In this article, William A. Haseltine, PhD, discusses findings that can help us understand why some people resist COVID-19 more effectively than others. He argues that we can use these findings to help us shore up the body’s defenses against SARS-CoV-2. In a companion article (Part II) that is scheduled to appear in the February issue of GEN, he will discuss biochemical details of the immune system’s struggle with the virus and how they may inform the development of antiviral drugs.
Why is SARS-CoV-2 so transmissible, infecting others before symptoms appear? Why do most people survive SARS-CoV-2 infection with little or no disease while some fall seriously ill and some die? The answers lie in the resolution of the age-old battle between invading microbes and our bodies’ response.
We bring to this struggle potent immune defenses, one innate and one adaptive. Our innate immune system, which is preprogrammed to recognize a broad array of microbes, unleashes a torrent of destructive enzymes within minutes to hours of initial infection. Our adaptive immunity is slower to respond. The adaptive immunity develops over the first two weeks but persists, recognizing and neutralizing specific invaders as they reappear. Vaccines stimulate adaptive immunity to equip us with antibodies and T cells that recognize and inactivate invading microbes.
SARS-CoV-2 wins the first phase of the encounter with our immune system, replicating wildly for the first three to four days by effectively silencing the early innate immune response. In these early days, virus concentration in the throat and nasal secretions reach astronomical numbers, sometimes exceeding one billion particles per milliliter. During this period, most of us are entirely unaware that we are infected.
Awareness of disease comes not from growth of the virus but rather activation of our defenses, primarily from production of interferon and other cytokines that cause fever, malaise, and cold-like symptoms. As we shall see, SARS-CoV-2 delays the production of interferon for several days. The absence of symptoms coincides precisely with the peak virus production. A global pandemic driven by asymptotic carriers is the consequence.
Survival depends on eventual control of virus replication. Looking at the trajectory of disease caused by the Delta SARS-CoV-2 variant, as documented in a preprint study conducted in China, it becomes clear that the innate immune response, not the adaptive immune response, is primarily responsible for protecting us in the initial encounter with the virus.1 On average, viral load peaks 3.7 days following infection and declines well before antibodies are produced as part of the adaptive immune response.
Fortunately, for most of us, our innate immune defenses are up to the job. The concentration of virus begins to drop precipitously about four days post infection. It is just before day six that symptoms appear as interferon and the full array of our innate immune defenses become fully active. From the timing, it is clear that it is our innate immune system that controls virus replication. The hallmark of the adaptive immune response, antibody production of virus-specific T cells, is delayed by 10 to 14 days (Figure 1).
Innate immune virus suppression is the end of the story for most of us, but unfortunately not for all. Increasing evidence suggests that it is a failure to fully mobilize innate immunity early on that results in serious disease and death. The impact of COVID-19 on the elderly is far greater than on children and young adults. Recent studies show that the innate immune response is strongest in those least affected, children and young adults, and weakens with age.2 Studies of genetic predisposition to serious COVID-19 disease all point to defects in interferon induction or function.3
Here I will focus on what occurs in those fateful few days. I will outline the powerful array of defenses our cells deploy to ward off the invading virus, describe the virus’s elaborate countermeasures, and detail weaknesses in our defenses that result in serious disease and death. I will end on a note of hope.
We can tip the balance in our favor so that few if any succumb to COVID-19. We now have vaccines that protect most people. Soon, we will have potent antiviral drugs that will provide additional protection to those with immune deficiencies and those who are infected.
Our experience with HIV tells us that if we are to avoid resistance and limit toxic effects, we will need combination antiviral drugs, each directed to unique viral proteins. We are fortunate that studies of the importance of innate immunity and SARS-CoV-2 countermeasures provide us the wealth of attractive targets that we need. Here I outline the key players in our innate immune response to SARS-CoV-2 and in the virus’s countermeasures. Being familiar with these players will give us the edge that we need.
Interferon is the key to our innate immune response to SARS-CoV-2. Virus entry and replication trigger the production of interferon, which in turn unleashes a torrent of hundreds of antiviral proteins. For clarity and simplicity, I will describe the pathways leading to the induction of one of the most critical and best understood of these antiviral proteins, 2′-5′-oligoadenylate synthetase 1 (OAS1). Those of us who have the inherited ability to produce the most active form of OAS1 rarely fall seriously ill.4 Those that inherit a less active OAS1 have a higher-than-average incidence of severe disease.
One way to think of cellular innate immunity is as a series of tripwires that signal the cell to produce interferon, which then activates antiviral defenses in the infected cells and alerts nearby cells to impending danger. In the case of SARS-CoV-2, the tripwires are proteins that sense the presence of the virus genome.
SARS-CoV-2 is an RNA virus—the genome is a long single strand of RNA. To reproduce, the virus must make multiple RNA copies of the genome as well as viral messenger RNAs. An array of ready-made cellular sensors are cocked and loaded in the cytoplasm, ready to spring into action the moment foreign RNA appears.
RNA species not normally present in the cell serve as triggers of the innate immune response (Figure 2A). The triggers include both short and long segments of double-stranded RNA, as well as RNAs that lack the 5′ cap structure and other modifications typical of cellular messenger RNAs. Replication of SARS-CoV-2 requires double-stranded RNA both of the full-length genome as well as shorter viral messenger RNAs.
Double-stranded DNA is detected by two protein sensors, retinoid-inducible protein gene 1 (RIG-1) and melanoma differentiation–associated gene 5 (MDA5). RIG-1 detects shorter double-stranded RNAs, whereas MDA5 detects longer duplex RNAs. Binding of double-stranded RNA triggers monomers of RIG-1 and MDA5 to self-aggregate into multiprotein complexes. The multimers then migrate to the surface of mitochondria where they encounter and activate the mitochondrial antiviral signaling protein (MAVS).
Once activated, MAVS initiates two separate antiviral pathways. One leads to the production of OAS1 via interferon induction. MAVS activates two cellular enzymes, TANK binding kinase 1 (TBK1) and inhibitor of nuclear factor kappa-B kinase subunit beta (IKK-β), to phosphorylate the transcription factor interferon regulatory factor 3 (IRF3). Phosphorylated IRF3 enters the nucleus and stimulates the production of both interferon alpha and beta (Figure 2A).
Activated MAVS also induces suicide of the infected cell, a process called apoptosis. MAVS activates the cellular protein caspase 8, initiating cell death.5 Programmed cell death is a protective response as it prevents further virus replication and destroys nascent virus particles.
Interferon-stimulated gene activation
Interferon alpha and interferon beta induce antiviral proteins within their infected neighbors (Figure 2B). The first step is binding of interferon to cell surface receptors. The interferon alpha-beta receptor (INFAR) consists of two proteins, INFAR1 and INFAR2. Interferon binds first to INFAR1. The complex then binds to INFAR2 to form a triplex comprised of interferon, INFAR1, and INFAR2.
The juxtaposition of the two receptors brings their associated protein kinases, Janus kinase 1 (JAK1) and nonreceptor tyrosine kinase 2 (TYK2), into close proximity, resulting in the phosphorylation of both receptors. The phosphorylated receptors recruit the signal transducer and activator of transcription proteins (STAT1 and STAT2).
Once associated with the receptors, the STAT proteins are themselves phosphorylated. Phosphorylated STAT proteins dimerize and translocate to the nucleus where they associate with interferon regulator protein 9 (IRF9) and together bind the interferon response stimulator sequence to induce the transcription of interferon-stimulated genes (ISGs). The ISG proteins are the primary effectors of the innate immune antiviral response. OAS1 is one such ISG protein.
OAS1 a key player in COVID-19 defense
OAS1 is one of the very first proteins identified as central to our defense against viral infections. OAS1 is part of a three-gene cluster that includes OAS1, OAS2, and OAS3. All the OAS proteins recognize short double-stranded RNAs. Upon RNA binding, the OAS enzymes synthesize 2′-5′-oligoadenylate (2-5A). Ribonuclease L (RNAse L) is present as an inactive monomer in the cytoplasm, ready to spring into action upon viral infection. The signal is 2-5A. In the presence of 2-5A, two RNAse L monomers associate to form a dimer. The RNAse L dimer cleaves single-stranded RNA, preventing further virus replication by fragmenting both viral genomic messenger RNAs.
Two recent papers, one in Nature Medicine and one in bioRxiv, highlighted the importance of RNAse L in our antiviral defense.4,6 The paper in Nature Medicine asked the question, which of the many interferon-stimulated genes is most effective in inhibiting SARS CoV-2 replication? The experimental conditions allowed evaluation of each ISG gene individually. OAS1 was found to be the most potent inhibitor of SARS CoV-2 of all the genes tested.
Both studies note that the OAS1 gene comes in two major forms, a 42K (42 kilodaltons) and a longer 46K protein. The 46K OAS1 protein is many times more potent in SARS-CoCV-2 inhibition than is the 42K. The two OAS1 genes differ by a single nucleotide—a single G-to-A substitution that inactivates the splice acceptor site of the seventh exon of the 42K variant. The 46K protein contains a long-chain fatty acid at the carboxy terminus, thanks to the prenylation signal at the end of the seventh exon. The 42K version, although active as a 2-5A synthetase, lacks a terminal fatty acid.
These two studies solved an outstanding mystery. Previous investigators noted that the OAS region plays an important role in resistance to SARS-CoV-2 and certain other RNA viruses. Those who inherit one genetic variant in the OAS are far less likely to end up hospitalized, severely ill, or dead following SARS-CoV-2 infection than those who inherit another form of the gene. The difference in disease response to infection turns out to be the single nucleotide that distinguishes the short from the long form of the OAS1. In technical terms, this is the difference between the re10774671 (G) or (A) allele. One report finds a 100-fold enrichment in the A allele for those hospitalized for COVID-19 as compared to gene frequency in the population.
William A. Haseltine, PhD, is the founder, chairman, and president of ACCESS Health International, a foundation dedicated to improving access to high-quality health services worldwide. He is known for his groundbreaking work on HIV/AIDS and the human genome, and he has founded more than a dozen biotechnology companies, including Human Genome Sciences.
1. Kang M, Xin H, Yuan J, et al. Transmission dynamics and epidemiological characteristics of Delta variant infections in China. medRxiv. August 13, 2021. DOI: 10.1101/2021.08.12.21261991.
2. Loske J, Röhmel J, Lukassen S, et al. Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children. Nat. Biotechnol. 2021; DOI: 10.1038/s41587-021-01037-9.
3. Zhang Q, Bastard P, Liu Z, et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 2020; 370(6515): eabd4570. DOI: 10.1126/science.abd4570.
4. Zhou S, Butler-Laporte G, Nakanishi T, et al. A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity. Nat. Med. 2021; 27(4): 659–667. DOI: 10.1038/s41591-021-01281-1.
5. Lei Y, Moore CB, Liesman RM, et al. MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins. PLoS One 2009; 4(5): e5466. DOI: 10.1371/journal.pone.0005466.
6. Iida K, Ajiro M, Muramoto Y, et al. Switching of OAS1 splicing isoforms mitigates SARS-CoV-2 infection. bioRxiv. August 23, 2021. DOI: 10.1101/2021.08.23.457314.