Did SARS-CoV-2 Cause The Decline of Influenza Through Viral Interference? it Seems Unlikely.

There seems to be a popular claim going around that the decline in influenza during the 2020 season is the result of viral interference, which is fascinating. Unfortunately it is being used to argue against the necessity of non-pharmaceutical interventions as means to control the spread of respiratory pathogens, which is much less fascinating and dishonest. I think that the source of this claim is likely this article from STAT which discusses the concept generally. In short, the concept refers to the propensity of having an infection with one virus disrupting your ability to become infected with another one. It’s a fairly well documented phenomenon at the level of cell culture, and it does make some intuitive sense. The immune system has a general network of pattern recognition receptors which overlap greatly for viruses, and viruses rely very strongly on their host cell for resources to replicate (they are parasites after all), which is why so many of these innate defenses converge on interferons. In particular RLRs seem to be very important sensors of viral nucleic acids as they are capable of recognizing the nucleic acids of viruses from every group in the Baltimore classification except for single-stranded DNA viruses (SARS-CoV-2 does indeed interact with RLRs and has machinery to disrupt their downstream interferon induction; a more global view of the innate immune response to SARS-CoV-2 can be found here). Interferons do a great many things, but among them, they rewire the metabolism of the cell to disrupt protein synthesis and as a result, the viruses can’t replicate their own proteins. I suppose that there’s a point of caution there about the terminology- it’s not so much that the first virus interferes with the second virus, but rather that it triggers a response from the host that makes them much more difficult to infect. Thus one could imagine a relatively simple mental model: virus 1 infects the cell, replicates some, triggers the intrinsic antiviral sensing mechanisms that result in production of interferon, and suddenly virus 2 has a really hard time establishing a productive infection in the same cell. A more detailed (though dated) discussion of interference can be found here.

Co-infection (where both pathogens are acquired at the same time) and superinfection (where hepatitis B is acquired first) have different trajectories in hepatitis D virus infection. This is considered the most severe form of viral hepatitis. Negro, F. Hepatitis D virus coinfection and superinfection. Cold Spring Harb. Perspect. Med. 4, a021550 (2014).

Beyond the cell culture level, the concept has therapeutic potential: one could imagine that if infected with a particularly dangerous virus, one could be inoculated with a harmless one (or relatively so) that would in turn disrupt the ability of the other virus to replicate and cause disease. This is known as superinfection therapy (SIT). There does appear to be some evidence of it occurring beyond the cell culture level as an elegant study from Wu et al showed, and it even pointed to interferons as the mechanism of interference. In their study, they performed a retrospective epidemiological analysis showing that there’s an inverse relationship between influenza A infections and rhinovirus infections over several years, and on statistical analysis there is indeed a significant divergence between the superinfection of the two (which is to say, if there were no effect and the phenomenon were solely due to random chance, there would be many more superinfections expected to observed than there actually were). They additionally show that infection of primary human airway epithelial cells with rhinovirus is really disruptive to future infection by influenza A virus, and upon treatment with a drug that blocks the induction of interferon, the effect disappears and co-infection readily occurs. This is really great news because rhinoviruses are relatively harmless, so one could imagine affording people a temporary protection in the setting of a pandemic influenza through deliberate infection with rhinoviruses. Of course, the issue is that you can only keep up production of interferon for so long before its effects become toxic- so that does raise concerns about the potential of superinfection as a prophylaxis. Additionally, the cell culture model is a bit reductive; there could be other components of the immune system mediating nonspecific protection (i.e. trained immunity- though I will note that I have some significant skepticism about this concept’s therapeutic potential beyond what has been established for BCG immunotherapy in bladder cancer; but the intellectually honest thing to do would be to explore it nonetheless). I think an animal model could have been valuable in assessing that- maybe even a human challenge study for the future. Finally, I think it would have been very valuable to see experimentally what happened when you inoculated the cells with influenza before rhinovirus, as, if the hope is a therapy, that would be the typical scenario you would be dealing with- a patient who has severe influenza rather than one in the throes of a brutal rhinovirus infection. That said, my read of the study was not that it was immediately striving for clinical application of these results but rather as an explanation of some key aspects of host-pathogen interaction and seasonality of respiratory viruses, and I think it accomplishes that quite well given the limitations of its retrospective design. However, given that the data are retrospective, and limited to a single site, and given that the supporting experiments are in vitro, we need to be very cautious with our interpretations of the study here. One could imagine these data used to justify a prospective cluster randomized trial where before flu season a large cohort of individuals is recruited to be inoculated with a rhinovirus and at another site they receive a sham control and comparing the incidence of influenza and its associated complications.

Some examples of how viruses avoid host cell induction of interferon. García- Sastre, A. Ten strategies of interferon evasion by viruses. Cell Host Microbe 22, 176–184 (2017).

I think you all know me well enough by now though to know there’s a “but” coming. The thing is, the picture presented until now might lead you to forget that superinfection and co-infection (when infection with both the pathogens occurs at the same time as opposed to one and then the other as in superinfection) do happen, and it’s typically not a good thing. Influenza for instance is known for being complicated by bacterial pneumonia (one of my favorite reviews- yes, I have favorite reviews. I’m a giant nerd)- though you could reasonably demur that this is quite different from two viruses superinfecting the same host, given that interferon can have more complex roles in the course of bacterial infection. Superinfection can take many complex forms though. For instance, patients who have hepatitis B virus infection can develop a much more severe form of the condition if they also acquire the hepatitis D (delta) satellite; hepatitis D cannot replicate unless hepatitis B is also present within the cell, and it leads to a more severe disease (though the form it takes depends on whether superinfection or co-infection occur, emphasizing the importance of timing). The thing is, the existence of viral superinfections that make things worse is kind of an important challenge to SIT. For one thing, given how broadly interferon acts to prevent viral infections, based on what we have thus far established, how could it even happen? Well, therein is the mess: interferon is such a powerful and ubiquitous mechanism of host defense, that for any viral infection, there needs to be some way of getting around it if productive replication is to occur. One of the most obvious ways is simply to hide. Coronaviruses for example can avoid detection of their nucleic acids (which would then trigger interferon signaling) by using double-membraned vesicles. Alternatively, the virus could take an active role in suppressing the induction of interferon-stimulated genes (ISGs) or interferon itself. Orf9b of coronaviruses disrupts key signaling at the mitochondria that can induce interferon production. We could go on- the point is viruses have to be really good at getting around interferon to function as viruses. A recent preprint even suggests that this is why B.1.1.7 variants are both more lethal and more transmissible than other variants of SARS-CoV-2: they are better at getting around the innate antiviral immunity we have. The fact that viruses can suppress interferon creates a problem because this would indicate some cells are at less than their baseline level of vulnerability in the course of a viral infection because there are processes at work actively preventing them from inducing their antiviral protective mechanisms. The thing is that the suppression of interferon, realistically, cannot be permanent (in fact the preprint about B.1.1.7 I just linked suggests that the delay in its production and then subsequently turning it on contributes to spread of the virus by activating an inflammatory cascade that prompts the host to cough, thereby allowing it to spread), so this suggests that there is actually a finite window of increased susceptibility to superinfection, reinforcing that whole theme of “timing is everything.”

Preinfection with influenza results in worse outcomes in mice and enhanced SARS- CoV-2 replication in the respiratory tract. Bai, L. et al. Coinfection with influenza A virus enhances SARS-CoV-2 infectivity. Cell Res. 31, 395–403 (2021).

Early on in the pandemic I remember some of my friends who treated patients describing those who had both influenza and COVID-19 at the same time (sometimes they even had influenza A, B, and COVID-19 at the same time), which sounds… just really terrible. There was also concern for the possibility of a twin-demic: influenza and SARS-CoV-2/COVID-19. That thankfully did not pan out. There was however a center in Wuhan which noted shockingly high rates of superinfection of influenza and SARS-CoV-2 (57.3 %), and in particular superinfection with influenza B and SARS-CoV-2 was associated with worse outcomes (studies are not entirely consistent on the effect this has on patient outcomes). Of course, that result needs to be interpreted with a lot of caution: it’s a single- center study, and it’s retrospective, but it did comprise the largest sample of superinfected patients that I could find in the literature. You might also expect the analysis of these results to be subject to some important confounders, e.g. individuals who are superinfected with both viruses might have poorer health at baseline or immunological deficiencies that would make the superinfection more serious. It’s hard to assess the meaning of these results without matching patient to singly infected patients. The study does also allude to the fact that COVID-19 mortality was noted to be lower in regions where uptake of influenza vaccines was higher, which is interesting but also likely not a reliable basis for making firm conclusions. A helpful starting point would be to examine how the two viruses interact in a cell culture system, which fortunately Bai et al did. Influenza A virus very clearly enhanced the ability of SARS-CoV-2 to infect multiple cell lines. They further validated this in a mouse model where some mice received both SARS-CoV-2 and influenza (influenza first 2 days earlier) and others received only SARS-CoV-2 and sacrificed 2 days after SARS-CoV-2 infection:

The lung histological data in Fig. 2e further illustrate that IAV and SARS- CoV2 [superinfection] induced more severe lung pathologic changes, with massive cell infiltration and obvious alveolar necrosis, compared to SARS-CoV-2 single infection or mock infection.

They called it coinfection in the paper but it didn’t occur at the same time, so it’s technically superinfection. They then demonstrate that at least part of this explainable by the fact that influenza infection enhances expression of ACE2, which is the receptor for SARS-CoV-2, and an interferon-stimulated gene (ISG). Bai et al also showed that using A549 cells, influenza virus, but not HPIV, HRSV, nor HRV3 enhanced infection by SARS-CoV-2.

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