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  • What is a virus? +

    A virus is a tiny, non-living infectious particle, which can infect all types life forms such as humans, animals, plants, fungi, and bacteria. Viruses infecting bacteria are called bacteriophages. The size of a virus is variable, but in general so small, that viruses cannot be seen by eye or even in a light microscope. With about 50 to 200 nanometers in diameter, this around 1/10000 of a millimeter. The concept of viruses was discovered in 1898 by Dimitri Ivanovsky, who described a non-bacterial pathogen infecting tobacco plants – although researchers at this time had no possibility to visualize these tiny pathogens. Since then, more than 6000 virus species have been discovered and described in more details.

  • How are viruses constructed? +

    The genomes of viruses are often very small and contain the genetic information to build proteins as either DNA or RNA. Therefore, we separate DNA viruses such as Herpes simplex, Cytomegalovirus, and Hepatitis B virus and RNA viruses such as Influenza, SARS-CoV-2 and Hepatitis C virus. The DNA or RNA contains the detailed information on how to construct a viral protein inside the infected cells. The genetic material of the virus is protected by a protein shell (and sometimes also with a lipid envelope) (REF 2). Many proteins serve important functions. The surface proteins of the virus are important to enter the cells of the host. Surface proteins are therefore very critical for the viral tropism. Surface proteins represent a certain weakness of the viruses, because they are so important but also exposed to the environment such as the host immune system. The immune response tries to build antibodies against these structures and thereby neutralizes the viral entry into the cell.

  • How do viruses work? +

    A main difference from so-called “living organism” is the fact, that viruses do not have their own metabolism or the ability to self-replicate. Therefore, a virus is dependent on a suitable host cell to replicate (REF 1). The so-called cellular tropism describes which type of cells are best suited for an infection and replication. For this purpose, very importantly, most viruses have proteins on their surface to bind to specific cellular receptors, which facilitates entry into the host cell. As an example, the new coronavirus SARS-CoV-2 infects mainly respiratory epithelial cells. On these cells, the so-called ACE-2 receptor is the main binding partner. Whereas the Hepatitis C virus mainly infects liver cells. Once inside the cell, the virus can hijack the host’s protein machinery and starts to replicate by using the cells' own proteins and mechanisms. Viruses can then follow in principle two strategies: (i) actively replicate and infect as many neighboring cells as possible, thereby increasing the chance to eventually spread to a new host organism or (ii) enter a sort of dormant stage, so-called latency, and wait for an ideal situation to reactivate and spread, e.g. when the immune system is weak. Moreover, viruses have evolved over millions of years and developed tricks to evade the immune response of plants and animals. Many viral proteins can for example modulate the immune response in their favor and interrupt an immunological signaling cascade in the body. The hosts and viruses have co-evolved over millions of years and specific aspects of the immune system are the result of these interactions. This race for supremacy will continue forever.

  • How are viruses transmitted? +

    Each organism must spread, otherwise it will risk extinction. This spread is also called transmission. Viruses spread in different ways for example: tiny respiratory droplets, body fluids such as blood, urine, faeces, or via insect vectors (REF 3). Based on the respiratory droplet size, we can differentiate between contact dependent transmission (>5 µm) and air borne transmission (<5 µm). Smaller droplets remain longer in the air, and can transmit viral particles over a longer distance, thereby largely affecting the contagiousness of a pathogen.

  • How does the immune system react to a virus? +

    Once a new host is infected, the virus starts to rapidly replicate, and produce as many offspring as possible. The host’s immune system tries to control the viral infection or even to eliminate the viral pathogen. The immune reaction is complex and differs from virus to virus and is also individual for each host. The first step of defense involves the innate immune response; this includes pattern recognition receptors of the immune system. Once initiated, an inflammatory response follows, which attracts members of the adaptive immune response. The adaptive immune response includes T- and B-cells, which provide a long-term immunological memory, which can prevent second infections with the same virus or viral reactivation (REF 4).

  • What is a Coronavirus? +

    A “coronavirus” belongs to a group of related RNA viruses with a relatively small genome of around 30’000 nucleotides. Coronaviruses typically cause respiratory tract infections in various animal species, including humans. The first coronaviruses described in the late 1920s in the US were causing a respiratory infection in chickens. There are currently four endemic coronaviruses circulating in humans, called OC43, HKU1, 229E, and NL63. All circulate mainly during winter months in the human population. Other members of human coronaviruses, include the Severe Acute Respiratory Syndrome 1 Coronavirus (SARS-CoV-1) and the Middle East Respiratory Syndrome (MERS) coronavirus, which are not endemic. SARS-CoV-1 was extinguished about 15 years ago and MERS-CoV is only prevalent in the middle east, mainly affecting camels with sporadic transmission to humans. The newest member in the coronavirus family is SARS-CoV-2, which was discovered in December 2019 and spread from Wuhan, China, around the globe. SARS-CoV-2 causes the disease COVID-19. COVID-19 can show diverse clinical courses from no, mild (common cold) to severe (pneumonia) respiratory symptoms and even life-threatening complications (REF 5) (REF8).

  • What is an epidemic? +

    An epidemic describes the rapid and often uncontrolled spread of (an infectious) disease within a specific group of people over a certain time period and in a defined geographical area. There are also non-infectious epidemics, however in this article, we will only focus on infectious epidemics. The spread of an epidemic caused by a pathogen is dependent on many factors and complex interactions. In principle, there are three main aspects involved: the pathogen, the host, and the environment. The pathogen provides specific aspects in terms of transmission routes, pathogenicity, immune evasion strategies. The hosts show specific characteristics which are also very important, such as the individual and population based immune response, vulnerabilities in specific populations, social behavior of a population. The environment can support the transmission of the pathogen e.g. respiratory viruses can survive longer on cold surfaces.

  • What is a pandemic? +

    A pandemic is an epidemic of an infectious pathogen that has widely spread across a large geographical area for example to multiple continents or even worldwide. Throughout the human history, there have been a number of pandemics such as influenza, smallpox, tuberculosis, or the plague. A pandemic is usually considered a global threat for public health and affects largely the economics. The World Health Organization (WHO) applies a six-stage classification system to describe the process for a novel virus, from the first infections to a global spread. These stages include: Investigation, Recognition, Initiation, Acceleration, Declaration, and Preparation

  • What is herd immunity? +

    The term herd immunity describes the collective immune response of a larger population forming a certain level of resistance against a specific pathogen based on the accumulation of its individual members. Depending on the contagiousness of a pathogen the percentage of immune individuals needs to be higher in order to interrupt the transmission chain and protect still vulnerable members of the society.

  • How can we describe the dynamic of an epidemic? +

    An epidemic often shows a bell-shaped curve of affected patients over time. There is usually a steep increase with an exponential amplification of case numbers. Then with countermeasures or increasing immune individuals a plateau of new transmissions is reached and in the final phase the number of new cases rapidly drop. The dynamic of an epidemic can be described with the reproduction number (see respective chapter). Epidemics can be mathematically modelled by using the number of susceptible, infected, and recovered individuals– these models are known as “S-I-R” models.

  • What are specific routes of transmission? +

    Transmission describes the process of pathogens being spread between two individuals or within a population or within the environment. The routes of transmission can be very broad and complex (REF 11). Some examples of transmission routes: Airborne transmission: Spread via very small droplets or dust (<5um) through the air e.g. measles. Arthropod transmission: Spread via an insect e.g. Plasmodium falciparum (malaria). Blood transmission: Spread via a transfusion of blood or transplantation of tissue e.g. the Hepatitis C virus in the 1980ies. Contact transmission: Spread via direct contact or larger droplets (>5um), e.g. Influenza or SARS-CoV-2. Fecal-oral transmission: The pathogen is spread from the infected host via feces and acquired by ingestion of contaminated material e.g. drinking contaminated water with the Hepatitis A virus. Sexual transmission: Transmission during sexual intercourse without protection e.g. HIV or Chlamydia trachomatis. Vertical transmission: From one generation to another e.g. during intrauterine infection from the mother to the fetus e.g. primary infection with Cytomegalovirus during pregnancy.

  • What is the basic reproduction number? +

    The basic reproduction number (also called R0) describes the average amount of subsequent infections from a single infected individual. The definition describes the state, where no other individual is infected and all individuals in a population are susceptible. The reproduction rapidly changes during an outbreak or epidemic, as increasingly more people either had the pathogen (or died), therefore the reproduction is not stable but changes – the reproduction number at a given timepoint is the effective reproduction number (Re).

  • What are the known reservoirs of Coronaviruses? +

    Normally viruses are host specific and have a narrow tropism, which means that only specific cells of a specific host are infected e.g. respiratory epithelial cells of humans. Viruses constantly evolve and adapt to their hosts and especially RNA viruses are prone to accumulate mutations. Sometime viruses gain the ability to jump from one host species to another (REF 9). The natural animal reservoirs for SARS-/MERS-CoV have been found to be bats, dromedary, and pangolins. From those natural reservoirs the spread of viruses can happen somewhat randomly and lead to the introduction e.g. into the human species. From there it is also possible that a virus gains the ability for a human to human transmission (REF 10).

  • What parts of viruses can we use in diagnostic tests? +

    In the diagnostic process, we can detect various elements of the virus (=direct diagnosis): The viral RNA or DNA can be detected using molecular methods such as the polymerase chain reaction (PCR). Viral proteins, so-called antigens, can also be detected. For this purpose, we can use specific antibodies binding to the antigens. These two methods allow to directly identifying an infected individual by detecting the infectious agents. Both methods usually require a certain amount of virus in order to be positive. This represents the limit of detection and provides valuable information on how sensitive a specific a diagnostic test is. Finally, we can also measure the immune response of the host (= indirect diagnosis). In most diagnostic tests, the antibody response of a previously infected or vaccinated individual is measured. The human body requires about 2-3 weeks to produce specific antibodies (IgG antibodies), which can then be measured. Therefore, this method is not suitable to determine an acute infection.

  • What is a PCR? +

    The polymerase chain reaction (also known as PCR) is a molecular method based on DNA amplification and detection of the amplified gene product. Usually, a short and highly specific DNA fragment is chosen as a target. This gene fragment can be used to detect the presence or absence of a whole gene, gene fragment or single point mutation (qualitative PCR) or it is used to quantify a certain amount of gene copies in a sample (quantitative PCR). The method is applied e.g. for selective DNA isolation for diagnostic purpose of genetic or infectious diseases or in forensics (REF 13).

  • How does a PCR work? +

    The PCR process uses two different steps to get millions to billions of copies of DNA. First, the separation of the double stranded DNA target by heating and in a second step, the enzymatic DNA replication via the DNA polymerase. In the laboratory, the reagents required for a PCR are mixed in a single tube and the separation and replication steps are repeated multiple times in a so-called thermocycler. The amount of cycle replications can influence the sensitivity of the method (REF12).

  • What is an antigen test? +

    An antigen is a molecular structure of a pathogen consisting of amino acids forming a protein. These antigens can be recognized by an antibody (REF 18). This antigen-antibody interaction is specific and can be used to detect e.g. a pathogen within a specimen of different body fluids like e.g. the nasopharyngeal swab for the detection of SARS-CoV-2 (REF 19). Another example of application of this method is the urine pregnancy test (REF 20). In contrasts to PCR tests, antigen tests do not amplify the pathogen material and thereby show a lower sensitivity. Some antigens among highly related pathogens may show a certain cross-reactivity. The specificity and sensitivity of any diagnostic method is usually evaluated against a gold or reference standard, when a diagnostic test is developed.

  • What is a serology test? +

    The term serology refers to the examination of the blood serum, a component of blood without the white and red blood cells, platelets and clotting factors. This term it is used to describe the search for specific antibodies in the serum. Serological tests serve as a method to test the immune response against an infection or in the diagnosis of an autoimmune illness (REF 14).

  • What are antibodies? +

    An antibody, also known as an immunoglobulin, is a highly specific protein (REF 15). They are produced by specific immune cells, the B-lymphocytes. B-lymphocytes are part of the adaptive immune system, to specifically target e.g. pathogens like bacteria and viruses. The function of an antibody is to recognize and bind to a unique pattern of amino acids of a pathogen, called an epitope. Most antibodies bind to different structures of a protein and can be used to tag the antigen. Sometimes, the antibody binds to a critical area of a protein and the protein loses its function – in such a case, the antibody has a neutralizing potential (REF 16). Neutralizing antibodies and B-lymphocytes play an important role in the defense against pathogens and can remain inside the body for years to decades in form of so called “plasma cells” to confer protection against a second infection of the very same pathogen (REF 17).

  • What does sensitivity mean? +

    Sensitivity is a statistical term widely used in medicine. It refers to the proportion of true positive compared to false negative numbers. In other words, it shows the proportion of positive results that are correctly identified, e.g. the percentage of sick people tested who are really carrying the illness (REF 21).

  • What does specificity mean? +

    Specificity is a statistical term widely used in medicine. It refers to the proportion of true negative compared to false positive numbers. In other words, it shows the proportion of negative results that are correctly identified, e.g. the percentage of healthy people tested who really do not carry the illness (REF 21).

  • What is a positive predictive value? +

    The positive predictive value is a statistical term to describe the proportion of the number of true positives compared to the number of all positives (true and false positives). In other words, it shows the performance of a statistical test to detect the true positive quantity (REF 22).

  • What is a negative predictive value? +

    The negative predictive value is a statistical term to describe the proportion of the number of true negatives compared to the number of all negatives (true and false negatives). In other words, it shows the performance of a statistical test to detect the true negative quantity (REF 22).

  • Up to what maximum Ct value are the samples analysed in Swiss laboratories to identify the SARS-CoV-2? +

    The ct value (cycle threshold) is an expression that corresponds to the number of amplification cycles performed where the amount of amplification of the target is sufficient to exceed the background and be considered positive. This numerical value is semi quantitative and allows to estimate the viral load in a sample. It is generally between 10 and 45. The higher the Ct value, the lower the viral load, and conversely, the lower the Ct value, the higher the viral load. However, this absolute value varies depending on the technique used. It is therefore difficult to compare this value between techniques. Moreover, the Ct value reflects the quantity of viral RNA in the sample, but the quality of the sample has an impact on this result. A poorly taken sample may underestimate the viral load. Moreover, it is not possible to distinguish by PCR between living and dead viruses in the sample.

  • What is the name of the manufacturer of tests you use to determine SARS-CoV-2? Have you always used the same test (same manufacturer) since the beginning of the corona crisis? If not: when and why did you change? +

    All labs have implemented PCR from several suppliers; none of them were able to use only one method during the pandemic. Some laboratories have developed initially "in house" methods to detect the virus, based on published genome sequences. We were completely at the mercy of the logistics of the production of the kits, machines or products related to the tests. Most of the reagents are not produced in Switzerland.

  • Does the manufacturer recommend a maximum Ct value? If so, do you follow these recommendations? If not, why not? +

    The number of cycles depends on the test used, the supplier and their PCR model. For the SARS-CoV-2 pathogen there are hundreds of certified PCRs on the market, all with their own characteristics. In Switzerland, each laboratory had to control the quality of the selected tests by comparing the quality of the results obtained with the samples exchanged between laboratories and then with quality controls distributed by recognized centers (CSCQ, MQ, QCMD, INSTAND).Technical information on PCR is the responsibility of the manufacturers via their certification (CE-IVD and others). Laboratories, their umbrella companies or reference centers verify and publish their results and recommendations on the tests used.

  • Since the beginning of the corona crisis, have you always used the same Ct value in tests from the same manufacturer? If not, have you increased or decreased it? By how many units? +

    It is well known that a positive response after a very high number of amplification cycles must be interpreted according to precise criteria and each system takes this into account. For example, the shape of the curve observable on all real-time PCR systems as well as the maximum value of the number of cycles where the result appears to be positive (cycle threshold) are part of the acceptance criteria of the result. Manufacturers are required to set up an algorithm and the laboratory to verify the relevance of the test.
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