Origins and Evolution of Seasonal Human Coronaviruses

Abstract

Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.

Keywords: 229E; HKU1; NL63; OC43; evolution; recombination; seasonal coronaviruses; zoonosis.

Figure 1

An illustration of the sHCoV genomes, not drawn to scale. The ORFs analyzed in this study are indicated in orange.

Figure 2

Maximum clade credibility (MCC) trees inferred from dataset D5 for full genomes (WGS), and the spike, nucleocapsid, membrane, and envelope ORFs, with the branches color-coded by the inferred coronavirus host. The upper panel shows MCC trees from alphacoronaviruses while the lower panel shows MCC trees from betacoronaviruses. Human, camel, and porcine coronavirus clades have been collapsed to increase readability. Human * is a lone human CoV (FJ415324) that clusters with ungulate and canine CoVs. Individual and more detailed MCC trees can be found in File S2.

Figure 3

Estimates of the evolutionary rate (A) and MRCA age (B) for full genomes and four open reading frames (dataset D5) of the seasonal human coronavirus species. The black horizontal lines in (B) are the dates of first isolation for the 229E (1966), OC43 (1967), NL63 (2004), and HKU1 (2005). The WGS is missing data points for HKU1_all (collective for both genotypes) and HKU1_genotype B as sequences for HKU1_genotype B were all removed in the generation of recombination-free WGS dataset D5.

Figure 4

Summarized within and between host/species recombination patterns identified by RDP4, for alphaCoVs (A) and betaCoVs (B). For each sHCoV species, recombining CoVs are shown; non-human and sHCoV (black arrows), within sHCoV species (blue arrows), and between sHCoV species (green arrows). In orange is a lone human CoV (FJ415324) that clusters with ungulate and canine CoVs. Figure generated using Biorender.

Figure 5

The number of inferred amino acid changes (AA) associated with the sHCoVs for AA positions in the envelope, membrane, nucleocapsid, and spike proteins from datasets D4 and D5. Panel (A) represents the aggregated AA changes from the alphaCoVs 229E and NL63 while (B) represents the aggregated changes from the betaCoVs OC43 and HKU1. At the top of each plot, the functional domains or regions of the respective proteins are shown; NTD = N-terminal domain, TM = transmembrane domain, CTD = C-terminal domain, RBD = receptor binding domain, LINK = central linker domain, LINK-Dimer = dimerization domain, S1 subunit, S2 subunit, FP = fusion peptide, IFP = internal fusion peptide, HR1 = heptad repeat 1, and HR2 = heptad repeat.