Recombinant bat coronavirus reported in wide-ranging Cambodian bat

By Dr. Liji Thomas, MDReviewed by Aimee MolineuxJan 20 2022

Coronaviruses (CoVs) are not a new occurrence, causing mild human infections for the most part. In 2002, an outbreak of severe respiratory disease traced to the severe acute respiratory syndrome coronavirus (SARS-CoV) focused scientific attention on a large scale on the severity with which these microbes can hit humans.

Further research showed that these viruses were harbored within bats of various species, and jumped into humans via the palm civet. The next outbreak occurred ten years later, with the Middle East Respiratory Syndrome coronavirus (MERS-CoV). The current pandemic, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been far more severe and deadly than the other two.

This has led to the recognition of the need for bat surveillance to predict the next bat-to-human jump of a potentially deadly CoV.

A new paper in the journal Viruses reports on the detection of recombinant CoVs in several bat species in Cambodia, and of a related species in China.

Background

The CoVs behind the three pathological outbreaks, referred to previously, belong to the family of beta-coronaviruses, which, along with alpha-CoVs, are found to infect bats as their primary host in over half the cases.

With their large 30 kilobase ribonucleic acid (RNA) genomes, despite a relatively efficient proofreading apparatus, these viruses are subject to mutation during replication, as well as viral recombination.

Recombination has been observed mostly in the viral spike, and encourages zoonotic spread as well as making it more difficult to diagnose and treat the virus. In a surprising case, a bat CoV of the Rousettus genus, related to the human seasonal CoV HKU9, was found to have undergone recombination with an orthoreovirus, a non-enveloped double-stranded RNA virus. The product was a new CoV, the Rousettus bat coronavirus GCCDC1 (RoBat-CoVGCCDC1), with part of the reovirus genome integrated into the CoV genome.

First found in China, in 2016, this virus was then discovered in Singapore bats in 2020, both containing the genes p10 and NS7c. These are absent in the HKU9 virus from Hong Kong. The current study reports the results of a metagenomic study of bat samples from 10 healthy bats from four different genera, captured from a variety of locales in Cambodia.

Virus isolation was unsuccessful, but RNA sequencing was carried out by next-generation sequencing (NGS) methods.

What did the study show?

The results confirmed its identity with GCCDC1. All the Cambodian genomes had the highest identity with the Chinese and Singapore strains of GCCDC1, but with variations that make Cambodia the hub for the bat hosts.

Despite the phylogenetic variations, there was close clustering of the strains found in the Cambodian bats, of different species, with less distance between them compared to the distance from the Chinese or Singapore bat strains. This was investigated using whole genome analysis of single nucleotide polymorphisms over all the GCCDC1 strains used in this study, whether current or from previous collections.

The researchers examined 33 sites in three genes – the ORF1ab, Spike and NS3 genes. Non-synonymous mutations occurring at these sites were compared for frequency between different bat hosts and countries.

This showed that there were no SNPs unique to the Chinese or Singapore CoV strains, but the Cambodian sequences showed multiple SNPs. Some SNPs were found more frequently in some geographic regions and some bat genera. Unique SNPs were found more often in the strains found in Cynopterus and Rhinolophus bats compared to those carried by Eonycteris and Rousettus genera.

In one sample, named PH201, sequence analysis showed an interesting situation. When the reads belonging to the GCCDC1 sequence were removed, the remaining reads formed an almost complete genome with 97% coverage, corresponding to a novel alpha-CoV.

In other words, the researchers had found an alpha-CoV coinfecting the bat with GCCDC1. The closest match to this sequence was with another alpha-CoV – RsYN14 – that infects the same genus of bat, but in Yunnan, China, but there was only 83% nucleotide identity between the full genomes of the two viral strains.

When the total gene sequences were compared, it was observed that the identity extends to 90%, though individual genes had different levels of identity. Thus, the PH201_AlphaCoV ORF4a shared 76% sequence identity with RsYN14, but for the membrane (M) protein it was 98%.

Phylogenetic analysis confirmed that these alpha-CoVs were closest to each other. Other closely related viruses included, first, Rousettus coronavirus HKU10 or Rhinolophus coronavirus Bt-CoV/Rh/YN2012, with the closeness varying with the genes selected for analysis.

Implications

The findings of this study show how important it is to keep a watchful eye on viruses that may one day become zoonotic, including bat CoVs, which could spill over into the human population due to the closeness of their habitats and the frequency of interactions between the two host species. The occurrence of recombination at genome level at a high level demonstrates that CoVs continue to change and present altered characteristics that could make them extremely dangerous to public health.

The researchers also report that GCCDC1 is found over a larger region of Asia than previously thought, requiring a wider field of investigation to detect the possible presence of the strain in bats outside Asia as well.

Another interesting finding is that GCCDC1 is capable of infecting different bat species, with samples from all four genera in this study were found to contain GCCDC1 RNA. Again, the pattern of SNP distribution could indicate a potential confounding effect on the species tropism attributed to the viral strains due to the spatial distribution of the bats themselves.

In other words, the viral strains are found in particular bat species, not because of the viruses are not able to cross-infect other bat genera but rather because the only bats in that region belong to certain specific genera.

It would appear that all the GCCDC1 strains detected in bats from China or Singapore derived from Cambodian bat hosts, in view of the detection of this strain in all the same bat species in Cambodia. It also indicates that there are abundant bat and viral strains in Cambodia.

The coinfection of a bat with both GCCDC1 and a novel alpha-CoV underlines the readiness of these viruses to spill over from one species to another. In fact, another study reported finding another bat CoV in the same bat species, a CoV closely related to SARS-CoV-2, in Cambodia.

This emphasizes the need for careful investigation of bat viruses for the occurrence of co-evolution of viruses. This changing genomic picture shows the effects of frequent and active recombination in bat CoVs.

Enhanced surveillance in a broad geographical area, in both bats and humans is required to monitor the evolution of this group of viruses and to assess potential zoonotic transmission into human populations.”