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dcyphr | Origin and evolution of pathogenic coronaviruses

Contents

Introduction

Coronaviruses cause respiratory and intestinal infections in animals and humans. They were not considered to be highly pathogenic to humans until the outbreak of severe acute respiratory syndrome (SARS) in 2002 and 2003. Ten years after SARS, another coronavirus: Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in Middle Eastern countries.

SARS Coronavirus uses "ACE2" (angiotensin-converting enzyme 2) as a receptor to infect specific lung cells (ciliated bronchial epithelial cells and type II pneumocytes). MERS uses "DDP4" (dipeptidyl peptidase 4) as a receptor to infect specific lung cells (unciliated bronchial epithelial cells and type II pneumocytes).

SARS and MERS were transmitted to humans from market civets and camels, respectively. Both viruses are thought to have originated in bats. Studies of these two coronaviruses have led to a better understanding of coronavirus biology and led to more coronavirus discovery in bats.

This review focusses on the origin and evolution of SARS and MERS. With a focus on the ecological distribution, genetic diversity, interspecies transmission and potential for disease development SARS and MERS related coronaviruses in bats. This information can help prepare countermeasures against new coronaviruses disease in humans.

Coronavirus Diversity

Coronaviruses are members of the subfamily Coronavirinae. This subfamily consists of four genera — AlphacoronavirusBetacoronavirusGammacoronavirus and Deltacoronavirus — based on their evolutionary similarity and genomic structures (Fig. 1). The alphacoronaviruses and betacoronaviruses infect only mammals. The gammacoronaviruses and deltacoronaviruses infect birds, but some of them can also infect mammals. Alphacoronaviruses and betacoronaviruses usually cause respiratory illness in humans and infectious diarrhoea in animals. SARSand MERS, cause severe respiratory syndrome in humans, and the other four human coronaviruses (HCoV-NL63, HCoV-229E, HCoV-OC43 and HKU1) cause mild upper respiratory diseases in people with weak immune systems, although some can cause severe infections in infants, young children and elderly individuals. Alphacoronaviruses and betacoronaviruses can pose a heavy disease burden on livestock.

Based on current databases, all human coronaviruses have animal origins: SARS-CoV, MERS-CoV, HCoV-NL63 and HCoV-229E are considered to have originated in bats; HCoV-OC43 and HKU1 likely originated from rodents. Domestic animals may be intermediate hosts that enable virus transmission from other animals to humans. Domestic animals themselves can suffer disease caused by coronaviruses: genomic sequences highly similar to PEDV were detected in bats, and SADS-CoV is a recent spread from bats to pigs (Fig. 2). Currently, 7 of 11 ICTV-assigned (International Committee on Taxonomy of Viruses)Alphacoronavirus species and 4 of 9 Betacoronavirus species were identified only in bats (Fig. 3). Thus, bats are likely the major natural reservoirs of alphacoronaviruses and betacoronaviruses.

Animal Origin and Evolution of SARS

At the beginning of the SARS epidemic, almost all inital patients had animal exposure before developing disease. Traces of antibodies linked to SARS were found in masked palm civets (Paguma larvata) and animal handlers in a market place. However, later, investigations of farmed and wild-caught civets revealed that the SARS-CoV strains found in market civets were transmitted to them from other animals. In 2005, two teams independently reported the discovery of  new coronaviruses related to human SARS-CoV,  in horseshoe bats (genus Rhinolophus). These were named SARS-CoV-related viruses or SARS-like coronaviruses. These discoveries suggested that bats may be natural hosts for SARS-CoV and that civets were only intermediate hosts. Many coronaviruses with evolutionary relations to SARS-CoV were discovered in bats from different provinces in China and also from European, African and Southeast Asian countries (Fig. 4; Supplementary Fig. S1a). According to the ICTV (International Committee on Taxonomy of Viruses) criteria, only the strains found in Rhinolophus bats in European countries, Southeast Asian countries and China are SARS related. Those from Hipposideros bats in Africa are less related to SARS-CoV and should be classified as a new coronavirus species. These data indicate that SARS related viruses have wide geographical spread and might have been present in bats for a very long time. A 5-year study revealed the existence of many different SARS-related viruses in bat populations in one cave of Yunnan province, China. This location the SARS-related viruses in this location contain all varieties found in other locations of China. Furthermore, the viral strains that exist in this one location contain all genetic elements that are needed to form SARS-CoV (Fig. 5). Since no direct predecessor of SARS-CoV was found in bat populations despite 15 years of searching, and as RNA recombination is frequent within coronaviruses, it is likely that SARS emerged through recombination of related viruses in bats. Previous data supports this idea. Given the prevalence and great genetic diversity of SARS-related viruses in bats, their close coexistence and the frequent recombination of the coronaviruses, it is expected that there will be new coronaviruses in the future. Because there were no SARS cases in Yunnan province during the SARS outbreak, it is believed that the predecessor of SARS-CoV was produced by within bats, spread directly or indirectly (via another mamal) to civets. When the virus-infected civets were transported to Guangdong market, the virus spread in market civets and further mutated before spreading to humans.

Variability of bat SARSr-CoVs

SARS-CoVs and SARS-Related viruses in bats mainly vary in three regions: S, ORF8 and ORF3 (Fig. 5). 

Receptor usage of SARS-CoV and SARSr-CoV
The binding of the ACE2 receptor is essential for a range of coronaviruses. Different strains of the virus bind to varying degrees. Those which bind more strongly to ACE2 in humans transmit more effectively between humans. Some virus may bind well to ACE2 in animals like civets but bind poorly in humans, leading to less human transmission. Understanding thee usage of receptors by coronaviruses is essential to prevent future disease outbreaks.

Origin and evolution of MERS-CoV

Most early cases of MERS came from camels. MERS strains found in camels were almost identical to those found in humans. MERS-specific antibodies were found in camels as well as infections detected in 1983 in camels. This suggests MERS was present in camels for 30 years. MERS related viruses have also been found in bats. 

Variability of human and camel MERS-CoV

MERS virus in humans and camels were over 99% identical. Mains variations were in S, ORF4b and ORF3, particularly in African camels.

Variability of bat MERSr-CoVs
Currently, MERS in bats and camels have similar genomic structures but different genomic sequences. The higher similarity between MERS related virus in bats and camels was ~85%. Several MERS strains in bats in China were similar enough to be considered the same species.

Receptor usage of MERS-CoV and MERSr-CoV
In contrast to SARS-CoV, which uses ACE2 as its receptor, MERS-CoV uses DPP4. MERS strains in camels and humans are quite similar, using DPP4 efficiently. Similar to SARS, receptor recognition is essential MERS to infect and animal.

SADS-CoV
From 28 October 2016 to 2 May 2017, swine acute diarrhoea syndrome (SADS) was observed in four pig breeding farms in Guangdong province. Up to 90%of piglets younger than 5 days old died. A new bat related coronavirus names SADS-CoV was the cause. The virus was almost identical in all 4 farms. Virus that were 96-98% similar were later found in other farms. Analysis indicates that currently known receptors like ACE2 and DPP4 were not used for SADS. Further study is required on this topic.

Conclusions and future perspectives

The collected data demonstrated that SARS likely originated in bats through recombination of related viruses. Recombination likely occurred in bats before SARS was introduced into Guangdong province through infected civets or other infected mammals from Yunnan. The introduced virus underwent rapid mutations in S and orf8 regions, successfully spreading in market civets. After several independent transmissions to humans, some of the strains further mutated in S and became the SARS epidemic in 2002–2003. However, a recent investigation revealed the presence of antibodies against SARS related viruses in humans living near a bat cave.These people did not show signs of disease, suggesting that the virus can infect humans through frequent contact.

A similar scenario might have happened for MERS. Since its outbreak in 2012, MERS and related viruses have been found in bat species in five continents. Given the massive number of coronaviruses carried by different bat species, and other features such as adaptive mutation and recombination, it is expected that there will be frequent transmission from bats to animals and humans.

Currently, no clinical treatments or prevention strategies are available for any human coronavirus. In addition, little information is available on HKU3-related strains that have much wider geographical distribution. Similarly, antibodies against MERS-CoV could not protect from infection with a virus bearing the MERS related virus in bats. Little is known about the replication and disease spread of these bat viruses. Thus, future work should be focused on the biological properties of these viruses. The resulting data would help the prevention and control of SARS-like or MERS-like diseases in the future.

It is widely accepted that many viruses have existed in their natural reservoirs for a very long time. The constant transmission of viruses from natural hosts to humans and other animals is largely due to human activities, including modern agricultural practices and urbanization. Therefore, the most effective way to prevent viral infections from animals is to maintain the barriers between natural reservoirs and human society.