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Important information about infectious diseases

Why do infectious diseases occur?

There is a large number of microorganisms both in the human body and in the surrounding environment, but not all of them cause infectious diseases. The development of a disease is linked to the ability of a microorganism to pass by the body’s defensive mechanisms (its degree of virulence), and the human immune system plays a significant role in this process.

The most frequently encountered infectious disease pathogens are bacteria, viruses and fungal infections. They can be localized in various organs and systems in the human body: the respiratory tract mucosa, gastrointestinal tract (from the oral cavity through to the distal intestine segments), blood, skin, etc. In addition, the transmission path of a pathogen from one person to another depends on its localization. For example, if a pathogenic microorganism is located in the respiratory system, the infection pathway will be predominantly airborne, while diseases that attack the gastrointestinal tract are spread through household contact and the fecal-oral route (filth-born disease). However, it should be noted that very rarely does a disease pathogen stay localized in a one single organ, and more often the microorganism quickly spreads to several organs and systems, and therefore there can be several transmission routes at the same time.

How does an infectious disease progress?

There are several distinct periods over the course of an infectious disease. Depending on the pathogen, they have various durations, clinical aspects and degrees of severity.

Incubation period

This is the time after a pathogen has already entered the human body, but no clinical signs have yet appeared (increased body temperature, runny nose, headache, etc.). During this time, the infected person does not experience any decline in his/her well-being, but can already act as a source of infection for others. This means that during this period the person is not yet sick but is already infected and contagious! Depending on the disease, the incubation period can last from several hours or days to several weeks, months, or, in some cases, even years.

The average incubation period for COVID-19 is five days. This means that after the initial contact with the virus, a person does not feel its effect for five days (on average), but is a source of infection for others. The insidiousness of the COVID-19 virus is due to the fact that in about 1% of all cases (around 100 people in 10,000) the incubation period can last for longer than 14 days (Lauer, Grantz, et al. 2020). This means that the first clinical symptoms can appear even after that widely accepted two-week period. During this entire time, an infected person is contagious.

At this stage, diagnostic testing can make a big difference, for if the method used is sensitive enough, it can detect an infected person before there are any clinical signs, and a decision about self-isolation can be made. This helps stop the spread of the disease, and protects those around the infected person.

Prodromal period (Pre-onset)

This is characterized by the appearance of “harbingers” of the disease: the body temperature starts to increase, the person’s appetite and ability to perform decreases, and, depending on the pathogen, local manifestations of the disease can appear (rashes, inflammation, etc.).

The pre-onset period often does not last for more than two days, and can be virtually or completely absent. However, its presence has great diagnostic value for certain infectious diseases.

Eruptive phase (clinical symptoms – Period of the actual illness)

Clinical symptoms and the degree of their severity are specific signs of an infectious disease, but are often accompanied by signs of general intoxication (high temperature, weakness, acute body pain, decrease in performance, headache, etc.). The degree of severity of clinical symptoms during this period is significantly impacted by the body’s immune system, the timeliness of diagnostic procedures, and the correctness of the chosen treatment.

Timely diagnosis helps to determine the specific pathogen and can also determine the sensitivity of the pathogen to drugs. For example, it is not a widely known fact that there are certain strains of bacteria that are resistant to many antibiotics. Also, antibiotics are useless against viral infections, as these need to be treated with antiviral therapy, something that has been developed for very few known viruses. This means that modern diagnostic methods can help:

  • provide timely information on whether a person is infected before clinical symptoms emerge and help make a decision about self-isolation in order to stop the spread of the disease to other people ;
  • make well-informed decisions about preventing the disease if a pathogen is detected;
  • make balanced decisions about treating the disease and choosing the most effective treatment and drugs;
  • understand what kind of drug is not effective for a certain disease to avoid using it, thereby decreasing the possibility of side effects caused by unproductive treatment.

Convalescent period

If the disease takes a favorable course, the period of active illness transforms into a convalescent period, which is characterized by gradual disappearance of clinical symptoms. During this period, in most cases both the pathogens and the byproducts of their vital activity and decay are completely excreted, and specific immunity is formed. This means that antibodies are created to allow the body to repeatedly resist the same infectious disease. However, it is noteworthy that the process of complete elimination of the pathogen from the body is slower than the disappearance of clinical symptoms. That is why guidance from a doctor should be followed until convalescence is complete.

Without doing any analyses, is it possible to ascertain what caused the disease: bacteria, viruses, or a fungal infection?

Yes, a clinical picture can give a lot of information to a physician about what is possibly causing the illness. At the same time differential diagnosis is often required between bacterial and viral infectious diseases. And, in many cases, the nature of the disease can be surmised even before any special tests are done.

For example, for viral infections a sudden start for the disease is quite typical: shivers, a sharp increase in body temperature up to 38◦С followed by a decrease after a few days, and signs of general intoxication of the organism manifested by pains throughout the body and sharp pains in the muscles and joints. Some nasal discharge might be present, but that is characterized by transparency and a liquid consistency.

Bacterial infectious diseases are marked by the gradual growth of symptoms, and they are not as acute at the beginning as viral diseases are. Body temperature increases slowly over several days, reaching up to 38 degrees and higher, but it might not decrease on its own for a long time. When the nasopharynx is affected, there is typically thick, purulent nasal discharge. As a rule, inflammation is localized, which brings about defined localized pain (pain in the affected organ).

At the same time, it is important to remember that a viral infection can be accompanied by one of bacterial origin that follows it, and as a result the disease becomes of combined origin. Suspicions arise when new clinical symptoms appear a few days after the onset of the disease, especially if there was an improvement in the patient’s condition shortly before, or if the body temperature is increased for a long time (five days or more).

As far as fungal infections are concerned, when a healthy person comes into contact with an infectious agent, the course of the disease is limited to local manifestations. The process can potentially spread, along with a corresponding increase in the severity of symptoms and general sickness, if there is a prolonged absence of treatment, a weakening of the body’s protective mechanisms, or a severe concomitant pathology.

This information will allow you to better understand the nature of a potential disease. However, you should not attempt to diagnose yourself and prescribe treatment on your own. If you experience fatigue, an increase in body temperature, or the onset of other clinical symptoms, it is essential that you seek medical help. Only a doctor can prescribe any required tests, establish the diagnosis and prescribe treatment based on your medical history and data obtained from laboratory analyses, physical examination, and instrumental examinations.

What kind of tests allow a doctor to establish the correct diagnosis?

To diagnose infectious diseases, specific and non-specific laboratory diagnostic methods are used. However, it is important to understand that using some methods does not eliminate the need in others, and frequently an integrated approach to diagnosis is necessary.

If specific methods for laboratory diagnosis exist, are non-specific ones really necessary?

Non-specific laboratory methods are always of use to the physician. They help assess the severity of the inflammatory process is and establish whether it is localized (the degree of damage to the body’s organs and systems due to the disease), as well as making assumptions about the cause of this process. These laboratory diagnostic methods include clinical blood tests, clinical urine tests and biochemical blood tests, among others.

Clinical blood tests

The level of white blood cells indicates the presence of inflammation of any etiology. When a bacterial infection is present, the level of neutrophils typically increases (an increase in the level of band neutrophils attests to a process of acute inflammation). In contrast, during a viral infection the quantity of white blood cells can decrease. Further, an increase in the number of lymphocytes with a possible increase in the quantity of monocytes is also in favor of a viral etiology.

One important indicator in infectious disease diagnosis is the ESR (erythrocyte sedimentation rate), which reflects the activity of the inflammatory process

Urine test

Clinical urine tests allow to evaluate the degree of severity for general body sickness and reveal any damage to the urinary tract system.

Biochemical blood test

If a doctor has any reason to believe that a patient has suffered damage to the organs because of an infectious disease (to evaluate the degree of severity and type of damage), when there are suspected complications from the disease, or if there are underlying health conditions, a biochemical blood test is prescribed.

What are the specialized laboratory diagnostic methods, which methods are currently used, and what are they used for?

To diagnose infectious diseases, a doctor might prescribe specialized tests. In modern-day medicine, there are many methods that are widely used. However, it is worth realizing that it is nearly impossible to choose the right kind of test that every specific case calls for by yourself without proper medical training.

Microscopic methods

Microscopy allows the identification of pathogens in biological microscopic material by using various types of microscopes. The specimen viewed in the microscope, if necessary, can either remain unchanged or can be coloured using special technologies.

Bacteriological culture technique

The bacteriological culture technique involves extracting a pure culture of a pathogen from a patient’s biological material and then identifying it and determining its sensitivity to pharmaceutical drugs. This testing method is used for suspected purulent-inflammatory disease of bacterial origin.

Serologic testing

Serologic testing methods are based on the specific interaction of an antigen (virus, bacteria, etc.) and the antibodies targeted at it. This allows for the determination (qualitatively and quantitatively) of both the antigens themselves and the antibodies to them.

The following serologic testing methods are used in laboratory diagnostics: an enzyme-linked immunosorbent assay (ELISA), immunofluorescence assay (IFA), immunoradiometric assay (RIA), and others. The most widespread in diagnosing infectious diseases is the ELISA method that allows for the quantitative and qualitative determination of antibodies. In the former instance, discovering antibodies (a positive test result) attests to the possible presence of an inflammatory process caused by a certain infectious agent. In the latter instance, it is not only possible to establish the presence of an infectious disease, but to evaluate the activity phase of the inflammatory process.

It is important to realize that ELISA testing makes sense when the body is starting to build immunity to the infectious disease and when antibodies are starting to appear, or when this immunity has been developed and all the antibodies have already been produced. Consequently, at the beginning of a disease using the ELISA method does not make sense, and even less so to detect infected people before any clinical symptoms have developed.

Molecular biological methods

The polymerase chain reaction (PCR) method falls under the category of molecular biological methods, its cornerstone being amplification (repeated replication) of small DNA/RNA fragments of a virus, bacteria, etc. PCR diagnostics allows for a direct detection of a pathogen’s genetic material in the patient’s biological material.

Unlike the ELISA method, PCR does not pinpoint the antibodies formed in response to a pathogen, but identifies the pathogen itself in the human body. Any sample of body tissue can be used: saliva, blood, sputum, etc. This is especially valuable for identification of infected people going through the incubation period. During this period of time an infected person who is not showing any signs of sickness, is already spreading the infection. This information allows decisions to be made such as whether it is necessary for a patient to self-isolate, or to temporarily separate an employee from the workforce to prevent the spread of an infection and preserve a workforce that is both healthy and able to perform optimally. This can also be beneficial for the patient him-/herself since in many cases there is an opportunity to start preventive treatment.

In addition, this method is quite useful during the first days of the disease, even before the body has begun to produce antibodies. PCR can provide valuable information about the pathogen and help a doctor choose the right treatment strategy, which will make the treatment as effective as possible, enable a mild course of the disease, minimize potential side effects, and accelerate the recuperation and recovery process.

What is PCR diagnostics?

As mentioned above, PCR is a molecular laboratory diagnostic method that makes it possible to identify the DNA/RNA of the pathogen of an infectious disease in biological material (in saliva, blood, etc.). This method is effective for the diagnosis of infectious diseases, even in the absence of a pronounced clinical picture. The main advantages of PCR are:

  • high specificity – the method detects a particular virus, and does not confuse viruses with each other;
  • high sensitivity – the method can detect the pathogen even when there is very little of it in the biomaterial;
  • both a qualitative and a quantitative identification of the pathogen of an infectious disease – the method not only recognizes a specific pathogen, but also determines how much of is present;
  • the ability to diagnose several pathogens simultaneously;
  • monitoring the effectiveness of therapy;
  • speed of testing.

Speed of PCR testing

A classic real-time PCR analyses takes about 2-4 hours to perform. Despite the method being quite old, it still widely used for its preciseness and cost-effectiveness. More modern PCR variants, the so-called isothermal PCR (a constant temperature is maintained throughout the reaction), are faster and take about 30 minutes. However, they may be less precise, which may increase the probability of error.

SmartAmp method

SmartAmp method is the latest development in PCR diagnostics, which combines both the speed of the isothermal reaction and the accuracy of conventional PCR (even exceeds it by a number of indicators). The sensitivity of the test reaches 50-100 copies of the virus in a sample (saliva, blood, etc.), with the accuracy reaching 99.99% with almost no risk of cross-reactivity with other viruses (the method identifies precisely the desired virus, but does not erroneously identify other similar virus).

Mutations of microorganisms and viruses

In addition, any microorganism, including viruses, constantly mutates and may, potentially, become invisible to PCR, since the reagents of the method (primers) are “tailored” to a clearly defined part of the genome. The SmartAmp system employs several primers at once, making it possible to detect a pathogen even if its DNA or RNA mutates in a given area. This makes the method particularly reliable.

Additional capabilities

An additional advantage of SmartAmp is its ability to detect genetic polymorphisms (variants of genetic rearrangements), somatic mutations and single-nucleotide polymorphism (mutations based on the replacement of only one nucleotide - SNP). Due to this ability, it is possible to determine the resistance of the pathogen to drugs.

Thus, all of the above-mentioned components of the SmartAmp method make it a highly specific, highly sensitive and rapid diagnostic system with additional capabilities for determining drug sensitivity.

Which material is needed for PCR diagnostics?

Tissues and body fluids, which may be hosting the pathogen, are used as material for PCR diagnostics. Depending on the pathogen, it can be blood, a swab from the nasopharynx/oropharynx, sputum, epithelial scrapings from the mucous membranes, biological fluids and biopsy samples.

How to prepare yourself for PCR testing?

All recommendations boil down to the fact that the material should be clean, free from contamination and in sufficient quantities.

Blood should be given on an empty stomach, and no alcoholic beverages or fatty foods should be consumed the evening before.

Before taking a swab from the nasopharynx/oropharynx and saliva, one should refrain from eating food and taking medicines, drinking (even water), brushing teeth and chewing gum for at least 2-3 hours before testing. For about 2-3 days prior to testing no antiseptic solutions should be used for rinsing the oral cavity and antiseptic sprays should be avoided, as should antimicrobial ointments, etc.

When performing genital scrapings, it is necessary to refrain from sexual intercourse for at least 36 hours prior to testing, refraining from washing and using antibacterial soap the evening before, and one should try to refrain from urinating for at least three hours prior to testing. Antibiotic course should be completed at least three weeks before the test.

Possible reasons for erroneous results

PCR diagnostics are constantly being improved, but the human factor is ever present. There may be technical issues, which, however, are usually identified quickly and resolved by the technical support service of the laboratory. One must always take into account the characteristics of the pathogen and have a good understanding of its biological and epidemiological properties.

Therefore, the possible reasons for false positive or false negative test results may include:

  • errors in the collection, transportation, storage and allocation of the material. This is especially important for RNA viruses, as RNA is less stable than DNA;
  • the laboratory in which the tests are performed may have little experience working specifically with RNA viruses, so it may make minor technical errors when working with the RNA-containing COVID-19 virus;
  • insufficient amount of the pathogen in the biomaterial, which may be the case at the very initial stages of infection;
  • the pathogen undergoes a wave-like increase and decrease in concentration in the biological material (for example, on the mucous membranes of the nasopharynx and oropharynx), which is due to the wave-like immune response of the human body;
  • errors in result interpretation.

How can ELISA test results indicate the stage of an infectious disease?

With quantitative ELISA, the antibody titer is determined in accordance with its class. There are five classes of antibodies: IgM, IgA, IgG, IgD, and IgE. In most cases, it is that the IgM and IgG antibodies are important for the diagnosis of infectious diseases. They form in the body at different time intervals, depending on when the active infectious process began, which makes it possible to determine the activity stage of the infectious process.

The following antibody combinations are possible depending on the stage of the disease:

  • IgM «-» and IgG «-»: the body did not come into contact with the virus, specific immunity is absent. In order to prevent certain infectious diseases, a similar ELISA indicates the need for vaccination.
  • IgМ «+» and IgG «-»: recent infection, acute stage of the inflammatory process.
  • IgM «+» and IgG «+»: a chronic course of the disease with exacerbation at the moment of testing or the end stage of the disease.
  • IgM «-» and IgG «+»: specific immunity formed as a result of having had the illness or having been vaccinated.

It should be taken in consideration that interpretation of ELISA results is complicated, therefore, should only be done by a professional physician who can determine the presence or absence of an infectious disease and its stage.

A positive ELISA result: is it always bad news?

No, it's actually rather good news! As noted above, the presence of antibodies of a certain class towards the pathogen of an infectious disease may indicate the presence of acquired (specific) immunity, which often reduces or almost completely eliminates the risk of reinfection by the same agent.

Is it possible to receive a false ELISA test result?

Despite the relatively high accuracy of ELISA, the likelihood of false-positive or false-negative results does still exist.

Possible causes of a false-positive ELISA result may be:

  • lack of necessary preparation of the patient before biological material is taken;
  • errors in the biological material acquiring and handling (its storage, transportation, processing);
  • technical errors during the actual reaction;
  • results interpreting errors.

What material is acquired for ELISA?

Most commonly venous blood.

How should one prepare for the test?

  • the last meal should be no less than 8-12 hours prior to testing;
  • no medication should be taken (only after consulting with your doctor) prior to testing;
  • refrain from smoking and drinking alcohol the night before the test;
  • it is advisable to have a good night’s rest, avoiding any physical exertion and stress as much as possible.

Does a negative ELISA result (absence of antibodies) always mean that there is no infectious disease?

No, unfortunately not. After initial infection, antibodies do not immediately begin to be produced in the body, but rather after the incubation period, about the onset time of obvious clinical manifestations of the disease. Meanwhile, an infected person may pose a danger to others, even if they do not display pronounced clinical symptoms. As mentioned above, the duration of the incubation period for each disease may differ. In this regard, the test can be repeated within a few days with positive results, but this time displaying positive results provided that the person was indeed sick, even in a mild form.

Do ELISA test results and PCR diagnostics always match?

No, there may be a discrepancy between the results of these diagnostic methods.

Below are possible combinations of results with matching explanations.


This combination is possible in case of a recent infection or the chronic stage of an infectious disease. In the former case, the immune system has not yet begun to produce antibodies against the pathogen, whose DNA/RNA was detected by PCR diagnostics. In the latter case, the pathogen of an infectious disease has been present in the blood for a long period of time, and therefore the immune system no longer responds to its presence.

It should be noted that in the absence of clinical symptoms, but with the pathogen present in the body, a person can be the source of infection (carrier) and can transmit the infection to others.


This combination indicates a previous infection, or an infection closer to recoalescence. Moreover, the ELISA result is positive due to the presence of immunoglobulins (not the DNA/RNA of the pathogen itself) that can circulate in the blood for several months and even years after complete recovery. The PCR method, in turn, makes it possible to determine only the DNA/RNA of the pathogen in the body, which will have left the body by the time antibodies are formed.

Specificity and cross-reactivity

Discrepancy may be due to the selectivity of the test systems used for ELISA. If the ELISA system is not selective enough (not specific enough), it may erroneously identify antibodies in response to other infections, and not to the infection at hand. Many microorganisms are normally found in the human body and do not cause disease in usual circumstances.

The same is possible for PCR systems, although the chances are lower. If the system is not specific enough, it may erroneously identify the presence of a pathogen, "confusing" it with another related pathogens.

This situation of erroneous identification of a similar pathogen is called cross-reactivity.

Discrepancy in the biological material under study

PCR diagnostics can detect the DNA/RNA of the pathogen only in the tissues and body fluids in which it is located at the time when the material is collected for testing.

Positive results of both tests allow for a high degree of probability regarding the presence of an infectious disease, while negative results point to its absence. However, in any case, only the attending physician can make the final diagnosis.

Technical reasons

It should also be noted that any modern molecular analysis, no matter how advanced it is, is always dependent on the technical equipment of the laboratory and on the “human factor”. Inaccuracies in the process of collecting the material, transporting it, and preparing it for testing mean there is always a slight possibility for error. Be sure to use trustworthy certified laboratories to perform the testing.

When does it make sense to take tests to diagnose infectious diseases?

  • when clinical symptoms of the disease are present;
  • after contact with a source of infection (a sick person or carrier of the pathogen, be it a virus or bacteria);
  • after returning from places with an unfavorable epidemiological environment;
  • when preparing for trips to places with unfavorable epidemiological indicators (in order to identify antibodies and make a vaccination decision);
  • when preparing for pregnancy (in order to identify antibodies and decide for or against vaccination).

Advanced methods for molecular diagnosis of infectious diseases are the best way to protect yourself and your loved ones from many dangerous diseases and choose an effective treatment against them. The most important thing is your conscious approach to each situation.

After all, your health and the health of your loved ones is your own responsibility!

Lauer, S. A., K. H. Grantz, Q. Bi, F. K. Jones, Q. Zheng, H. R. Meredith, A. S. Azman, N. G. Reich and J. Lessler (2020). "The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application." Ann Intern Med.