Unpacking Pandora From Its Box: Deciphering the Molecular Basis of the SARS-CoV-2 Coronavirus

Abstract

An enigmatic localized pneumonia escalated into a worldwide COVID-19 pandemic from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This review aims to consolidate the extensive biological minutiae of SARS-CoV-2 which requires decipherment. Having one of the largest RNA viral genomes, the single strand contains the genes ORF1ab, S, E, M, N and ten open reading frames. Highlighting unique features such as stem-loop formation, slippery frameshifting sequences and ribosomal mimicry, SARS-CoV-2 represents a formidable cellular invader. Hijacking the hosts translational engine, it produces two polyprotein repositories (pp1a and pp1ab), armed with self-cleavage capacity for production of sixteen non-structural proteins. Novel glycosylation sites on the spike trimer reveal unique SARS-CoV-2 features for shielding and cellular internalization. Affording complexity for superior fitness and camouflage, SARS-CoV-2 challenges diagnosis and vaccine vigilance. This review serves the scientific community seeking in-depth molecular details when designing drugs to curb transmission of this biological armament.

Keywords: 2019-nCoV; COVID-19; RNA; bats; coronavirus; pandemic; virus.

Figure 1

Schematic overview of the SARS-CoV-2 single stranded RNA genome. Upper line (green) represents the Severe Acute Respiratory Syndrome Coronavirus 2 isolate Wuhan-Hu-1 accession number NC_045512 version 2 entry in the National Centre for Biotechnology Information database. Numbers (black) represent the beginning and end of a coding region. Of note, coding regions do not run consecutively (numbers in red). Polyproteins 1ab (pp1ab) and 1a (pp1a) are translated from ORF1ab (265–21,555 bp) via a ribosomal slippage site (black rectangle) and stem loop formation. Non-structural proteins (NSP 1–11) are cleaved from both polyproteins. Cleavage of NSP12–16 occurs only from pp1ab enabling the formation of various listed enzymes. Structural proteins spike (S), envelope (E), membrane (M) and nucleocapsid (N) are encoded by the genes S (21,563–25,384 bp), E (26,245–26,472 bp), M (26,523–27,191 bp), and N (28,274–29,533 bp). Open reading frames (ORF) ORF3a, 6, 7a, 7b, 8, 9, and 10 are encoded by intermediate genomic segments as indicated. The location of two stem loops is shown adjacent to the 3′UTR representing pseudoknot stem loop (left) and s2m (right). The overall structure of SARS-CoV-2 is illustrated with abbreviations as indicated above.

Figure 2

Sequences within the SARS-CoV-2 genome are involved in ribosomal frameshifting and RNA stem-loop structural formation. (A) The predicted standard coronavirus heptanucleotide shift site U_UUA_AAC is present and shown with the slippery sequence (brown box) and frame shift site (FSS) followed by a guanine conservation sequence (bold). An unpaired G:U nucleotide quartet (UNQ: boxed) may offer stability to the stem loop I and II. Binding between the stem loops and a downstream nucleotide region (13,538–13,542 bp) results in “kissing” stem loop II formation. A variant in SARS-CoV-2 (13533C->A) compared to SARS-CoV is indicated. Potential pseudoknot stem loops occur between 29,609–29,657 bp (grey box). Conservation element s2m (stem-loop II motif, pale green box) is shown that may partake in 16S ribosomal RNA macromolecular mimicry. Ribbon diagram (left of arrow) showing the similarity in the backbone folds between the s2m structure (red) and the 530 loop of the 16S rRNA (blue). (B) Sequence and base-pairing of three different coronavirus stimulatory elements; SARS three-stemmed pseudoknot [24,25], the avian infectious bronchitis virus (IBV) two-stemmed pseudoknot [26], and the kissing loops of the human coronavirus 229E stimulatory element [17]. The heptameric slippery sites are shown (yellow rectangles). (C,D) Models of mimetic relationships corresponding to the representamen: R, the model to the object: O and the operator to the interpretant: I [27]. A molecular example (C): the tRNAPhe is considered to be the object, the untranslated end of the plant virus TYMV genome is the representamen, while the interpretant is the tRNA precursor processing enzyme RNase P Modified from [23]. In (D), the plant’s thorn is the object, the thorn bug is the representamen and the predatory bird that the prey eludes is the interpretant. Modified from [23].

Figure 3

Summary diagram illustrating the non-structural proteins (Nsp) 1–16 cleaved from polyproteins pp1a (white partial circle) or pp1ab (yellow center). Numbers represent the molecular weight of Nsps in kilodaltons. Secondary structure prediction of each Nsp is shown except for Nsp11 which is unknown (Source PDB101.rcsb.org [30]. Nsp function is provided in the outer ring.