Corona virus

SARS-CoV-2

Profile

SARS-CoV-2 (Severe acute respiratory syndrome coronavirus - type 2) is the causative agent of the infectious disease COVID-19 (Coronavirus Disease 2019). It is a single-stranded RNA virus and belongs to the beta-coronavirus family.

Occurrence

Worldwide

Pathogen reservoir

Various domestic, pet, and wild/zoo animal species, such as felines (including large cats such as tigers, lions, etc.), dogs, ferrets, tanuki, deer, golden hamsters, rabbits, and various primates (e.g., gorillas) can be infected with SARS-CoV-2. In all known cases of natural infection, it most likely occurred via infected humans. The severity of clinical signs ranges from asymptomatic to mild clinical signs, depending on the species affected (primarily felines and ferrets, as well as minks); according to current knowledge, animals play no role in the spread of infection. An exception is mink from commercial fur farms, where infection of exposed humans has been documented.

Currently, it is not considered necessary or advisable to separate from pets in case of infection of humans or animals.

Infection route

Transmission of SARS-CoV-2 occurs mainly via virus-containing particles that are excreted, for example, when infectious persons speak loudly, sing, or cough or sneeze. Aerosols (finest airborne liquid particles) and droplets play a crucial role in this process. Aerosols can remain suspended in the air for prolonged periods of time and disperse in inadequately ventilated indoor spaces, leading to infection.

The relative risk of environmental SARS-CoV-2 transmission through contaminated surfaces is considered low compared with direct contact, droplet transmission, or airborne transmission.

Incubation period

For earlier variants of SARS-CoV-2, an average of five to six days, in some cases up to 14 days.

For the omicron variant, the incubation period is often shorter, with estimates averaging three days

Symptomatology

The symptomatology of SARS-CoV-2 infections depends in its duration, frequency, and severity on the circulating variant, among other factors. The most common symptoms observed to date include: Fever, chills, and sore throat. Also common are cough, difficulty breathing, general symptoms such as fatigue and aching limbs, loss of smell and taste, nausea and vomiting, dizziness, and difficulty sleeping.

In more severe cases, the infection causes severe shortness of breath (at rest or when speaking), confusion, drowsiness or loss of consciousness, chest pain or pressure, and pale to bluish skin color, among other symptoms. Severe courses can lead to death.

There are also asymptomatic courses.

Infections with SARS-CoV-2 can have long-term consequences. A distinction is made between long-COVID and post-COVID (see the technical information). The symptoms can be of a physical and/or psychological nature. Frequently, a so-called "fatigue" is reported by those affected.

This list does not contain all possible symptoms, the course can be very different (see technical information). The symptoms vary depending on the SARS-CoV-2 variant and the immune status of the affected person.

Therapy

Treatment of mildly symptomatic patients without risk factors for a severe course is basically symptomatic, i.e., by alleviating the symptoms of the disease, e.g., by administering antipyretics.

For high-risk patients and patients with a severe course, various pharmaceutical agents are available (e.g., paxlovide, veklury, or corticosteroids).

The use of antibiotics is not recommended (unless there is a bacterial superinfection), as antibiotics are not effective against SARS-CoV-2.

Prevention

Vaccination, depending on the circulating variant and the timing and level of immunization, partially protects against infection and, in particular, against severe courses and death(ECDC: Public health control measures for COVID-19).

To protect against infection, it is recommended that hands be washed with soap and water or disinfected with an alcohol-based disinfectant several times a day. It is also recommended to ventilate indoor areas regularly and spend time outdoors whenever possible. To minimize the risk of infection, in addition to vaccination, WHO advises continuing to keep your distance and wearing a well-fitting mask if distance is not possible and the room is poorly ventilated. As a general rule, when sneezing, it is always advised to cover the mouth and nose with a cloth or bent elbow, not the hands.

These preventive measures generally reduce the risk of colds and are especially recommended when infection or hospitalization rates increase.

If symptoms appear, it is advised to stay at home and avoid contact.

Situation in Austria

By 30 June 2023, 6,084,529 cases had been reported in Austria. The graph on the development of the 7-day incidence shows the course of the pandemic from 28 February 2020. The peak of the 7-day incidence was reached in March 2022, with the most cases reported in one day on 15 March 2022 (63,468). Since 30 June 2023, COVID-19 is no longer a notifiable disease in Austria.

The SARI dashboard shows inpatient admissions to Austrian hospitals with diagnoses of Severe Acute Respiratory Infections (SARI). These include COVID-19, influenza, RSV and other severe respiratory diseases.

Variants in Austria

AGES is carrying out whole genome sequencing of SARS-CoV-2 positive samples in order to break down the spread of known variants and discover new SARS-CoV-2 variants.

BA.2.86 is the dominant variant in the samples sequenced in recent weeks. Within BA.2.86, the subline JN.1 accounts for the majority: of 12 BA.2.86 samples in week 0 6 (05.02.-11.02.2024), 11 could be assigned to JN.1. In CW 07, all four samples were JN.1. The other variants, XBB.1.5*, XBB.1.9.1*, XBB.1.9.2*, EG*, XBB.1.16*, and XBB.2.3* were only sporadically represented in the Austrian samples.

The number of samples has fallen sharply in recent weeks, so sequencing will be carried out monthly from February 2024 until further notice.

A detailed breakdown of the SARS-CoV-2 variants registered since the beginning of July 2023 can be found in the .csv file at the bottom of the page under "Downloads".

Percentage distribution of variants since the beginning of July 2023

7-day incidence over the entire course of the pandemic

Prozentuale Variantenverteilung der erfolgreich sequenzierten Stichproben bis 03.07.2023

International variants

The SARS-CoV-2 variants are categorised by the ECDC and the WHO into different categories, depending on how their characteristics and further development are assessed: Variant of Concern (VOC), Variant of Interest (VOI) and Variant under Monitoring (VUM). Currently, no variant is considered a "Variant of Concern".

At the WHO, the variants XBB.1.5 (incl. XBB.1.5 + L455F + F456L), XBB.1.16, BA.2.86, EG.5, BA.2.86 and JN.1 are categorised as VOI. In ECDC, XBB.1.5-like, "XBB.1.5-like with an F456L mutation" and BA.2.86 are declared as VOIs.

BA.2.86 circulated at an average of 93.4 % across Europe in calendar week 5. A large proportion of BA.2.86 cases are caused by the BA.2.86-derived subline JN.1.

The proportion of "XBB.1.5 variants with additional F456L mutation", which include EG.5, FL.1.5.1 and XBB.1.16.6, is decreasing in Europe. These "XBB.1.5 variants with additional F456L mutation" currently account for 1.7 %, averaged across the EU/EEA countries.

An overview of the exact categorisation can be found in the table below.

Variants under observation
Variant WHO ECDC
BA.2.86 VOI VOI
JN.1 VOI
BA.2.87.1 VUM
XBB* VUM
XBB.1.5* VOI VOI
XBB.1.5 + F456L VUM VOI
XBB.1.5 + L455F + F456L VOI VUM
XBB.1.9.1* VUM VOI
XBB.1.9.2* VUM VOI
EG.5 (XBB.1.9.2.5) VOI VOI
XBB.1.16* VOI
FE.1* (XBB.1.18.1.1*) VUM VOI
XBB.2.3 VUM VOI

VOC = Variant of Concern, VOI = Variant of Interest, VUM = Variant under Monitoring

Mutations repeatedly lead to a line splitting into several, slightly different lines. These are known as sublines. They are often given their own names and numbers, which means that the relationship is not always obvious (as in the case of subline FE.1, which belongs to XBB.1.18.1, see legend).

Legend:

VOC = Variant of Concern

VOI = Variant of Interest

VUM = Variant under Monitoring

* = Variant including associated sublines

BA.2.86 = B.1.1.529.2.86

JN.1 = BA.2.86 + S:L455S

BA.2.87.1 = B.1.1.529.2.87.1

XBB = recombinant from BA.2.10.1 + BA.2.75

XBB.1.5 = XBB + S:G252V, S:F486P

XBB.1.9 = XBB + S:G252V, S:408S, ORF1ab:G1819S, ORF1ab:T4175I, ORF8:G8

XBB.1.9.1 = XBB.1.9 + S:F486P

XBB.1.9.2 = XBB.1.9 + S:F486P, S:Q613H

EG.5 = XBB.1.9.2 + S: F456L; Incl. EG.5.1: EG.5 + S:Q52H

XBB.1.18.1 = XBB + S:G252V, A8001G, S:F486P

FE.1 = XBB.1.18.1 + S: F456L

XBB.2.3 = XBB + S:D253G, S:F486P, S:P521S

Specialized information

Symptomatology

Via entry into cells through the ACE2 receptor, manifestations are possible in all tissues where these receptors are present; the type and severity of manifestation depends, among other things, on the density of the receptors. In addition, in some cases there are exaggerated immune reactions and circulatory disturbances as a result of increased blood clotting.

Pulmonary manifestations are very common. In addition to colds, pneumonia can develop during the course of the disease, which can subsequently turn into Acute Respiratory Syndrome (ARDS). This may necessitate extracorporeal oxygen saturation by ECMO.

Neurologically, COVID-19 may manifest neuropsychiatrically in addition to headache, dizziness, and confusion; strokes, (meningo) encephalopathies, Guillain-Barré and Miller-Fisher syndromes also occur.

Cardiovascularly, myocardial damage, myocarditis, acute myocardial infarction, heart failure, cardiac arrhythmias, and various thromboembolic events resulting from the infection have been described.

Especially in severely ill COVID-19 patients, renal failure (requiring dialysis) may occur.

If hyperinflammatory syndromes occur, damage to various organs occurs as a consequence (multi-organ failure). The mortality is high(RKI - Coronavirus SARS-CoV-2 - Hyperinflammation Syndrome in COVID-19 (27.07.2020)).

Co-infections frequently occur, including with Mycoplasma pneumoniae, Candida albicans, and Aspergillus spp.

Known risk factors for a severe course include: Hypertension, diabetes mellitus, chronic liver and kidney damage, coronary artery disease, COPD (chronic obstructive pulmonary disease), cerebrovascular disease, regular use of immunosuppressive drugs, cancer, obesity, arrhythmias, and ischemic heart disease(see ECDC).

Infections with SARS-CoV-2 may involve long-term sequelae. A distinction is made between long-COVID and post-COVID. Long-COVID is when symptoms that occurred during the confirmed infection persist for more than four weeks after the onset of illness. Symptoms that do not appear until twelve weeks after the onset of the disease or reappear, persist for at least two months, and cannot be explained in any other way are referred to as post-COVID. The symptoms can be of a physical and/or psychological nature. Fatigue is frequently reported by those affected, as well as shortness of breath, concentration and memory problems, sleep disturbances, muscle weakness and muscle pain.

Therapy

The current therapy recommendations for the treatment of an infection with SARS-CoV-2 can be found here:

AWMF Guideline Register

RKI - Coronavirus SARS-CoV-2 - COVID-19: Therapy notes and recommendations

Diagnostic

Diagnosis of infection with SARS-CoV-2 is made by means of a secretion obtained from the upper respiratory tract, for example by means of a mouth or nasopharyngeal swab. Samples should be taken as close as possible to the onset of symptoms. The samples obtained can be used to perform rapid antigen tests, for which the result is usually available within ten to 30 minutes. The most reliable detection method is PCR testing for SARS-CoV-2 RNA. Saliva samples can also be examined by PCR; antigen tests are too unspecific here.

In hospitalized patients, secretions from the lower respiratory tract can be obtained for PCR diagnosis.

Blood tests for the detection of SARS-CoV-2 antibodies can detect infections that have already occurred, but are not important for acute diagnostics. The test for antibodies may also be positive as a result of previous vaccination. A negative result does not exclude a previous infection with SARS-CoV-2, as the number of antibodies decreases again with time.

Last updated: 27.02.2024

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