SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective

Abstract

In less than five months, COVID-19 has spread from a small focus in Wuhan, China, to more than 5 million people in almost every country in the world, dominating the concern of most governments and public health systems. The social and political distresses caused by this epidemic will certainly impact our world for a long time to come. Here, we synthesize lessons from a range of scientific perspectives rooted in epidemiology, virology, genetics, ecology and evolutionary biology so as to provide perspective on how this pandemic started, how it is developing, and how best we can stop it.

Keywords: Coevolution; Coronavirus; Host susceptibility; Immune system; Pandemics; Phylodynamics.

Fig. 1

Comparative analysis of SARS-CoV-2 with other coronaviruses. Maximum-likelihood phylogenetic trees of the NTD (A) and RBD (B) regions of SARS-CoV-2 (red), RaTG13 (green), RmYN02 (light blue), Pangolin coronaviruses (Guangdong lineage, grey; Guangxi lineage, orange), and other Asian (dark blue) and non-Asian (brown) bat coronaviruses belonging to the Sarbecovirus subgenus. Trees are based on amino acid sequences and were built using PhyML (Guindon and Gascuel, 2003). Trees are mid-point rooted. (C) Combined variability in S1 (grey) and S2 (red) domains of SARS-CoV-2 when compared to RaTG13 and pangolin coronaviruses spike sequences. (D) Sequence alignments showing absence of the YLTPGD insert in bat sarbecoviruses, and the sequence of the RBD region involved in the interaction with ACE2. (E) The position of YLTPGD inserts forming conformational clusters (red spheres) at the NTD of SARS-CoV-2 spike protein is shown (left). The ribbon structure of the spike protein-ACE2 interaction surface is represented to show polar interactions (right). Polar interactions were analyzed using PyMol using PDB id: 6m0j (Lan et al., 2020). (F) Alignment of the region carrying the polybasic amino acid insertion (red) at the S1/S2 cleavage site. GenBank/GISAID accessions for the sequences included in trees are: NC_045512.2 (SARS-CoV-2), MN996532.1(RaTG13), EPI_ISL_412977 (RmYN02), MT084071.1 (MP789 or Guangdong 1), EPI_ISL_410544 (Guangdong P2S), MT040334.1 (GX-P1E),MT072865.1 (GX-P3B), MT040335.1 (GX-P5L), KY417148 (Rs4247), DQ071615.1 (Rp3), GQ153547.1 (HKU3–12), GQ153542 (HKU3–7), MK211378.1 (BtRs-BetaCoV/YN2018D), DQ648856.1 (BtCoV/273/2005), JX993987.1 (Rp/Shaanxi2011), KJ473816 (BtRs-BetaCoV/YN2013), MG772933 (CoVZC45), MG772934 (CoVZXC21), KY417151.1 (Rs7327), KF569996 (LYRa11), NC_014470.1 (BM48–31/BGR/2008), KY352407.1 (BtKY72). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Onset of bat-borne viral diseases in Asia and the Pacific since 1990 (see Table 1) in relation to El Niño Southern Oscillation (ENSO) driven climate anomalies using ‘NINO 3.4’ index retrieved from the National Oceanic and Atmospheric Administration (NOAA, https://www.noaa.gov).

Fig. 3

Time-stamped maximum likelihood phylogenetic reconstruction of SARS-CoV-2 isolates deposited to GISAID.org and rendered by https://nextstrain.org/ncov. Isolates are represented by colored circles with the color code corresponding to time of sampling as detailed in the legend.

Fig. 4

The same reconstruction of SARS-CoV-2 phylogeny, now denoted by geography. Isolates originated and initially diversified in China (purple), followed by multiple and independent introductions to Oceania (blue), Europe (green and yellow), and North America (red). Less information is known about Africa, India, South America, and other populations of major concern in the Global South. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)