Guidance

COVID-19: epidemiology, virology and clinical features

Updated 17 May 2022

Who this information is for

This page contains information for professionals and the public on the epidemiology, virology and clinical features of coronavirus (COVID-19), the infection caused by SARS-CoV-2.

Epidemiology

On 31 December 2019, the World Health Organization (WHO) was informed of a cluster of cases of pneumonia of unknown cause detected in Wuhan City, Hubei Province, China. On 9 January 2020, it was announced that a novel coronavirus had been identified in samples obtained from these cases and initial analysis of virus genetic sequences suggested that this was the cause of the outbreak.

In February 2020 this new virus was formally named as SARS-CoV-2, and the disease caused by it was named COVID-19, in line with best practice guidance. On 11 March 2020 WHO declared the COVID-19 outbreak a global pandemic due to the rapid spread and severity of cases around the world.

Scientific consensus is that SARS-CoV-2 is zoonotic in origin, however the source of the original outbreak is yet to be determined. An intermediate host between the source and intoduction into humans has been considered to be ‘likely to very likely’, and investigations are ongoing. For further information see the report from the WHO-convened Global Study of the Origins of SARS-CoV-2 virus.

The WHO coronavirus dashboard provides information on cases, deaths and vaccine doses administered internationally. WHO also publishes weekly international epidemiological and operational updates.

A summary of key information about the COVID-19 pandemic is published on a dashboard on GOV.UK.

Virology and characterisation

Coronaviruses are a large family of related viruses that cause diseases in animals and humans. Some cause less severe disease, such as the common cold, and others cause more severe disease, such as Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS). They are a different family of viruses to the influenza viruses that cause seasonal influenza.

SARS-CoV-2 is genetically related to the coronavirus responsible for the SARS outbreak of 2003 (SARS-CoV) and to viruses that have been isolated from bat populations. It is less closely related to the coronavirus responsible for MERS (MERS-CoV).

The 2019 emergent SARS-CoV-2 strain, usually referred to as the original or ‘wild- type’ strain has mutated over time. These mutations have given rise to new variants. Variants of the SARS-CoV-2 virus are being monitored across the globe.

Most of these mutations have little effect. Where mutations have the potential to increase how easily the virus spreads, escapes immunity or causes more severe disease, the variant is designated a variant of concern (VOC).

On 31 May 2021, the WHO recommended a naming system for SARS-CoV-2 variants that uses the Greek alphabet. The UK Health Security Agency (UKHSA) incorporates this recommended naming system in its surveillance of SARS-CoV-2 variants, and releases weekly information on SARS-CoV-2 variants.

Transmission

When someone with COVID-19 breathes, speaks, coughs or sneezes, they release droplet and aerosol particles containing SARS-CoV-2 virus. SARS-CoV-2 is primarily transmitted between people through these infectious respiratory particles (droplet and aerosol) when they are inhaled, or come into contact with the eyes, nose or mouth. Aerosol generating procedures (AGPs) can result in the release of aerosols from the respiratory tract when these are performed in health and care settings. Transmission risk is highest in close proximity to an infectious person (particularly within 2 metres). The number of infectious respiratory particles is greatest close to the nose and mouth. Being in poorly ventilated indoor spaces, particularly for an extended period of time, also increases the risk of becoming infected.

Indirect transmission can occur through contact with surfaces contaminated with the virus (fomite transmission); the relative risk is likely to be lower than other routes of exposure, however this route may still be important in higher risk settings.

The risk of transmission in a specific setting depends on factors including:

• contact patterns, such as the proximity, number of contacts, and duration of contact with other people
• individual infectiousness and susceptibility, including viral load and immune status
• activities taking place in the setting, for example singing or exercising, which increase the volume and propulsion of respiratory particles
• environmental factors, including ventilation

Once an individual has been infected, SARS-CoV-2 viral load has been shown to peak in the upper respiratory tract within the first week after symptom onset, and later in the lower respiratory tract. Contact tracing studies show that the highest risk of transmission occurs a few days before and within the first 5 days after symptom onset. Infected individuals who are pre-symptomatic and asymptomatic can still transmit virus to others, and viral loads at the start of infection appear similar between those who are asymptomatic and those who are symptomatic.

After 10 days from symptom onset or a positive test result, the likelihood of infectiousness is low in individuals who are not immunocompromised. Fragments of inactive virus may however be detected by PCR in respiratory tract samples following infection for prolonged periods (frequently up to 90 days, sometimes beyond) when the individual is no longer infectious.

It is possible for humans to transmit SARS-CoV-2 to other mammals including dogs, cats, and farmed mink. The risk of transmission from mammals to humans is likely to be low, however this varies by species.

Disease course and clinical features

The incubation period for SARS-CoV-2 varies according to the circulating variant. The mean incubation period for wild type and the Alpha variant was around 5 to 6 days (ranging from 0 to 14 days), whereas the mean incubation period for the Delta and Omicron variants have been found to be shorter, at around 4 days (ranging from 3 to 5 days) and 3 days (ranging from 0 to 8 days) respectively.

COVID-19 presents with a range of symptoms with varying severity. It is estimated that 1 in 3 people have COVID-19 without displaying any symptoms.

The main symptoms of COVID-19 include fever, a new and continuous cough, anosmia (loss of smell) and ageusia (loss of taste). Examples of other symptoms include shortness of breath, fatigue, loss of appetite, myalgia (muscle ache), sore throat, headache, nasal congestion (stuffy nose), runny nose, diarrhoea, nausea and vomiting. Atypical symptoms, such as delirium and reduced mobility, can present in older and immunocompromised people, often in the absence of a fever.

Data relating to the initial wild type variant demonstrated that most people with symptomatic COVID-19 developed mild (40%) or moderate (40%) disease. Approximately 15% developed severe disease requiring oxygen support, and 5% had critical disease with complications such as respiratory failure, acute respiratory distress syndrome (ARDS), sepsis and septic shock, thromboembolism, and/or multi-organ failure, including acute kidney injury and cardiac injury.

The severity of illness with successive strains has differed, with decreasing case fatality rates and risk of hospitalisation observed in Delta and Omicron variants compared with Alpha and earlier variants.

The observed reduction in risk of severe illness and hospitalisation is likely to be, and will continue to be, due to a combination of a reduction in intrinsic severity of the virus, and other factors such as protection provided by prior natural infection, vaccination, and the availability and use of therapeutics.

Risk of severe disease is influenced by factors such as age, obesity, ethnicity, and the SARS-CoV-2 variant causing infection. Risk of severe disease and death from COVID-19 is higher in people who are older, male, from deprived areas or from certain non-white ethnic backgrounds. Certain underlying health conditions, as well as obesity, also increase risk of severe disease and death in adults.

Infants and children generally appear to experience milder symptoms than adults and require admission to hospital less frequently. The risk of death in children is extremely low and appears to be linked to severe co-morbidities. There are a number of ongoing surveillance programmes to monitor the course, progression and outcomes of COVID-19 in children. A very rare multisystem inflammatory response in children and adolescents (paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 (PIMS-TS) or multisystem inflammatory syndrome in children (MIS-C)) has been noted.

There is growing evidence to suggest that individuals who have suffered from both mild or severe COVID-19 can experience prolonged symptoms or develop long-term effects. Refer to NICE guidance on managing the long-term effects of COVID-19 for further information.

Further information on the management of COVID-19 is available in NICE guidance.

Vaccination

The first vaccine for COVID-19 was approved for use by the Medicines and Healthcare products Regulatory Agency (MHRA) in the UK on 2 December 2020. A further 3 have now been added to the list of approved vaccines. COVID-19 vaccination has been shown to reduce the risk of infection, severe illness, hospitalisation and death. However, fully vaccinated individuals can still become infected with SARS-CoV-2 and transmit the infection to other people.

Vaccine effectiveness (VE) data is continuously monitored and is important for surveillance and monitoring of SARS-CoV-2 variants. Estimates for VE have changed over time and with the emergence of new variants of SARS-CoV-2. Overall, these data have shown that 2 doses of vaccine provide a level of protection against symptomatic disease, hospitalisation and death, however the observed waning effect after 2 doses over time has necessitated the introduction of the booster programme for optimal protection.

For further information on the effectiveness of vaccines in England see UKHSA vaccine surveillance reports and the variant technical briefings.