Mutational spectra of SARS-CoV-2 isolated from animals

Introduction

The outbreak of the novel coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been reported in Wuhan City, Hubei Province, China, and posed unprecedented challenges to global health. Despite the ongoing efforts to control the COVID-19 outbreak, the disease is still spreading worldwide with increasing numbers of infected cases and deaths. The World Health Organization (WHO) officially declared it as a pandemic on 11 March 2020 (Wu et al., 2020; Zhou et al., 2020).

Severe acute respiratory syndrome coronavirus-2 belongs to the order Nidovirales, suborder Cornidovirineae, family Coronaviridae, subfamily Orthocoronavirinae, genus Betacoronavirus, and subgenus Sarbecovirus. The virus is enveloped with a single-stranded positive-sense RNA genome of 29,903 nucleotides. SARS-CoV-2 has a monopartite genome that consists of two untranslated regions (5′ and 3′ UTRs) and 11 open reading frames (ORFs) encoding 27 proteins. ORF1ab constitutes the first two-thirds of the genome (21,290 nucleotides) and encodes 16 non-structural proteins (nsp1–nsp16). The last third of the genome encodes four structural and six accessory proteins. The structural proteins are the Spike (S), Envelope (E), Matrix (M), and Nucleocapsid (N) proteins, while the accessory proteins include the ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 (Chan et al., 2020).

The N protein coils the RNA segment into a helical nucleocapsid that is incorporated into a virion of icosahedral symmetry, whereas the M and E proteins are required for virus morphogenesis, assembly, and budding (Paraskevis et al., 2020). The S glycoprotein (1273 aa) is a fusion viral protein that consists of two subunits: S1 (681 aa) and S2 (588 aa). The S1 subunit comprises a signal peptide (SP), an N-terminal domain (NTD), and a receptor-binding domain (RBD) that interacts with the angiotensin-converting enzyme 2 (ACE2) (Hoffmann et al., 2020; Letko, Marzi & Munster, 2020; Walls et al., 2020; Zhao et al., 2020). The S2 subunit comprises a fusion protein (FP) that mediates membrane fusion and two heptad repeats known as HR1 and HR2, which form the coiled structures surrounded by the protein ectodomain. A furin cleavage site (RRAR▾) for furin proteases exists between the interface of S1 and S2 subunits of SARS-CoV-2 but not SARS-CoV (Canrong et al., 2020; Coutard et al., 2020). It mediates the initial attachment of the virus to the host-cell receptors and subsequent fusion with the cell membrane allowing virus entry. Like SARS-CoV, SARS-CoV-2 binds to ACE2 for cell entry as mediated by the viral surface S glycoprotein (Hoffmann et al., 2020; Walls et al., 2020; Yan et al., 2020; Zhou et al., 2020). Subsequently, the S protein is cleaved by the transmembrane serine protease 2 (TMPRSS2) to S1 and S2 subunits (Hoffmann et al., 2020) allowing the entry of the virion core.

There is a broad acceptance that SARS-CoV-2 has an animal origin, although the animal reservoir has not yet been identified (Abdel-Moneim & Abdelwhab, 2020). Bats may be considered a potential reservoir host for SARS-CoV-2 since they are the reservoir of several SARS related coronaviruses. One of these viruses is the horseshoe bat (Rhinolophus affinis) coronavirus RaTG13, which shares a high identity (96.3%) with SARS-CoV-2 at the genome level (Helmy et al., 2020). Wong et al. (2020) suggested that pangolin might be the intermediate host as it shares 98% identity with SARS-CoV-2 at the receptor-binding motif (RBM) of S protein. The receptor recognition by the S glycoprotein is the major determinant of host range, tissue tropism, and pathogenesis of coronaviruses. Human-to-human transmission has been confirmed even from asymptomatic carriers and pre-symptomatic infected persons (Rothe et al., 2020; Zou et al., 2020). Several cases of SARS-CoV-2 infections in animal hosts (cat, dog, mink, and tiger) have been reported (Gollakner & Capua, 2020; Tazerji et al., 2020), although none of them developed typical clinical features as COVID-19 patients. The dynamics of the disease concerning the transmission of the virus from humans to animals and vice versa requires further explanation. Additionally, there is inadequate information on whether animals have a role in the evolution of SARS-CoV-2. Hence, the mutation rate could drive viral evolution and genome variability, thereby enabling viruses to escape host immunity and develop drug resistance. In the present study, the genetic diversity and mutations in SARS-CoV-2 isolated from cats, dogs, mouse, minks, and tiger were characterized and compared with human isolates to investigate the mutational spectra that might play a role in the virus evolution, transmission, and pathogenesis.

Materials and Methods

Phylogenetic analysis

Forty SARS-CoV-2 genomes were used for phylogenetic analysis (Fig. 1). The phylogenetic tree was constructed based on the coding sequences of all genes. The 3′ UTR, 5′ UTR, and non-coding sequences were excluded. Sequences were aligned using Kalign3 (Lassmann, 2020). The phylogenetic tree was constructed in IQ-TREE (Nguyen et al., 2015) using the maximum likelihood method, ModelFinder (to identify the best fitting model (s)), and ultrafast bootstrap approximation (1,000 replicates). The best-fitting models were TN (Tamura-Nei) + F (Felsenstein) + I (proportion of invisible sites). The tree was drawn to scale with branch length representing the number of substitutions per site. The tree was visualized in MEGAX (Kumar et al., 2018) and rooted on the midpoint.

Results

Mutational spectra of spike (S) protein

The spike gene of animals SARS-CoV-2 consists of 3,822 nucleotides (21,563–25,384) that encode 1,273 amino acids. The domain structures and critical ACE2-binding residues of S protein from animal SARS-CoV-2 are illustrated in Fig. 2. The analysis of mutations in the S gene of the studied isolates from animals revealed a total of 25 unique substitution mutations, 22 of which occurred in mink isolates (Table S2). The cat isolates had one unique substitution, while the mouse had two unique substitutions and one deletion mutation. No mutations were identified in the S gene from the dog or tiger isolates. Of the 25 substitutions, 17 were non-synonymous, while nine substitutions were synonymous (Table S2).

The non-synonymous mutations reported for spike protein in Table 2 were distributed as follows: one in the signal peptide (SP), two in the N-terminal domain (NTD), six in the receptor-binding domain (RBD), one downstream of the RBD (D614G), and one in the heptad repeat 1 (HR1) (Refer to Fig. 2 for the map of spike protein). In the mouse isolate, two unique amino acid substitutions (Q498H and N969S) were identified, with one of them (Q498H) located within the RBM (Fig. 3). Fifteen unique mutations were identified in mink isolates (Table S2), four of which (L452M, Y453F, F486L, N501T) were located within the RBM of S protein (Figs. 2 and 3; Table 2). The deletion of five amino acid residues in the isolate from the mouse was close to the furin cleavage site. No mutations were identified at the furin cleavage site of SARS-CoV-2 isolates from other animals. All mutations reported for spike protein in Table 2 are unique for animal isolates except the mutation in the SP for the dog (L8V). The position and structure of each amino acid substitution in the RBM compared to normal residues are illustrated in Fig. 3.

Discussion

The novel coronavirus (SARS-CoV-2) has been identified as the causative agent of the coronavirus disease 2019 (COVID-19) outbreak in Wuhan City, Hubei province, China in December 2019 (Huang et al., 2020; Zhou et al., 2020). Like other coronaviruses, the interspecies transmission of SARS-CoV-2 is possible. Bats are the natural host of human coronaviruses 229E, SARS-CoV, NL63, and MERS-CoV (Corman et al., 2015, 2016; Donaldson et al., 2010; Ge et al., 2013; Hu et al., 2015; Huynh et al., 2012; Samara & Abdoun, 2014; Tao et al., 2017), while rodents are the natural host of HKU1 and OC43 (Cui, Li & Shi, 2019). The intermediate hosts of both NL63 and HKU1 are not yet unidentified, while the intermediate hosts of 229E, OC43, SARS-CoV, and MERS-CoV are camelids, bovines, palm civets, and dromedary camels, respectively (Corman et al., 2015; Cui, Li & Shi, 2019; Donaldson et al., 2010; Ge et al., 2013; Hu et al., 2015). This study aimed to identify the genomic features that might be associated with interspecies jumping of SARS-CoV-2 between humans and animals. To this extent, SARS-CoV-2 genomes from different species including humans, cats, dogs, mouse, minks, and tiger were fully characterized and compared with geographically and phylogenetically close SARS-CoV-2 human isolates.

Phylogenetic analyses of hCoV-19/tiger, hCoV-19/mouse/Harbin, hCoV-19/mink, hCoV-19/cat, and hCoV-19/dog revealed a close relationship (99.7–100%) with SARS-CoV-2 human isolates. It is speculated that bats are the natural source of SARS-CoV-2, hence the phylogenetic analysis of SARS-CoV-2 revealed a nucleotide homology of 96.3% with the bat CoV RaTG13 (Zhou et al., 2020). Additionally, the nucleotide sequence homology between pangolin and analyzed human SARS-CoV-2 isolates in this study is 89%. Although pangolin could not be excluded as one of the intermediate animal hosts of SARS-CoV-2 (Lam et al., 2020), a direct transmission of pangolin SARS-CoV-2 might not be possible due to the sequence divergence.

Generally, coronaviruses can easily cross species barriers. There are three main reasons for interspecies transmission of coronaviruses; firstly, the high mutation rates (Su et al., 2016), although the mutation rate of SARS-CoV-2 is lower than SARS-CoV (Ye et al., 2020). Secondly, the large RNA genome of coronaviruses, which increases the incidence of mutations and recombination leading to the emergence of novel CoVs (Ye et al., 2020). Thirdly, the interaction of coronaviruses with different ACE2 receptors (Bolles, Donaldson & Baric, 2011). The SARS-CoV and HCoV-NL63 bind with ACE2 for interspecies transmission (Graham & Baric, 2010; Hofmann et al., 2005). However, HCoV-229E and HCoV-OC43 use aminopeptidase N (APN) and 9-O-acetylated sialic acid (9-O-Ac-Sia) receptors, respectively, which helps successful adaptation in humans after interspecies transmission from their animal hosts (Huang et al., 2015; Liu, Liang & Fung, 2020). Although SARS-CoV-2 uses the ACE2 receptor for host cell entry (Hoffmann et al., 2020; Zhou et al., 2020), it remains unclear whether any other coreceptor might be required for its transmission.

In the present study, sequence analysis of the SARS-CoV-2 revealed several unique amino acid substitutions within the S, M, N, and nsps proteins. These mutations may indicate that the virus is not yet adapted to these animals. Duffy (2018) reported that the mutation rate is often high when coronaviruses are not well adapted to their hosts. Several amino acid substitutions may not significantly switch the amino acid properties as the involved amino acid residues were either from the same class or shared some properties. In S protein, for example, L452M involved leucine and methionine, and both are neutral and hydrophobic. Similarly, Y453F involved tyrosine and phenylalanine, and both are hydrophobic and aromatic. However, Q498H in mouse isolate may have a significant change in the properties of the amino acid residues because glutamine is neutral while histidine is positively charged, and both have significant differences in the structure of the side chain.

Mutations in the S protein could change the tropism of the virus, pathogenicity, and interspecies transmission (Wan et al., 2020). In our study, several unique mutations were found in the SP, NTD, RBD, downstream to RBD, and in the HR1 of S protein. Ortega et al. (2020) reported that slight modifications of some residues within RBD of SARS-CoV-2 could improve the interaction with the human cellular receptors. The D614G mutation downstream of the RBD could be associated with higher transmission, pathogenicity, and evasion of immune interventions (Happi et al., 2020; Korber et al., 2020). It was found that K479N and S487T of SARS-CoV are associated with human ACE2 receptor recognition. These amino acids are corresponding to Q493 and N501 in SARS-CoV-2, respectively (Ortega et al., 2020). In our study, all analyzed SARS-CoV-2 from animals had Q493 and N501 except mink isolates which had N501T (Figs. 2 and 3). However, the question whether other reported mutations contribute to further adaptation, and subsequently impact the virus pathogenicity require further investigation. Computational models and data have identified additional mutations that might further strengthen the binding affinity of SARS-CoV-2 to ACE2 receptors (Wan et al., 2020). Yao et al. (2020) found that S protein mutations of SARS-CoV-2 are capable of changing its pathogenicity. Further studies are required to investigate the impact of these mutations on virus evolution.

The N protein of SARS-CoV-2 consists of 1,260 nucleotides that encode 419 amino acids. It is a multifunction protein and an important determinant of the virus pathogenicity, viral transcription efficiency, and coiling the RNA segment into a helical nucleocapsid incorporated into virion of icosahedral symmetry (McBride, Van Zyl & Fielding, 2014; Paraskevis et al., 2020). In our study, the N protein had four amino acid substitutions: three in mink isolates (R41L, P80L, and P199Q) with a frequency of 2.7% each, and one in cat isolates (T247I) with a frequency of 16.7%.

Generally, the nsps (nsp1-16) of coronaviruses play essential roles in virus replication (Lei, Kusov & Hilgenfeld, 2018; Zeng et al., 2018), polypeptide cleaving (Lei, Kusov & Hilgenfeld, 2018; Zhu et al., 2017), and inhibition of host immune response (Lei, Kusov & Hilgenfeld, 2018; Shi et al., 2019; Zhu et al., 2017). The ORF1ab polyprotein of SARS-CoV-2 plays an important role in viral RNA synthesis (Banerjee et al., 2020). In SARS CoV, it was found that nsp2 binds to the host proteins (prohibitin 1 and prohibitin 2) which are involved in several cellular functions including cell cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis (Cornillez-Ty et al., 2009). Analysis of ORF1ab nsp2 (638 aa from A181-G818) polyproteins of SARS-CoV-2 isolated from animals revealed six characteristic mutations, one in cat (H388Y) and five in mink (E352Q, A372V, R398C, A405T, and E743V) isolates. The impact of these mutations on the function of nsp2 and virus evolution is still unknown, although stabilizing mutation falling in the endosome-associated-protein-like domain of the nsp2 protein, could explain why SARS-CoV-2 is more contagious than SARS-CoV (Angeletti et al., 2020).

The papain-like proteinase (PLpro) and 3C-like main protease (3CLpro) are encoded by nsp3 and nsp5, respectively. Both PLpro and 3CLpro play a role in virus replication and antagonize the host’s innate immunity (Harcourt et al., 2004; Li et al., 2016). They are also a popular target for antiviral drugs (Wu et al., 2020). Sequence analysis of the nsp3 and nsp5 of SARS-CoV-2 isolated from animals revealed eight and three unique amino acid substitutions, respectively. The role of these mutations in nsp3 on virus replication and susceptibility to antiviral drugs should be investigated. The nsp3 mutation could explain the difference in pathogenicity between SARS-CoV-2 and SARS-CoV (Angeletti et al., 2020). Furthermore, unique mutations were found within the nsp9, nsp10, nsp12, and nsp13. Although no direct evidence exists about their roles, continued evidence-based analysis of evolutionary change is important.

Additionally, the ORF3a protein of coronaviruses showed a pro-apoptotic activity. The SARS-CoV-2 is less virulent than SARS-CoV due to diminished pro-apoptotic activity (Ren et al., 2020). Herein, different mutations were found within ORF3a (Table 3; Table S2). However, the impact of mutations within ORF3a of SARS-CoV-2 on the apoptotic activity and consequently on the virus pathogenicity is unknown.

In conclusion, although the dynamics of SARS-CoV-2 transmission from humans to animals and vice versa is still unclear, further human-animals interface is possible due to the similarity of ACE2 receptors in humans and some animal species. In the present study, unique amino acid substitutions were reported in almost all animal SARS-CoV-2 proteins such as the ORF1ab, S glycoprotein (including critical ACE2-binding sites), ORF3a, and N proteins. Our study draws the attention of scientists worldwide on the role of mink as an animal host to SARS-CoV-2 due to several unique amino acid substitutions recorded in its proteins (specially S protein) that might play a role in the virus evolution, pathogenesis and transmission to human. This study also recommends continuous molecular surveillance of SARS-CoV-2 animal isolates. Also, it is essential to furtherly investigate if these mutations could impact the virus evolution, including virus adaptation, changes in the pathogenicity, and the emergence of drug-resistance viral phenotypes.

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