In December 2019, cases of pneumonia of an unknown aetiology were detected in Wuhan City in the Hubei Province of China. The number of cases increased very rapidly, and by March 2020, more than 150 countries across the globe reported COVID-19 infections, prompting WHO to classify it as a pandemic disease. This erratic outbreak has forced governments in these countries to take drastic measures, including a complete lockdown of states and cities to contain the outbreak. These measures have had a major impact on the global economy, with job losses seen in every sector.
Global efforts are being made to understand the virus and the disease it causes to help develop vaccines, therapeutics and diagnostics to combat this unprecedented pandemic. In January 2020, a new strain of coronavirus (CoV), SARS-CoV-2, was identified to be the cause of this pandemic. CoVs are enveloped, non-segmented, positive-sense single-stranded RNA viruses and are classified into α−, β−, γ−, and δ– CoVs. While α– and β-CoVs infect mammals, the γ– and δ-CoVs generally infect birds. Previously, α-CoVs HCoV-229E and HCoV-NL63, and β-CoVs, HCoV-HKU1 and HCoV-OC43, have been found to infect humans, leading to mild symptoms. Two β-CoVs, severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 and Middle-East respiratory syndrome coronavirus in 2012 (MERS-CoV), have crossed the species barrier to infect humans, resulting in fatal respiratory illnesses including pneumonia. SARS-CoV-2 is a β-CoV and seems to have acquired higher infectivity as compared to the previous two β-CoV outbreaks.
SARS-CoV-2 is like a sub-microscopic tennis ball with little spikes jetting out of its surface. It has four major structural proteins, including spike (S), envelope (E), membrane (M) and the nucleocapsid (N) covering the viral genome. The spike protein (S) on the viral surface are primarily used by the virus to attack the human epithelial cells in the airway and the lungs. The S-protein is a glycosylated transmembrane protein, composed of the S1 subunit and S2 subunit. The S1 subunit contains a receptor-binding domain (RBD) that binds to the angiotensin-converting enzyme 2 (ACE2) on the host cell surface and uses it as a gateway to enter the host cell. ACE2 is a carboxypeptidase acting in the Renin-Angiotensin pathway to regulate blood pressure in our body. Once inside the cell, the virus uses the host’s cellular machinery to make tens of thousands of copies of itself which eventually gets out to infect other neighbouring cells.
ACE2 and infectivity
With the spread of the disease, it became clear that certain regions, like Italy, had severe infectivity and higher associated death rates, which suggested that underlying genetic differences could alter the susceptibility of individuals to the infection.
The interaction of SARS-CoV-2 with ACE2 is a key event in the pathogenesis of the virus and it is possible that certain natural variants on the gene encoding this enzyme can make its interaction stronger, making individuals more susceptible to the infection. To test this possibility, as a part of a collaborative effort, we started looking at natural variants in the ACE2 gene across global populations using different publicly available genomic data sets, including datasets from India (GenomeAsia 100K). Here, the ACE2 sequencing data from about 300,000 individuals across the globe was analysed and specific natural ACE2 variants were identified in each region. With a structural analysis of these variants, one could predict the variants that would facilitate or inhibit its interaction with the viral S-protein and make an individual more or less susceptible to the viral infection. Even though the variants that increase or decrease susceptibility are not very common (<1%), they are likely to be a factor in the varying disease severity observed in infected individuals.
The SARS-CoV2 infections and its deadly effects in humans are more recent and thus the pathogenic and protective variants have not been subject to purifying selection and therefore the variants we observe are predictably rare. The results from this study were published in BioRxiv recently.
The effort will enable studies that can correlate clinical symptoms with the reported ACE2 variation types. If verified in clinical settings, gene sequencing of ACE2 can become a tool to predict the risk of getting affected by this viral infection. This work can be further extended to other mammals and one can predict the probability of other mammals getting infected by this virus based on ACE2 sequence variations.
With no immediate availability of a vaccine or a specific drug, it is inevitable that the virus will linger for some more and we will be forced to live with this virus. An easy, point-of-care screening device and novel therapeutics to monitor and combat this disease are some immediate unmet requirements. Other than its direct implication in predicting the disease risk in individuals, this work also paves the way to the development of novel, simple and more effective strategies for virus screening and therapeutics.
ACE2 proteins carrying the variants that make their interactions stronger with the virus can be expressed recombinantly in cell culture. This modified recombinant protein can be used as a screening/diagnostics tool to effectively capture the SARS-CoV-2 virus from human saliva or nasal swabs using ELISA. Such screening/diagnostics tools can be further developed into sensitive point-of-care test kits. The same modified recombinant ACE2 can also be used to neutralise
the SARS-CoV-2 in COVID-19 patients. Here, the recombinant protein will act like a sink that adsorbs the virus and prevent it from sticking to ACE2 receptors on the cell surface and infecting it. Recombinant ACE2 has already been shown to have therapeutic potential to control blood pressure in animal models. By introducing some alterations using protein engineering tools, a modified ACE2 can be developed into a recombinant drug and can be tested for the treatment of COVID-19 patients with serious symptoms.
Taken together, the findings can be leveraged in multiple ways, ranging
from identifying the disease risk to finding a cure as the world comes to terms with the new reality of living with the virus.