warned that the virus is likely to spread to nearly all countries of the Americas, except perhaps Canada and continental Chile, where it is too cold for Aedes mosquitoes to survive. Large outbreaks may also be expected in Asia.

More than a hundred of pregnant women in the US has been tested positive for Zika (May 2016)

The Asian strain that causes Brazil outbreak is now found in Africa

Prevention

There is currently no vaccine for Zika; the best way to prevent the disease is to avoid mosquitoes. Pregnant women are advised not to travel to affected areas and women living in affected countries to delay getting pregnant.

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