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 30.06.2023, 6,084,529 cases were reported in Austria. The graph on the development of the 7-day incidence shows the course of the pandemic from 28.02.2020. The peak of the 7-day incidence was reached in March 2022, the most cases in one day were reported on 15.03.2022 (63,468). As of 06/30/2023, COVID-19 is no longer a reportable 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 illnesses.

7-Tage-Inzidenz im gesamten Pandemieverlauf

Variants in Austria

AGES performs whole genome sequencing of SARS-CoV-2 positive samples to dissect the distribution of known variants and to discover new SARS-CoV-2 variants. Due to the current very low volume of SARS-CoV-2 positive samples, a representative representation of variant distribution as shown in the graph below is not reasonably possible for the time being. The samples received will of course continue to be subjected to whole genome sequencing. Should sufficient SARS-CoV-2 positive samples be submitted, the graph on the variant situation will be updated.

Ergebnisse der AGES Ganzgenomsequenzierung seit 03.07.2023

Prozentuale Variantenverteilung der erfolgreich sequenzierten Stichproben bis 03.07.2023

Varianten international

Das ECDC hat am 14.09.2023 einen Überblick der Variantenlage in den europäischen Ländern veröffentlicht. Bei den 14 EU-Ländern, die für die Kalenderwochen 34 bis 35 (21. August bis 3. September 2023) mindestens zehn Ergebnisse der SARS-CoV-2-Sequenzierung meldeten, waren die „Variants of Interest“ (VOI) folgendermaßen verteilt: 60,6 % waren XBB.1.5-Varianten, die zusätzlich eine F456L-Mutation aufweisen; 35,2 % entfielen auf andere XBB.1.5-Varianten, 2,8 % auf BA.2.75 und 1,1 % auf XBB.

Das aktuellste „Weekly epidemiological update“ der WHO zu COVID-19 wurde am 01.09.2023 veröffentlicht: In den weltweit in KW 32 (07.08. bis 13.08.2023) gemeldeten Daten ist EG.5 nun mit 26,1 % an der Gesamtprävalenz die am häufigsten vorkommende Variante. EG.5 hat damit XBB.1.16 überholt, deren Anteil seit KW 32 stabil bei 22,7 % liegt. EG.5 und XBB.1.16 wurden aus 109 bzw. 57 Ländern gemeldet.  XBB.1.5* weist weiterhin einen abnehmenden Trend auf und hatte in KW 32 weltweit einen Anteil von 10,2 %. Die Prävalenz von XBB.1.9.1* liegt in KW 32 bei 13,2 %. Die Prävalenz von XBB.1.9.2 ist auf 4,6 % gesunken. XBB.2.3* hat einen Anteil von 5,5 % an der Gesamtprävalenz. Andere XBB‑Sublinien hatten einen Anteil von 5,0 %. Der Anteil der BA.2.75‑Sublinie CH.1.1* betrug 0,8 %, andere BA.2.75-Sublinien machten etwa 0,9 % aus. 10,7 % der Sequenzen entfielen auf Linien, die keiner VUM oder VOI angehören und auch nicht von den Omikron­Linien BA.1­BA.5 abstammen.

EG.5 wurde von der WHO am 09.08.2023 auf eine VOI hinaufgestuft. EG.5 ist eine Sublinie von XBB.1.9.2 mit einer zusätzlichen Mutation, F456L, am Spike Protein. Basierend auf der bisher vorliegenden Evidenz wird das Public Health Risiko von EG.5 auf globalem Level als niedrig eingestuft. EG.5 zeigt eine zunehmende Prävalenz, einen Wachstumsvorteil und Immunflucht-Eigenschaften. Veränderungen in der Krankheitsschwere wurden bisher nicht gemeldet.

Das ECDC hat alle XBB.1.5-ähnlichen Linien mit zusätzlicher Spike Protein Mutation F456L als VOI eingestuft. Zu diesen XBB.1.5-ähnlichen Linien mit zusätzlicher Spike Protein Mutation F456L zählen, unter anderem, EG.5, FL.1.5.1, XBB.1.16.6 und FE.1. Grund für diese Einstufung ist der schnelle proportionale Anstieg dieser Linien im EU/EEA-Raum zusammen mit einer leichten Zunahme der epidemiologischen Indikatoren. Zudem konnte dieser Mutation in in‑vitro Studien eine erhöhte Immunflucht im Vergleich zu früheren Varianten nachgewiesen werden. Das ECDC hat daher die ganze F456L-Gruppe hervorgehoben, da auch andere Linien innerhalb der Gruppe genauso wie EG.5 erhöhte Wachstumsraten aufweisen. Bisher erfüllen die F456L-Varianten nicht die Kriterien für eine Variant of Concern, da u.a. weder von schwereren Krankheitsverläufen noch von einer reduzierten Impfeffektivität ausgegangen wird.

Am 17.08.2023 hat die WHO BA.2.86 zu einer Variant Under Monitoring ernannt. ZZu BA.2.86 liegen bisher weltweit 146 Sequenzen aus 17 Ländern vor. In Europa stammen die meisten Meldungen aus dem Vereinigten Königreich, Schweden und Dänemark (Quelle: GISAID, Stand 19.09.2023). Bisher sind in den gemeldeten BA.2.86-Fällen keine Todesfälle aufgetreten. Die Schweiz hat BA.2.86 in Abwasserproben detektiert. Die Einstufung als VUM wird dadurch begründet, dass die Variante mehr als 30 Mutationen am Spike Protein trägt. Die potenziellen Auswirkungen dieser Mutationen sind derzeit noch unbekannt und werden einer sorgfältigen Beurteilung unterzogen. Die WHO ruft weiterhin zu einer besseren Surveillance, Sequenzierung und Berichterstattung von COVID-19 auf, da dieses Virus weiterhin zirkuliert und sich weiterentwickelt.

Variants under observation
Variant WHO ECDC
BA.2.75* VUM VOI
CH.1.1* VUM VUM/VOI
BA.2.86 VUM VUM
XBB* VUM
XBB.1.5* VOI VOI
XBB.1.5 + F456L VOI
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 VUM
FE.1* (XBB.1.18.1.1*) VUM VOI
XBB.2.3 VUM VOI
BQ.1* VOI

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

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

Legend:

* = variant including associated sublines

BQ.1 = BA.5 + S:K444T, S:N460K

BA.2.75 = BA.2 + S:K147E, S:W152R, S:F157L, S:I210V, S:G257S, S:G339H, S:G446S, S:N460K, S:R493Q

CH.1.1 = BA.2.75 + S:L452R, S:R346T, S:K444T, S:F486S

XBB = recombinant of 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.1.16 = XBB + S:E180V, S:K478R, S:S486P, ORF9b:I5T, ORF9b:N55S

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: 19.09.2023

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