Host Immune Defenses Against Viral Infections, Part I: Innate Immunity

By Elene Tsopurashvili ( & Katelyn C. Cook (

July 2nd, 2020


Viruses are everywhere! We encounter them every day at work, on a train station, and in an ice cream shop. We are exposed to viruses constantly, and not only when the person next to us sneezes – trillions of viruses drop from the atmosphere on a daily basis, and just a thimble of seawater contains millions of viral particles. Despite living in a world dominated by viruses and other microbial pathogens, we rarely get sick from them. How is this possible?

We are protected from pathogen invasions by our immune system, which consists of both the innate and adaptive (covered in our next post!) branches. The innate immune system is our first line of defense, encompassing passive and active processes that prevent viruses, bacterial pathogens, and other foreign substances (e.g., pollen) from infiltrating the body. Large structures, such as skin, mucosal membranes, tears, and saliva, impede viruses from reaching interior cells to initiate an infection. Within these barriers, specialized immune cells including macrophages, dendrites, and neutrophils are constantly monitoring our tissues to detect, engulf, and destroy invading germs. If a virus successfully evades these defenses and enters a host cell, it is further met with a series of anti-viral sensing and defense mechanisms geared towards inhibiting virus replication. Triggering these innate cellular immune pathways will mark the cell as infected, signaling to natural killer (NK) white blood cells to eliminate the cell, thus preventing the spread of infection.

Within an invaded cell, a key step in initiating innate danger signals is the detection and recognition of the infectious agent. This process is largely accomplished by sensing foreign molecules, such as proteins, lipids, carbohydrates and/or nucleic acids, the genetic material of invading pathogens (e.g., DNA, RNA). Numerous proteins – many conserved throughout eukaryotic organisms – are positioned across the cellular landscape for this purpose, including Toll-like receptors (TLRs), RIG-I like receptors (RLRs), AIM2-like receptors (ALRs), NOD-like receptors (NLRs), and anti-viral nucleotidyltransferases (NTase), among others. These proteins can rapidly bind to foreign particles and initiate a cascade of anti-viral signaling events, ultimately resulting in the production and release of interferons (IFN), molecules that warn white blood cells about the pathogenic invasion.

A significant challenge for these sensors is distinguishing foreign material from that of the host cell. In the case of nucleic acid sensing, one way this is accomplished is by detecting aberrant structures (e.g., dsRNA, which is not made by eukaryotic cells) and/or localization outside of the nucleus. For example, TLRs, RLRs, and anti-viral NTases, such as cyclic-GMP-AMP synthase (cGAS), patrol other organelles and the cytoplasm, searching for pathogenic RNA/DNA and complexing with other cytoplasmic proteins to achieve anti-viral signaling. Many of these signaling axes have been well-described during infections with viruses that replicate in the cytoplasm, such as the flaviviruses dengue (DENV) and hepatitis C (HCV).

However, this does not explain how cells sense nuclear-replicating viruses, which includes common human pathogens like the orthomyxovirus influenza A, the alpha-herpesvirus herpes simplex type 1 (HSV-1), the beta-herpesvirus human cytomegalovirus (HCMV), and the Kaposi sarcoma-associated gamma-herpesvirus (KSHV). This mystery was partially resolved by the finding that cells possess nuclear DNA sensors, such as the ALR interferon-inducible protein 16 (IFI16). This protein can recognize viral genomes within the nucleus, suppress viral gene expression, and initiate IFN production, making it a core player in innate immune responses. In the decade since its discovery, our lab – among many other research groups – has worked to elucidate the mechanisms underlying the anti-viral roles of IFI16.

For example, in HSV-1 and HCMV infections we identified distinct functions for IFI16 protein domains, showing that its anti-viral capacity relies on binding to viral DNA at the nuclear periphery. IFI16 then recruits additional proteins to coordinate immune processes, a key focus in other studies that demonstrated IFI16 can assemble multi-complex signaling hubs at invading viral genomes. This includes a “restrictosome” at replicating HSV-1 DNA, which restricts viral gene expression, and an “inflammasome” at KSHV genomes, which activates programmed cell death. Linking nuclear to cytoplasmic DNA sensing, the Knipe lab at Harvard, in collaboration with our lab, discovered that IFI16 interacts with and is stabilized by cGAS, demonstrating the importance of collaboration between anti-viral sensors across the cell. Current investigations are largely focused on characterizing the dynamic regulation of IFI16-mediated immune complexes, and determining how IFI16 functions are specific to pathogenic rather than host nuclear DNA, a conundrum with broad implications (esp. auto-immune disorders).

Despite the diversity and abundance of innate immune defenses, ultimate protection against intracellular microbes is not guaranteed. Nearly all viruses have co-evolved strategies to manipulate and subvert innate defenses, enabling the progression of infection. This can be accomplished by degrading, sequestering, or inactivating the anti-viral sensors. For example, multiple groups have shown that HSV-1 evades IFI16-induced immune responses by causing its proteasomal degradation, and we found that HCMV uses viral proteins to inhibit IFI16 from reaching its genome. In comparison, DENV bypasses host detection by changing cytoplasmic membrane structures to obscure its genetic material from RNA sensors. Similarly, coronaviruses (e.g., SARS-CoV-2 of COVID-19 fame) use a specialized viral protein to shield untranslated RNAs from cytoplasmic anti-viral receptors.

The innate immune system is also vulnerable to other types of malfunction that can mount serious health concerns, such as a “cytokine storm” that has received much focus during the ongoing COVID-19 pandemic. This occurs when disease agents cause the immune system to overproduce anti-viral signaling molecules known broadly as “cytokines” (e.g., IFNs described above), which can be lethal in high amounts. Cytokine storm responses have been described during various virus infections, including avian H5N1 influenza virus, HCMV, and SARS-CoV-2. In SARS-CoV-2 infected individuals, this can cause acute respiratory distress syndrome (ARDS), a major factor in the severity and mortality rate of COVID-19. Treating these cases can require therapeutic intervention with anti-inflammatory drugs, augmenting intrinsic cellular mechanisms to prevent or turn off rampant cytokine production.

In fact, cells have numerous strategies to rapidly terminate the innate immune response. Anti-viral sensors can engage in regulatory cross-talk, suppressing the activation and downstream signaling of other immune proteins. We recently described this during HSV-1 infection, whereby the immune response factor OASL negatively regulates cGAS and reduces cGAS-mediated IFN production. This phenomenon has also been demonstrated for other proteins; some TLR pathways, for example, require the zinc finger protein A20 to turn off after danger signals have passed. In addition, direct changes to protein structure (e.g., post-translational modifications) can toggle active versus inactive signaling states, as we and others recently showed for cGAS. The existence of such gatekeepers highlights the importance of finely tuning innate immunity to maintain a healthy system. Accordingly, ongoing investigations geared towards revealing the underlying mechanisms of host defense and viral evasion strategies are critical for the scientific community to better understand and combat immunopathologies.