SARS-CoV-2 and the COVID-19 pandemic

SARS-CoV-2 and other human coronaviruses

Human coronaviruses (hCoV) were identified in 1965 as causing around 30% of the cases of common cold and flu-like illnesses in humans. The CoVs belong to the order Nidovirales, subfamily Orthocoronavirida, family Coronoviridae . They owe their name to the club-shaped glycoproteins on their surface or ‘spikes’ that give them a crown-like appearance ( corona in Latin).

CoVs are classified into four genera according to their genomic organization: α-CoV, β-CoV, γ-CoV and δ- CoV. The α-CoVs and β-CoVs infect various mammals (such as bats, cattle and domestic animals) including humans. All hCoV are zoonotic (able to jump from animals to humans) and most originate in bats that are considered their natural reservoir, including SARS-CoV-2. Zoonotic transmission then can occur using domesticated animals or other animals that are in closer contact with humans, such as the palm civets for SARS-CoV or camels for MERS-CoV. The emergence of novel variants of CoV was predictable owing to their genetic variability and frequent recombination between strains.

Seven strains of hCoV have been identified. Four are responsible for causing mild respiratory infection: NL63, 229E, OC43 and HKU1. A further three highly pathogenic strains have also been identified as causes of acute respiratory distress syndrome with high fatality rate: SARS-CoV, MERS-CoV and SARS-CoV-2. In 2002, SARS-CoV caused an outbreak that spread to 27 countries, infecting approximately 8000 people with 774 deaths. In 2012, an outbreak of MERS-CoV started in the Arabic peninsula where it remains endemic; so far, it has involved around 2500 individuals with 30% mortality. SARS-CoV and MERS-CoV are both beta coronaviruses.

The first reports of an atypical pneumonia originated in November 2019 in Wuhan province, in China. The viral agent responsible was identified shortly thereafter as a new beta coronavirus and was initially called 2019 novel coronavirus (2019-nCoV). The virus was renamed SARS-CoV-2 in February 2020. The genome of SARS-CoV-2 was fully sequenced in January 2020 and it was found to be 96.2% identical to the bat CoV RaTG13 and 79.5% identical to SARS-CoV indicating that both SARS-CoV and SARS-CoV-2 originated from a common ancestor.

Genomic organization and structure of SARS-CoV-2

SARS-CoV-2 is an enveloped, single-stranded, positive sense RNA virus with a genome of 29 Kb in size. Its genome contains a 5’ leader untranslated region (UTR) followed by a replicase (R), spike (S), envelope (E), matrix (M), nucleocapsid (N) genes and a 3’ UTR with a poly (A)tail. It also contains 6 to 12 open reading frames (ORFs) between the conserved genes (S,E,M and N), 9 transcription regulatory elements and 9 subgenomic RNAs. The first ORF is ORF1a/b and it constitutes two-thirds of the genome at the 5’end. It codes two long polypeptides that can produce 16 non-structural proteins after processing by proteases encoded by the virus. At the 3’ end are ORFs 10 and 11 encoding the 4 structural proteins SEMN ( Fig. A1 ).

The viral particle has a pleomorphic structure; on its surface are located the spikes that are peplomers formed by projections of glycoproteins with an important role in the immunogenicity and pathogenesis of the virus. The M protein lies between the viral nucleocapsid and the envelope. The E protein is a transmembrane protein that, along with S and M, constitutes the viral envelope. Proteins E and M have important roles in the viral replication. The N protein is associated with genomic RNA forming the nucleoprotein ( Fig. A2 ).

Emergence of variants of SARS-CoV-2

A large number of mutations in the original Wuhan strain of SARS-CoV-2 have emerged owing to the huge number of infections that have occurred in a small period of time. Most changes are expected to have no or minimal consequence for virus biology, but tracking these changes allows a better understanding of the virus evolution and its impact on treatment or vaccine effectiveness. Data sharing and dissemination are crucial for the surveillance of any organism, particularly in the setting of a pandemic. To this end, global initiative on sharing avian influenza data (GISAID), a public and private initiative that was established in 2008 as a result of the H1N1 influenza pandemic, provided a free platform on which information on SARS-CoV-2 sequences could be uploaded and shared. This allowed the analysis of data from all over the world. Making use of this sequenced data, CoV-GLUE analysed the mutations that resulted in amino acid replacements in viral proteins or changes in sequence lengths as a result of insertions or deletions (indels). CoV-GLUE is thus an amino acid database.

In March 2020, a new strain of SARS-CoV-2 emerged with a mutation in position 614 of the viral S protein that resulted in the substitution of an aspartic acid (single-letter code: D) with glycine (single-letter code: G). This mutation (D614G) was associated with a selective advantage that resulted in this variant taking over the original strain and becoming the dominant strain circulating all over the world. This variant was not associated with higher mortality or disease severity, but appeared to be more transmissible, which probably explained its fixation in the global population. Towards the end of 2020, more variants started to be identified all over the world. The identification of these variants was of particular concern because it coincided with the approval of COVID-19 vaccines, the efficacy of which could be threatened by the new variants or lineages of SARS-CoV-2. Lineage B.1.1.7 is a variant of SARS-CoV-2 that was identified originally in November 2020 in the southeast of the UK and was termed the ‘Kent variant’. It was calculated to be 40–80% more transmissible than the wild-type SARS-CoV-2 or D614G. It rapidly spread first in the UK and then all over the world and this is thought to be at least partly owing to some of the mutations that this variant presents in its spike protein, such as E484K and N501Y.

One of the mutations, N501Y, was also identified in further variants of concern (VOC), such as one identified originally in South Africa (Lineage B.1.351) and another one identified in Brazil (Lineage B). More recently, another VOC has been identified in India (B612.7) that appears to be replacing the previous B.1.1.7 in the UK. The nomenclature of the different variants has been changed by the WHO and they are all now denominated with Greek letters rather than numbers or the place where they were first identified ( Table A1 ). An updated list of variants can be found in updated list of names that can be found at https://www.who.int/activities/tracking-SARS-CoV-2-variants .

SARS-CoV-2 pathogenesis

The spike protein (S) of SARS-CoV-2 has a receptor-binding domain (RBD) that binds the angiotensin-converting enzyme 2 (ACE2) receptor in tissue and triggers a conformational change that produces membrane fusion between the virus and host cell. The S protein has two subunits (S1 and S2). S1 contains the RBD in its C-terminal domain that determines cellular tropism. S2 mediates the fusion of the viral envelope and the cellular membrane. The binding affinity of RBD with ACE2 determines its transmissibility; it has been observed that the affinity of the S protein of SARS-CoV-2 is higher than, for example, SARS-CoV or MERS-CoV.

Diagnosis