Coronaviruses

(Page last reviewed: 15 September 2021)

General background

Coronaviruses (CoV) were identified as human pathogens in the 1960s. They are enveloped positive stranded RNA viruses in the order of Nidovirales (Figure) [1]. With their characteristic surface, the virions have a crown-like appearance under the electron microscope, which is why the viruses are named after the Latin word ‘corona’, meaning crown or halo.

Most coronaviruses infect animals (i.e. bats, birds and mammals) which act as an intermediate host reservoir. Sometimes they change host and infect humans.

There are currently seven coronaviruses known to infect humans (Figure). Four of them cause mild-to-moderate disease. More specifically, HCoV-OC43, HCoV-HKU1 and HCoV-229E cause common colds, and severe lower respiratory tract infections among people in the youngest and oldest age groups, while HCoV-NL63 is an important cause of (pseudo) croup and bronchiolitis in children [2]. The other three cause more severe, and even fatal disease and have emerged more recently (in the last 20 years): SARS-CoV responsible for the Severe Acute Respiratory Syndrome (SARS) which emerged in 2002, MERS-CoV the Middle East Respiratory Syndrome (MERS) which emerged in 2012 and SARS-CoV-2, identified through a cluster of pneumonia cases in Wuhan, China in late 2019 [3,4].

Illness in humans mostly affects the respiratory tract, with symptoms ranging from those of a common cold to very severe lower respiratory infection [5].

Figure: Human coronavirus taxonomy 

Coronavirus taxonomy
The human coronavirus are depicted in yellow and SARS-CoV-2 responsible for COVID-19 in red. Source: based on the International Committee on Taxonomy of Viruses (ICTV)

SARS-CoV-2 virus evolution

The GISAID EpiCoV database (www.gisaid.org) holds SARS-CoV-2 genome sequences. Some caution needs to be taken when interpreting the results in the database due to variations in reporting and sampling timeframes between countries.

A meta-analysis of time estimates to the last common ancestor of the virus suggested that the pandemic started sometime between 6 October and 11 December 2019 [6]. The current hypothesis is that the virus emerged in or close to Wuhan, China, where it was first detected, but so far no direct ancestor to the virus has been found that can fully explain its emergence [7]. The earliest detection of the presence of the virus in the EU/EEA comes from retrospective analysis of sewage samples in Milan and Turin, which showed that the virus was present in northern Italy on 18 December 2019 [8].

Three different time-calibrated phylogenetic analyses of closely-related coronaviruses suggest that the lineage giving rise to SARS-CoV-2 diverged from the most similar known bat coronavirus between 1948 and 1982 [9]. Bats are the most likely original animal reservoir of the virus, with an intermediate animal host probably involved in the transmission to humans, as has been the case for other coronaviruses [9, 10]. However, the recombinant nature of coronaviruses complicates longer-term phylogenetic analysis, making it difficult to disentangle the ancestry of SARS-CoV-2. Genomic evidence also indicates that the virus is unlikely to be a product of in-vitro manipulation, passaging in cell-culture, or of synthetic origin [7, 11].

As for all viruses, the SARS-CoV-2 virus will constantly change through mutation and, indeed, many variants of the SARS-CoV-2 virus with different sets of mutations have been observed worldwide. While most emerging SARS-CoV-2 variants will not have a significant impact on the spread of the virus, some mutations or combinations of mutations may provide the virus with a selective advantage, such as increased transmissibility or the ability to evade the host immune response. These variants could increase the risk posed by SARS-CoV-2 to human health which is why they are considered to be variants of concern (VOCs).

ECDC is continuously monitoring the emergence and circulation of SARS-COV-2 variants of concern (VOCs) in the European Union (EU).

References

  1. International Committee on Taxonomy of Viruses (ICTV). Virus Taxonomy: The Classification and Nomenclature of Viruses. The 9th Report of the ICTV (2011). Available from: https://talk.ictvonline.org/ictv-reports/ictv_9th_report/
  2. Yin Y, Wunderink RG. MERS, SARS and other coronaviruses as causes of pneumonia. Respirology (Carlton, Vic). 2018;23(2):130-7.
  3.  World Health Organization (WHO). WHO Statement regarding cluster of pneumonia cases in Wuhan, China 2020. Available from: https://www.who.int/china/news/detail/09-01-2020-who-statement-regarding-cluster-of-pneumonia-cases-in-wuhan-china
  4. World Health Organization (WHO). Disease outbreak news update. Novel Coronavirus – China 2020. Available from: https://www.who.int/csr/don/12-january-2020-novel-coronavirus-china/en/
  5. Channappanavar R, Perlman S. Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology. Seminars in Immunopathology. 2017;39(5):529-39.
  6.  van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infection, Genetics and Evolution. 2020;83:104351.
  7.  Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nature Medicine. 2020;26(4):450-2.
  8. La Rosa G, Mancini P, Bonanno Ferraro G, Veneri C, Iaconelli M, Bonadonna L, et al. SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring. Sci Total Environ. 2020;750:141711.
  9.  Boni MF, Lemey P, Jiang X, Lam TT-Y, Perry BW, Castoe TA, et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology. 2020.
  10. Hu B, Zeng L-P, Yang X-L, Ge X-Y, Zhang W, Li B, et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLOS Pathogens. 2017;13(11):e1006698.
  11. Othman H, Bouslama Z, Brandenburg J-T, da Rocha J, Hamdi Y, Ghedira K, et al. Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism. Biochemical and Biophysical Research Communications. 2020;527(3):702-8.