How did it get here? The origins of SARS-CoV-2
Coronaviruses have likely been around for millions of years, transmitted through birds, domesticated animals and wildlife.1 Middle East respiratory syndrome (MERS) coronavirus first appeared in 2012 in Saudi Arabia after it was transmitted to humans from camels.2 SARS-CoV (SARS) originated in bats and was first identified in humans in 2003. SARS was also the first severe and readily transmissible emerging infectious disease in the 21st century. The spread of SARS was exacerbated by modern ways of life, highlighting the importance of understanding host-pathogen interactions to predict and prevent the emergence, spread and evolution of novel infectious diseases.
SARS-CoV-2 is an enveloped RNA virus and owes its name as a coronavirus to its crown-like appearance under an electron microscope. This crown-like appearance is caused by a glycosylated protein, the Spike (S) protein, that envelops the virus. The genome of SARS-CoV-2 was sequenced in record time,3 but several variants have been reported.4 Gene- and transcript-level analyses are vital contributors to understanding host-virus interactions, particularly regarding approaches to the development of vaccines and treatments.
How does SARS-CoV-2 enter cells? Routes to infection
Determining how viruses get into the host cells is fundamental to understanding their pathology. Years prior to the emergence of SARS-CoV-2, studies revealed that coronavirus cell entry is mediated by the S protein. First, the S protein binds to cell-surface receptor angiotensin-converting enzyme 2 (ACE2) and it is then cleaved by serine proteases such as TMPRSS2.5 Interfering with receptor binding may be one approach to identifying possible antiviral treatments or vaccines. For example, Wei et al. used small interfering RNA (siRNA) followed by a combination of gene expression, flow cytometry and immunohistochemistry to determine that antagonists to an ACE2 entry cofactor inhibit S protein attachment and viral entry.6 Inhibition of endocytosis is another approach to antiviral investigation, as Zang et al. demonstrated by using gene-knockout screening to identify an interferon-stimulated gene and its protein product that restrict S protein-catalyzed membrane fusion.7
What are the primary sites of infection? Virus tropism
Inhalation of airborne viral particles appears to be a primary source of SARS-CoV-2 infection. To understand the mechanisms of infection in the airway, one study on FFPE tissues from deceased individuals used RT-qPCR to identify SARS-CoV-2 gene expression in the lungs, bronchi, lymph nodes, and spleen that was coincident with alveolar damage.8 Hou et al. studied living donors to understand at what point in the respiratory pathway infection occurs. They used a reverse genetics approach that revealed a gradient of infectivity in cells from the proximal to the distal respiratory tract.9
SARS-CoV-2 infection symptoms can affect multiple areas of the body, and other diseases such as cardiovascular disease and diabetes are associated with increased risk of developing severe infection. For example, Bulfamante et al. reported that about 20-40% of individuals hospitalized with SARS-CoV-2 also develop cardiac injury.10 The team demonstrated that SARS-CoV-2 can be expressed in the cardiomyocytes of individuals, even in those who showed no signs of cardiac involvement. Expression of a wide range of genes associated with SARS-CoV-2 infection has also been demonstrated in intestinal cells.11 Studies on the effects of SARS-CoV-2 on different types of tissues may reveal causes and treatment opportunities for co-morbidity factors and non-pulmonary complications of SARS-CoV-2 infection.
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Host response to infection
In host individuals, hyperinflammatory response correlates with severity of disease and mortality.12,13 Different inflammatory pathways may contribute to different individual outcomes.14 In severe cases, a hyperinflammatory response can result in what is referred to as cytokine storm syndrome.15 In one study, Vanderheiden et al. revealed a misdirected immune response following SARS-CoV-2 infection in airway epithelial cells. Importantly, treatment of the infected cells with interferons reduced SARS-CoV-2 viral burden as measured with RT-qPCR.16 Looking at other contributors to immune response, Olagnier et al. investigated the expression of genes associated with antioxidant response in SARS-CoV-2 immunopathology.17 They identified two agonists to a key antioxidant response regulator that inhibited both SARS-CoV-2 replication and expression of associated inflammatory genes. These studies suggest that different aspects of the immune system might provide opportunities for therapeutic or vaccine development.
Role of human genetics in disease outcome
In some cases, the severity of disease and risk of death from SARS-CoV-2 infection appear to depend more strongly on characteristics of the host rather than genetic variations of the virus. For example, individuals with blood group A have been shown to have an increased risk of severe disease while blood group O appears to have protective effects. Studies have also identified rare ACE2 haplotypes that are likely to predispose individuals to severe SARS-CoV-2 infection and may account for certain differences in severity of the outcome.18 Even Neanderthal-derived haplotypes have been identified as genetic risk factors for severe SARS-CoV-2 infection.19
Disease risk also varies among different demographics, with younger people less likely to develop severe disease, and men more likely to do so. A study of six young men with severe SARS-CoV-2 infection revealed rare loss-of-function variants in the TLR7 gene that were associated with defects in interferon response. Interestingly, the rare variants are located on the X chromosome, as are other TLR7 variants that have been proposed as explanations for the male sex bias in SARS-CoV-2 infection.20 There is great interest in understanding the role that human genetics might play in either resistance or susceptibility to SARS-CoV-2 disease.
Impact of virus evolution on disease pathogenesis
New genotypes of SARS-CoV-2 have been reported several times during the pandemic. While data on pathogenicity of these new genotypes is incomplete, general theories of viral evolution may help predict the evolutionary trajectory of the continued adaptation of SARS-CoV-2.
The evolutionary success for a single viral genotype depends on the number of hosts it can infect. An infected host surviving for a long time will contribute to the spread of the virus, which in turn will select for lower virulence. If, however, a host is infected by different viral genotypes, the genotype with highest pathogenicity will prevail and spread to more cells within the host. Within a single host, selection for higher virulence can take place, while among hosts, selection for lower virulence is more likely.
Close monitoring and in-depth analysis of emerging SARS-CoV-2 strains may help us make predictions and adapt not only public health responses but also vaccine development. One such attempt at broadening our understanding of SARS-CoV-2 evolution was published by Plante et al.21 The team engineered a SARS-CoV-2 strain with a known single-nucleotide A-to-G mutation that has become more common as the pandemic has spread. They found that the mutation enhances viral replication by increasing the infectivity and stability of virions. Higher titers of viral RNA in the upper respiratory tract compared to lungs, determined via RT-qPCR, may also indicate an increase in transmissibility.
Conclusion
The range of disease responses among people who become infected with SARS-CoV-2 spans the complete spectrum, including complete lack of symptoms, mild flu-like symptoms, severe multi-organ distress and death. Symptoms also vary by demographics and co-morbidities. With such a broad range of symptoms and rapid pandemic spread, efforts to control, treat and prevent SARS-CoV-2 infection span all aspects of the virus pathology, including mechanisms of infection, tropism, host response, human genetics and viral evolution. RT-qPCR panels that are readily available and already curated to contain the most-cited genes related to tropism, infectivity, pathogenesis, inhibition and immune signaling can save researchers significant time in their own literature reviews.
Genetic analysis technologies including RT-qPCR to quantify viral RNA and expression of experimental host genes, fragment analysis methods to prepare and validate genetic constructs, Sanger sequencing to confirm intended genetic regions and next-generation sequencing to identify key genomic elements have all become essential tools in the search for vaccines and therapeutics.
Learn more: Advancing your SARS-CoV-2 research through genetic analysis solutions
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References
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