​The danger in the bat: a novel tool to detect sarbecoviruses

Infections with different coronaviruses can lead to various symptoms and their virulence is in no way deducible from their genomes. A study by Wassenaar and Zou published in Letters in Applied Microbiology in February 2020 described how the non-conserved regions of coronaviruses could be used in diagnostic PCRs to detect unknown species. The authors also raised concerns about the use of bats in Traditional Chinese Medicine as a potential risk for introducing virulent coronaviruses into the human population.

Coronaviruses are classified into alphacoronaviruses, betacoronaviruses and gammacoronaviruses, with all human coronaviruses belonging to the alpha- and betacoronavirus genera, which also contain several coronaviruses of bat origin. The betacoronaviruses are further divided into five subgenera: Embecovirus, Sarbecovirus, Merbecovirus, Hibecovirus and Nobecovirus. Human coronaviruses like the Embecovirus OC43 can cause common colds, while HKU1, also an Embecovirus, can lead to more severe illnesses like bronchiolitis and fever. The Merbecovirus MERS-CoV causes a respiratory syndrome with pneumonia, fever, chills and renal impairment and has a mortality rate of 42%. The reservoirs of MERS-CoV were shown to include bats and alpacas while its transmission also involves camels. SARS-CoV and the novel SARS-CoV-2 belong to the Sarbecovirus subgenus together with other bat-derived coronaviruses. Both SARS-CoV and SARS-CoV-2 cause fever, headaches, breathing difficulties, chills and sometimes diarrhoea. During the outbreak in 2002/2003, which lasted for 8 months, SARS-CoV had a mortality rate of 10%. The emergence of the novel SARS-CoV-2 causing the COVID-19 pandemic, affecting people of all ages and resulting in a mortality rate between 2% and 10%, is another reminder of how diverse coronaviruses are and that better preparations for future pandemic threats are required.

Coronaviruses contain a positive-sense single strand of RNA that is 26–32 kb in size, rendering it the largest known genome for RNA viruses. Two thirds of the genome codes for ORF1ab, which is translated into two polyproteins and processed into 16 non-structural proteins required for genome transcription and replication, in addition to structural proteins, amongst them the spike S, envelope E and nucleocapsid N proteins. Even though coronavirus RNA polymerase contains a proofreading function, leading to a stable genome, genetic recombination amongst RNA viruses is frequent. This led to the hypothesis that a novel recombinant coronavirus could emerge at any given time, while it would be challenging to predict its virulence solely from its genome.

To prepare for novel emerging coronaviruses, a study by Wassenaar and Zou aimed at identifying conserved regions within the Sarbecovirus genomes that would allow the design of PCR primers to detect any Sarbecovirus. Notably, the maximum degree of conservation within the ORF1ab over a sliding window of 60 nucleotides was 85% for different viral species belonging to the Sarbecovirus subgenus. When analysing the 5′ and 3′ non-coding flanking regions, the authors found that the conservation was a lot higher within the same sliding window. Moreover, the gene for the envelope protein E showed conservation of 95% within a sliding window of 60 nucleotides and the longest stretch of conserved nucleotides was 32 nucleotides long. For future pandemic threats, these regions are ‘where one should target one’s PCR primers to detect an unknown Sarbecovirus’, explains Dr Trudy Wassenaar, the lead author of the study.

Although genetic variations between the Sarbecovirus species are extensive, the genome of SARS-CoV-2 seems to have remained relatively stable so far during the current pandemic. Different SARS-CoV-2 isolates were shown to only differ in a very few polymorphic nucleotide sites, leading to different lineages. These variations can be as few as 5 to 15 polymorphic nucleotides, out of a genome of 30,000 nucleotides, with additional single nucleotide mutations in individual isolates. This genomic stability could mean that when ‘a vaccine turns out to be protective, it won’t likely lose its effectiveness due to genetic drift’, thinks Dr Trudy Wassenaar, as is often the case for the influenza virus vaccine.

Coronaviruses commonly have bats as their natural reservoirs and the novel SARS-CoV-2 is also thought to propagate naturally in bats, which are often used in Traditional Chinese Medicine. Hence, the authors compared the 5′ flanking region of SARS-CoV-2 with the flanking regions of coronavirus isolates from several bats from the region around Wuhan, where the first COVID-19 cases were reported. Interestingly, the coronavirus isolate to which SARS-CoV-2 showed the highest similarity was derived from the bat species Rhinolophus sinicus, corroborating the idea that SARS-CoV-2 uses bats as a reservoir. Bats, their body parts or faeces are commonly used in Traditional Chinese Medicine to treat different conditions by application to the human body or by oral intake. If an infected bat were used for such treatment, this is a possible explanation of how SARS-CoV-2 entered the human population and such treatment should be reconsidered. Another explanation could be that the collection of bat faeces from their natural roosting sites led to a host-jump involving the faeces-collector.

Independent of the true connection between a SARS-CoV-2-infected bat and any human involved, handling bats or bat products represents a severe risk of introducing any zoonotic coronavirus into the human population. The current pandemic caused by yet another zoonotic virus raises concerns about the use of bats in Traditional Chinese Medicine and one might even suggest completely forbidding the use of bats in human treatment