Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a previously unknown betacoronavirus that was discovered in bronchoalveolar lavage samples taken from clusters of patients who presented with pneumonia of unknown cause in Wuhan City, Hubei Province, China, in December 2019.
Coronaviruses are a large family of enveloped RNA viruses, some of which cause illness in people (e.g., common cold, severe acute respiratory syndrome [SARS], Middle East respiratory syndrome [MERS]), and others that circulate among mammals and birds. Rarely, animal coronaviruses can spread to humans and subsequently spread between people, as was the case with SARS and MERS.
SARS-CoV-2 belongs to the Sarbecovirus subgenus of the Coronaviridae family, and is the seventh coronavirus known to infect humans. The virus has been found to be similar to SARS-like coronaviruses from bats, but it is distinct from SARS-CoV and MERS-CoV. The full genome has been determined and published in GenBank. GenBank external link opens in a new window
All viruses, including SARS-CoV-2, change over time. Over 665,000 variants of the virus have been sequenced by the COVID-19 Genomics UK Consortium (COG-UK) as of 20 July 2021. COG-UK: data external link opens in a new window
The World Health Organization has introduced new easy-to-pronounce and non-stigmatising labels for SARS-CoV-2 variants based on the Greek alphabet. WHO: tracking SARS-CoV-2 variants external link opens in a new window
SARS-CoV-2 variants of concern (VOC) include the following.
Alpha (VOC-20DEC-01; B.1.1.7 lineage): first identified in Kent, South East of England in September 2020, and reported to the World Health Organization in December 2020. The origin is unclear. The variant has been reported in at least 137 countries, and community transmission has been reported in 35 of these countries (as of 19 April 2021). There is evidence that suggests this variant may be more transmissible. Secondary attack rates have been reported to be higher if the index case has this variant. The reported secondary attack rate is 10.2% in household contacts of people with the variant (who have not travelled). However, secondary attack rates for non-variant forms are known to vary quite widely (see Secondary attack rate below). The variant appears to be associated with an increased risk of hospitalisation and intensive care unit admission (suggesting more severe disease), but not mortality, compared with the wild-type virus, although data are conflicting. The variant was not associated with changes in symptoms reported or their duration. There is consistent evidence of cross-neutralising activity in convalescent sera (i.e., sera from individuals who have been infected with B.1.1.7 shows neutralising activity against viruses from other lineages, and the converse is also true). There is evidence that there is no increase in reinfection rate, and that vaccine performance is preserved against this variant. The variant has mutations that have been associated with attenuation in other variants.
Beta (VOC-20DEC-02; B.1.351 lineage): first detected in Nelson Mandela Bay, South Africa in October 2020. The variant has been reported in at least 97 countries, including the UK (as of 19 April 2021). The variant has similar spike protein mutations to the B.1.1.7 lineage. Sequence analysis reveals that the N501Y mutation reported in the UK and South Africa originated independently. These mutations may affect its transmissibility and antigenic profile.
Gamma (VOC-21JAN-02; P.1 lineage): a descendant of the B.1.1.28 lineage first detected in Japan in travellers from Brazil. The variant has been reported in at least 55 countries (as of 19 April 2021), including the UK. Based on modelling and laboratory data, it is plausible that there is some degree of immune escape, or increased transmissibility, or both with this variant. However, the magnitude and clinical significance of these effects are yet to be determined.
Delta (VOC-21APR-02; B.1.617.2): first identified in India in April 2021. It is now the dominant variant in the UK. There are also a small number of cases of the Delta variant with a K417N mutation (AY.1 lineage). Preliminary evidence suggests that this variant is likely to be more transmissible than the B.1.1.7 variant based on available data. The secondary attack rate among household contacts of cases that have not travelled is 10.9% (as of 5 July 2021), and the rate has been decreasing. This is slightly higher compared with the B.1.1.7 variant, which is currently 10.2% among household contacts of cases that have not travelled (see above). An increase in cases has not been associated with a similar proportional increase in hospitalisations or deaths in the UK. This variant has been reported in many countries around the world. The crude case fatality rate is estimated to be 0.2%, with the majority of deaths occurring in people aged 50 years and older (as of 5 July 2021). Emerging evidence suggests that current vaccines may be effective against the variant after two doses, but with reduced efficacy after one dose. Efficacy is comparable to vaccine efficacy against hospitalization from the Alpha variant, but may be less effective against infection compared with the Alpha variant. Data on this variant are still evolving.
Epsilon (B.1.427 and B.1.429 lineages): first detected in California in the US, these variants have been classified as variants of concern by the US Centers for Disease Control and Prevention, but not the World Health Organization or Public Health England. They may have an increased risk of transmission, may cause more severe disease, and may not be as responsive to certain treatments; however, data are limited.
Further investigations are required to more fully understand the impact of these variants. There are many other variants under investigation.
Origin of virus
A majority of patients in the initial stages of this outbreak reported a link to the Huanan South China Seafood Market, a live animal or ‘wet’ market, suggesting a zoonotic origin of the virus. An initial assessment of the transmission dynamics in the first 425 confirmed cases found that 55% of cases before 1 January 2020 were linked to the market, whereas only 8.6% of cases after this date were linked to the market. This suggests that person-to-person spread was occurring among close contacts since the middle of December 2019.
Some studies suggest that SARS-CoV-2 may be a recombinant virus between a bat coronavirus and an origin-unknown coronavirus. Pangolins and minks have been suggested as possible intermediate hosts. However, there is currently no evidence to demonstrate the possible route of transmission from a bat reservoir to human through one or several intermediary animal species. Further research is required to determine the origin of SARS-CoV-2.
More recent studies suggest that the virus may have emerged earlier than previously thought.
Respiratory transmission is the dominant mode of transmission, with proximity and ventilation being the key determinants of transmission risk. Available evidence suggests that transmission between people occurs primarily through direct, indirect, or close contact with infected people through infected secretions such as saliva and respiratory secretions, or through their respiratory droplets, which are expelled when an infected person coughs, sneezes, talks, or sings.
Airborne transmission can occur in healthcare settings during aerosol-generating procedures. There are also some outbreak reports that suggest aerosol transmission is possible in the community under certain conditions; however, these reports relate to enclosed indoor crowded spaces with poor ventilation where the infected person may have been breathing heavily (e.g., restaurants, choir practice, fitness classes). A detailed investigation of these clusters suggests that droplet and fomite transmission could also explain the transmission in these reports. While the air close to, and distant from, patients has been found to frequently be contaminated with SARS-CoV-2 RNA, few of these samples contained viable virus. The risk of transmission is much lower outdoors compared with indoors, with a limited number of studies estimating a transmission rate of <1%. Evidence that nebuliser treatments increase the risk of transmission of coronaviruses similar to SARS-CoV-2 is inconclusive, and there is minimal direct evidence about the risk for transmission of SARS-CoV-2.
Fomite transmission (from direct contact with fomites) may be possible, but there is currently no conclusive evidence for this mode of transmission. In the few cases where fomite transmission has been presumed, respiratory transmission has not been completely excluded. While the majority of studies report identification of the virus on inanimate surfaces, there is a lack of evidence to demonstrate recovery of viable virus. The virus has been found to be more stable on plastic and stainless steel (up to 72 hours) compared with copper (up to 4 hours) and cardboard (up to 24 hours) under experimental conditions, but this does not reflect real-life conditions.
Faecal-oral transmission (or respiratory transmission through aerosolised faeces) may be possible, but there is only limited circumstantial evidence to support this mode of transmission. The pooled detection rate of faecal SARS-CoV-2 RNA in patients with COVID-19 is approximately 51%, with 64% of samples remaining positive for a mean of 12.5 days (up to 33 days maximum) after respiratory samples became negative.
Transmission via other body fluids (including sexual transmission or bloodborne transmission) has not been reported. While the virus has been detected in blood, cerebrospinal fluid, pericardial fluid, pleural fluid, urine, semen, saliva, ocular tissue including the cornea, tears, and conjunctival secretions, as well as in the middle ear and mastoid, the presence of virus or viral components does not equate with infectivity. While SARS-CoV-2 is not sexually transmitted, it may have an effect on male fertility, although this is yet to be confirmed.
Vertical transmission occurs rarely and transplacental transmission has been documented. There is limited evidence on the extent of vertical transmission and its timing. Overall, 6.3% of infants born to mothers with COVID-19 tested positive for SARS-CoV-2 at birth. Transmission was reported in both preterm and full-term infants. There is also evidence for antibodies against SARS-CoV-2 among infants born to mothers with COVID-19 who tested negative for SARS-CoV-2. The rate of infection appears to be no greater when the baby is born vaginally, breastfed, or allowed contact with the mother. Viral fragments have been detected in breast milk; however, this finding is uncommon and, when it occurs, has been associated with mild symptoms in infants. Anti-SARS-CoV-2 antibodies are more prevalent in breast milk compared with viral fragments. Vertical transmission is unlikely to occur if correct hygiene precautions are taken.
Nosocomial transmission was reported in 44% of patients in one systematic review; however, this review was limited to case series conducted early in the outbreak in Wuhan before the institution of appropriate infection prevention and control measures. Hospital-acquired infections (defined as patients diagnosed more than 7 days after hospital admission) accounted for approximately 17% of infections in the NHS England as of 26 October 2020, and rates have been as high as 25% in some areas. Studies of healthcare workers exposed to index cases (not in the presence of aerosol-generating procedures) found little to no nosocomial transmission when contact and droplet precautions were used.
Transmission dynamics in relation to symptoms
Transmission appears to mainly be spread via droplets and close contact with infected symptomatic cases. Transmissibility depends on the amount of viable virus being shed and expelled by a person (viral load is highest just before or around the time of symptom onset and during the first 5-7 days of illness), the type of contact, the setting, and what infection prevention and control measures are in place.
Transmission from asymptomatic cases (laboratory-confirmed cases who never develop symptoms) has been reported; however, most of the evidence is based on early data from China and has limitations (e.g., small number of cases, cases may have been presymptomatic). The World Health Organization states that asymptomatic cases are not the major driver of the overall epidemic dynamics. Numerous studies have reported no evidence of asymptomatic transmission from carriers of SARS-CoV-2. In a post-lockdown screening study in nearly 10 million residents in Wuhan, there were no positive tests among 1174 close contacts of asymptomatic cases. In addition to this, virus culture was carried out on samples from asymptomatic positive cases and all cultures were negative, indicating that asymptomatic positive cases in the study were not infectious.
Estimating the prevalence of asymptomatic cases in the population is difficult. A meta-analysis of over 50,000 people found that 15.6% of confirmed cases were asymptomatic at the time of testing (range 2% to 75%), and nearly half developed symptoms later. The overall estimate of the proportion of people who become infected and remain asymptomatic throughout infection has been estimated to be 17% to 33%.
Healthcare workers may play a role in asymptomatic transmission. About 7.6% of healthcare workers who worked in hospital units with infected patients tested positive for SARS-CoV-2 antibodies; however, only 58% of these workers reported prior symptoms. A cross-sectional study of nearly 2800 healthcare workers found that 5.4% of COVID-19-facing asymptomatic healthcare workers tested positive, compared with 0.6% of non-COVID-19-facing asymptomatic healthcare workers.
Children are more likely to be asymptomatic. The pooled proportion of asymptomatic cases in children was thought to be significant (around 40%). However, recent studies have found that the rate of asymptomatic infection in children was very low (1% compared with 9% in adults in one study, and 0.6% compared with 1.8% in adults in another study), indicating that children appear not to be particular drivers of the pandemic.
Superspreading events have been reported. These events are associated with explosive growth early in an outbreak and sustained transmission in later stages.
Reported events include church/religious gatherings, family or social gatherings, weddings, choir practices, overnight youth camps or high school retreats, fitness classes, indoor recreational sporting activities, business conferences, and working in call centres. Widespread transmission has also been reported in long-term care facilities, homeless shelters, prisons, immigration detention centres, and meat and poultry processing facilities, as well as on board cruise ships.
Limited transmission has been reported in childcare, school, and university settings, and infected cases may transmit the infection to their household members. There is limited high-quality evidence to quantify the extent of transmission in schools, or to compare it with community transmission. However, emerging evidence suggests a lower overall infection attack rate in students (0.15%) compared with school staff (0.7%).
Some individuals are supershedders of virus, but the reasons underlying superspreader events are often more complex than just excess virus shedding and can include a variety of behavioural, host, and environmental factors.
Viral transmission factors
Reproduction number (R₀)
Reports suggest that the reproduction number, the number of people who acquire the infection from an infected person, is estimated to be 2.2 to 3.3. However, there is very high heterogeneity across studies and the number varies between countries. The US Centers for Disease Control and Prevention gives a current best estimate of 2.5 (as of 19 March 2021).
The R₀ decreases when public health measures (e.g., social distancing) are put in place.
The time between the start of symptoms in the primary patient and the onset of symptoms in the patient being infected in a chain of transmission has been estimated to be approximately 5.45 days (range 4.2 to 6.7 days).
Secondary attack rate
The secondary attack rate is the proportion of people exposed to an index (or primary) case that go on to develop the disease as a result of the exposure.
The pooled secondary attack rate among all close contacts of an index case has been estimated to be 7%.
The secondary attack rate differs between contact settings. More familiar prolonged contact increases the potential for transmission. Pooled estimates of the secondary attack rate range from 1.2% to 5.9% in social settings (depending on level of contact and whether contact is with strangers or family and friends), 1.9% in workplaces (based on limited data), 3.6% in healthcare facilities, and 21.1% for household settings (increases with exposure >5 days).
Another systematic review and meta-analysis of household transmission estimates the pooled household secondary attack rate to be slightly lower at 16.6%. The rate is higher for symptomatic index cases (18%) compared with asymptomatic cases (0.7%), and adults have a higher susceptibility to infection compared with children. Spouses of the index case are more likely to be infected compared with other household members.
The secondary attack rate increases with the severity of the index case (i.e., 0.3% for asymptomatic cases to 6.2% for severe/critical cases) according to a study of 3410 close contacts of 391 index cases.
The secondary attack rate for close contacts of presymptomatic people has been estimated to be approximately 7%, compared with 1% in asymptomatic people and 6% in symptomatic people.
Children aged <5 years had lower secondary attack rates compared with older children, and the risk of infection was higher if the household index case was the mother. The secondary attack rate was 1.2% in children in a childcare setting or school.
Secondary attack rates for SARS-CoV-2 variants may differ (see Emerging SARS-CoV-2 variants above).
Viral load is highest in the upper respiratory tract (nasopharynx and oropharynx) early in the course of infection (usually peaks in the first week of illness), and then increases in the lower respiratory tract (sputum). Viral load decreases after symptom onset. Patients with severe disease have higher viral loads compared with those with mild disease. Viral load in the upper respiratory tract is comparable in asymptomatic and symptomatic patients; however, most studies demonstrate faster viral clearance among asymptomatic people compared with symptomatic people.
Viral load appears to be a leading driver of virus transmission. In one cohort study, the secondary attack rate was 17% among 753 contacts of index cases, with a variation from 12% when the index case had a viral load lower than 1x10⁶ copies/mL to 24% when the index case had a viral load of 1x1010 copies/mL or higher (in nasopharyngeal swabs). Higher viral loads in swabs of asymptomatic contacts were associated with a higher risk of developing symptomatic disease, and these contacts had shorter incubation periods than those with a lower viral load.
The mean duration of shedding was 17 days in the upper respiratory tract, 14.6 days in the lower respiratory tract, 17.2 days in stool, and 16.6 days in serum samples. The maximum duration of shedding was 83 days in the upper respiratory tract, 59 days in the lower respiratory tract, 126 days in stool, and 60 days in serum samples. However, no live virus was detected beyond day 9 of symptoms, despite persistently high viral loads. Duration of viral shedding was longer in symptomatic patients compared with asymptomatic patients, and in patients with severe illness compared with those with non-severe illness.
The period of infectiousness is far shorter than the duration of detectable viral shedding. No viable virus has been isolated in patients with mild or moderate disease after 10 days of symptoms, or after 20 days in those with severe or critical disease, despite ongoing viral shedding. Data about the dynamics of viral shedding in people with persistent asymptomatic infection are inconsistent. There is no convincing evidence that duration of viral shedding correlates with duration of infectivity.
Factors associated with prolonged viral shedding include male sex, older age, comorbid hypertension, delayed admission to hospital after symptom onset or severe illness on admission, and use of invasive mechanical ventilation or corticosteroids. Immunocompromised patients may shed for at least 2 months.
The pathophysiology resembles that of other coronavirus infections. However, emerging evidence indicates that COVID-19 has distinctive pathophysiological features that set it apart from respiratory failure of other origins.
SARS-CoV-2 attaches to the angiotensin-converting enzyme-2 (ACE2) receptor on target host cells, followed by internalisation and replication of the virus. ACE2 receptors are highly expressed in the upper and lower respiratory tract cells, but are also expressed in myocardial cells, renal epithelial cells, enterocytes, and endothelial cells in multiple organs, which may explain the extrapulmonary manifestations associated with the disease. The virus uses host transmembrane protease serine 2 (TMPRSS2) for viral spike protein priming and fusion of viral and host cell membranes. The SARS-CoV-2 spike protein plays a key role in the recognition of the ACE2 receptor and cell membrane fusion process. A unique structural feature of the spike glycoprotein receptor-binding domain confers potentially higher binding affinity for ACE2 on host cells compared with SARS-CoV-1. This furin-like cleavage site does not appear to exist in other coronaviruses. The binding energy between the spike protein and ACE2 was highest for humans out of all species tested in one study, suggesting that the spike protein is uniquely evolved to bind to and infect human cells expressing ACE2. Emerging evidence suggests that the spike protein alone may damage endothelial cells by downregulating ACE2 and consequently inhibiting mitochondrial function. Further research is required on whether the spike protein can by itself trigger cell signalling that could lead to various biological processes. SARS-CoV-2 variants may be more transmissible, at least in part, due to enhanced spike protein binding affinity for the ACE2 receptor.
In addition to direct cytopathic viral injury, severe disease is frequently complicated by an infection-induced microangiopathy or hypercoagulable state that causes capillary, venous, and/or arterial thrombosis, which may lead to end-organ damage due to distant thrombotic or embolic disease. The predominant pathological findings in fatal cases were diffuse alveolar damage, coagulopathy, and haemodynamic compromise. Involvement of non-pulmonary organs was limited to mild parenchymal inflammation (e.g., myocarditis, hepatitis, encephalitis). Direct viral cytopathic injury of extrapulmonary organs in general was not regarded as the cause of organ failure. SARS-CoV-2-induced endotheliitis may play a role in both the respiratory and non-respiratory manifestations.
World Health Organization: COVID-19 disease severity
Symptomatic patients meeting the case definition for COVID-19 without evidence of hypoxia or pneumonia.
Common symptoms include fever, cough, fatigue, anorexia, dyspnoea, and myalgia. Other non-specific symptoms include sore throat, nasal congestion, headache, diarrhoea, nausea/vomiting, and loss of smell/taste. Additional neurological manifestations reported include dizziness, agitation, weakness, seizures, or findings suggestive of stroke. Children may not report fever or cough as frequently as adults.
Older people and immunosuppressed people may present with atypical symptoms (e.g., fatigue, reduced alertness, reduced mobility, diarrhoea, loss of appetite, delirium, absence of fever).
Symptoms due to physiological adaptations of pregnancy or adverse pregnancy events (e.g., dyspnoea, fever, gastrointestinal symptoms, fatigue) or other diseases (e.g., malaria) may overlap with COVID-19 symptoms.
Adolescent or adult: clinical signs of pneumonia (i.e., fever, cough, dyspnoea, fast breathing) but no signs of severe pneumonia, including blood oxygen saturation levels (SpO₂) ≥90% on room air.
Children: clinical signs of non-severe pneumonia (i.e., cough or difficulty breathing plus fast breathing and/or chest indrawing) and no signs of severe pneumonia. Fast breathing is defined as:
<2 months of age: ≥60 breaths/minute
2-11 months of age: ≥50 breaths/minute
1-5 years years of age: ≥40 breaths/minute.
While the diagnosis can be made on clinical grounds, chest imaging may assist in diagnosis and identify or exclude pulmonary complications.
Adolescent or adult: clinical signs of pneumonia (i.e., fever, cough, dyspnoea, fast breathing) plus one of the following:
Respiratory rate >30 breaths/minute
Severe respiratory distress
SpO₂ <90% on room air.
Children: clinical signs of pneumonia (i.e., cough or difficulty in breathing) plus at least one of the following:
Central cyanosis or SpO₂ <90%
Severe respiratory distress (e.g., fast breathing, grunting, very severe chest indrawing)
General danger signs: inability to breastfeed or drink, lethargy or unconsciousness, or convulsions
Fast breathing (<2 months: ≥60 breaths per minute; 2-11 months: ≥50 breaths per minute; 1-5 years: ≥40 breaths per minute).
While the diagnosis can be made on clinical grounds, chest imaging may assist in diagnosis and identify or exclude pulmonary complications.
Presence of acute respiratory distress syndrome (ARDS), sepsis, septic shock, acute thrombosis, or multisystem inflammatory syndrome in children.
National Institutes of Health: clinical classification of COVID-19
Asymptomatic or presymptomatic infection
People who test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using a virological test but have no symptoms consistent with COVID-19.
People who have any of various signs and symptoms (e.g., fever, cough, sore throat, malaise, headache, muscle pain, nausea, vomiting, diarrhoea, loss of taste and smell) without shortness of breath, dyspnoea, or abnormal chest imaging.
People who have evidence of lower respiratory disease by clinical assessment or imaging and an oxygen saturation (SpO₂) ≥94% on room air at sea level.
People who have respiratory frequency >30 breaths per minute, SpO₂ <94% on room air at sea level, ratio of arterial partial pressure of oxygen to fraction of inspired oxygen (PaO₂/FiO₂) <300 mmHg, or lung infiltrates >50%.
People who have respiratory failure, septic shock, and/or multiple organ dysfunction.
Persistent symptoms or organ dysfunction after acute COVID-19
People who experience persistent symptoms and/or organ dysfunction after acute disease. Also known as post-acute COVID-19 syndrome or long COVID. See the Complications section for more information.
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