On bat-like immune systems, and “living with the virus”
Dr. Noor Bari, Emergency Medicine • 21 July 2022
❦ “So, we want to “live with the virus”. Is there any evidence of this occurring successfully anywhere?
Yes!
In bats... and it has taken 64 million years of evolution to get there.
To “live with the virus”, bats have better host defences – they don’t overdo inflammation, and they can get rid of toxic compounds and deal with reactive oxygen species much better than humans.
They literally live with the virus.
📖 (20 Jan 2021 ~ Nature) Lessons from the host defences of bats, a unique viral reservoir ➤
For humans to “live with the virus”, we would need to have similar mechanisms to permit SARS-CoV-2 to be part of our biome – without causing all of the autoimmune disease and other damage.
We would have to have fundamentally different biochemistry and immune systems.
We can mimic this using therapeutics to some extent, and this may help us treat Long COVID.
However, I don’t think that we will naturally become resilient to SARS-CoV-2 for a very long time.
What I’m trying to say is that mass-infecting this generation of children is unlikely to result in them developing a bat-like immune system within their lifetimes.
It’s ridiculous that the attempt was ever made.
I genuinely think that putting ventilation upgrades into every building and wearing good-quality masks will be easier than building a genetically modified SARS-resistant human.
I keep trying to give you the easy way out!
The coronavirus is moving into our bodies and is attempting to stay there, just like it does in bats.
The problem is that our bodies try to fight it.
We fight it well enough to reduce detectable virus-shedding on our breath, but there is evidence (persistent spike RNA) that the virus is hiding somewhere else in our body anyway.
So our bodies keep fighting it. The collateral damage is the problem.
What are our choices?
1. Figure out how to change human physiology so that we don’t burn ourselves out fighting an elusive and persistent enemy.
2. Or figure out how we can stop transmission.
The second is easier, and economically sound.
The ability to completely clear coronavirus is also a potential goal – but again, therapeutics will be needed because we have places where, if the immune system is left to do it, it causes damage – and coronavirus has many tricks to help it hide from detection.
Needless to say, coronavirus can evolve a lot faster than we can, so we need to use our brain cells in a different way to fight COVID-19.
Instead of using microglia, we need to think...”
➲ Video: ‘SARS-CoV-2 infection triggering cell fusion and cell death in bat (Myotis myotis) brain cells’ by © Sophie-Marie Aicher.
“The above image is SARS-CoV-2 destroying bat brain cells. In vitro mind you...
So we don’t know how a bat immune system might have dealt with this in the wild… It’s possible that even bats won’t do so well with COVID-19!”
© 2023 Dr. Noor Bari. ➲
“We are drunk-driving in healthcare... with a pathogen that has a 10% fatality rate in that setting.”
❦ “If you are letting yourself get infected and taking no precautions against passing it on, you are not a passive bystander for your next infection. You’ve participated in creating it.”
❦ “It’s not like I’ve never seen people die of causes that are a result of their lifestyle... but it’s awful seeing people die as a result of other people’s lifestyles... and now that includes their healthcare provider! It feels very similar to watching people die from another person’s drunk-driving... That’s the closest similar situation I can think of. We are drunk-driving in healthcare... with a pathogen that has a 10% fatality rate in that setting.”
❦ “If y’all are busy weakening your immune systems with one virus, let me assure you that there are packs of other pathogens out there waiting to chew on the leftovers.”
❦ “Anything that is more transmissible will kill in two ways. Infecting more people. Worsening pressure on healthcare.”
❦ “In real life, no-one… and I mean no-one… is actually living a normal life if they have abandoned C-19 precautions. Either they are suffering the effects of illness themselves, are caring for someone that is sick, grieving, or all of the above. It’s not all people of one race/genotype either. It’s across a broad spectrum of people. It’s not even segregated by money. People with money that did not take it seriously enough to seek treatment have also fallen foul of problems. At this point in my social world the denial is being peeled away… and people are opening up about issues. However many still feel unable to prevent further problems. I’m seeing everything from acute COVID deaths to long COVID deaths. Every kind of autoimmune disease seems to be on the cards, colitis, hearing loss, joint problems… One common thread… people either have not made the connection to C-19, or think they are the odd one out. That they have somehow personally failed to be tough enough to weather the SARS storm. One can only congratulate the ghouls that have allowed that feeling to spread. I mean no-one I know… So all these people that I see on-and-off are living in their own quiet bubble of difficulty… and no-one is brave enough to tackle anything because no-one wants to be different… or perceived as a failure… or in many cases, they don’t know what to do anyway… This is a massive failure of public health. The anti-maskers are out on social media, loud and proud; public health departments barely whisper some diluted numbers once a week. Literally, things tick along “normally” in the conversation until you hit that bump. Ever since my last infection I _____. Fill in the blank. It’s often something that sounds really minor… but those that have read the data know what it really means. Quit the gym. Food is bland. Ringing in ears. Headaches. Joint pain. Stomach upset. Dizzy. Heart races. Tired. Stopped driving or stopped driving long distances. Quit the booze. Rashes. Keep getting xyz infections. Just going to tack on here that the first sentence contains an omission. “Real life” = People I know in real life. My real-life home village is sick or grieving or caring. Pretty much every household.”
❦ “Dear economy enthusiasts... The only humane way to avoid locking down for airborne disease control ever again is to set up safer indoor-air infrastructure... globally. Everyone that is slowing down this process is asking for another lockdown. Or mass murder. More likely another lockdown though because in the end, if bird flu takes off or MERS has an interesting offspring... the public will not stomach as much death as the anti-lockdown and dirty-air proponents would like.”
❦ “There is no such thing as “personal risk assessment” for the vast majority of people. A tiny number of dominant personalities in your life (and it could be you) have decided what to do, and the rest will follow. Even those that are making the decisions are not making a personal risk assessment. They are making a group risk assessment and taking their whole family/community with them. People may not even realise this – that they have made the decision on behalf of their entire household/class/company... but they have... If there is no responsible public health leadership, someone else is leading... because that is how we work, by and large, as a species. Someone is in charge... someone is always in charge, and unfortunately... misinformation is rife.”
❦ “No-one said life was gonna be easy. No-one said living through a pandemic was going to be easy. It’s all about what you think is important and worth fighting for. I chose health, lives, and sticking together. I chose to try to solve problems, not hide them. You can rewrite history. You can say that the mass overseas graves didn’t matter. You can say that we didn’t need to lock down in Australia in 2020 (when we had no PPE, no vaccines, and no therapeutics). I know different. I was there. Shed enough tears, attended enough zoom funerals… I know it wasn’t easy. I saw the tears when I said that a family on the breadline needed to isolate. I saw the heartbreak as I led a person away from their family, across the red line into the “red zone”. Even as I walked away from my family every day into the red zone, I felt your effort with me. When I said goodbye to my kid every day, and isolated away from my family to protect them from any accidental breaches... I know you all sacrificed too... ...and I was so grateful, and so proud... I wasn’t the one saving lives, you all were. You saved my life... I’m sure of it. We didn’t have enough PPE... Don’t ever forget that, and don’t let those bombastic characters writing rubbish articles about lockdown ever take that away from you.”
❦ “I’m vaguely following the chatter on the comparisons of COVID with HIV. I’ve never been a fan of this, because there are so many unanswered questions. One thing I am sure of. Research shows the immune system does get damaged. It does. Which bits? How much? Recovery? What opportunistic infections? Impact on global disease patterns? Impact on animal disease patterns (ecology and food-chain threats)? All questions that will be answered over time. No-one should be surprised by this. It should not be even vaguely controversial. Plenty of viruses damage the immune system . We will find out exactly the extent of the nature of COVID on this aspect of health. Another thing I can say with some certainty. Your chances of recovery from a depressed post-viral immune system will not be improved by further [SARS-CoV-2] infections. I can see a lot of people directly comparing COVID with HIV. Rest assured. I am concerned. I just don’t find that particular comparison helpful. As many have already pointed out, there are significant differences too. You don’t walk into the supermarket and catch a new strain of HIV starting a whole new acute infection every 6-8 months, for example. But there are also signs that some immune cells are recovering many months after infection too – then again, there are probably reservoirs in the body that could potentially continue to mutate, and then cause other pathology down the line – as some animal coronaviruses do. I think COVID is quite an interesting and horrible disease. I expect we will see what repeated infections really do as time goes on. Excess deaths are already through the roof. One last attempt to clarify. Trying to make COVID into either a cold, or HIV, and ending up with “half-way between” – when in reality COVID is doing 100% COVID, which is turning out to be really, really bad in its own right… and it’s airborne… and we are catching it all the time. That’s the part I find frustrating with this comparison. SARS is a dangerous, dangerous disease. It always has been. Both of them [SARS-1 and SARS-2] . Yes, there are threads of similarities, and we can use our wealth of knowledge to extrapolate possible outcomes, and test treatments… But SARS is not half-way to anything. It is, in itself, a giant problem.”
❦ “No. We haven’t gone back to normal. We have gone forward into abnormal. Really abnormal. Kill your elders abnormal. Douse the kids in viruses abnormal. Ignore and kill disabled people abnormal. Please go back to normal... because I don’t believe for a second that when you wake up and look in the mirror, that this is what you ever wanted to see looking back at you. It’s not too late.”
❦ — “How was your New Year?” — “S’ok...” Sad face... young adult person... “I got sick... kind of like a cold...” (But face says, “It ruined my New Year.”) So much is left unsaid. So many assumptions that everyone else is having fun – why not me? Guilt about being a let-down. (‘Am I not strong enough? My immunity not good enough?’) Others move on to chat about dining out at restaurants... This young person turns away, and continues to work. Isolated in her thoughts... How desperately I wanted to go over to her and say, “You are not alone...” But I’m a stranger, just passing... I think about how people in power are misleading and hurting young people. It’s deplorable.
❦ “COVID-19 causes lung fibrosis. It affects the immune system, and it causes liver fibrosis . COVID-19 causes brain inflammation and heart inflammation, strokes, heart attacks and large blood clots. COVID-19 causes diabetes . COVID-19 can cause kidney failure. I could go on... and on. Bone necrosis, joint pain, hair and teeth falling out. Do you normally expect a cold to make your teeth fall out ? Look up ‘lung fibrosis’ and ‘liver fibrosis’. Google them, and read about the complications. Read how patients that have these progressive diseases die. (Apologies to patients that already know.) Time and again, these patients have said to me (particularly when I was a young medical student): “Don’t do what I did.” “Don’t smoke.” “Alcohol is...” “I wish I had never...” “Save yourself...” Of those dying of infectious causes of lung and liver fibrosis: “Why me...?” “I wish I could have avoided that infection...” Stop. Stop as many COVID infections as you can. Stop now. Now is your chance to avoid treading these terrible paths. Once COVID has weakened your organs and immune system, every other pathogen – and even some environmental/commensal bugs – can move in... You will feel nothing wrong, nothing wrong, nothing wrong... then... the cascade of deterioration will snowball. Stop now while you are still in the “I feel nothing wrong” phase. There may well already be stuff wrong, but it’s better to try to stay in this phase than accelerate towards death any faster than is avoidable. No, not everyone will get every effect to the same extent, but macrophages do get activated by COVID (as well as other immune pathways and cells). Some of the inflammation in the body has been observed for months. That is a recipe for damage and fibrosis. I wrote this after hearing – again and again – “I have a cough, it just won’t budge, and it’s not COVID”. I don’t know what's causing all the coughing. Could be anything... but this is one of the ways I would expect widespread prevalence of lung damage to present. It’s also one of the ways I would expect chronic infections with slow-growing pathogens (like TB or atypical pneumonias) to present... Chronic coughs can also have other malignant or serious causes. These should be assessed and monitored by a GP if it’s not budging. Please... try to look after yourselves.. .”
❦ “Lymphopenia is present during and after some viral infections, and this also varies between individuals. It is very transient in most cases, and by that I mean a couple of weeks. The viruses that cause longer derangement are already known to be associated with long-term immune system derangement – including secondary infections, immune amnesia and cancers. COVID-19 lymphopenia has been recorded present for months. COVID-19 has been found to destroy (engulf in syncytia), directly infect, stimulate, and suppress a lot of white-cell function. Reinfections are frequent. Secondary infections/reactivations observed. It’s a huge worry. As a general rule, efforts are made to control/treat viruses that cause prolonged immune system derangement. COVID-19 is wildly exceptional in that we are ignoring it, pretending the lymphocytes bounce back like after a cold, and are frequently infecting people with it. We are also losing naive lymphocytes in large numbers due to superantigen stimulation. This is very different to transient suppression of peripheral blood lymphocytes due to cytokines or migration. This is another example of people making assumptions (huge and wrong), based on entirely dissimilar pathogens. It’s very important to look at what happens in similar situations, such as post-other-super-antigen-carrying infections. (Nothing good.) I could have saved my energy today and just let everyone play with a super antigen and find out… but sadly, the people finding out the hardest lessons are not the people deciding to play with it. So… here we are…”
❦ “This is quite possibly the most absurd thing you will read today. Let’s take this one step at a time. For the purposes of this short essay, I will be ‘vulnerable’.”
❦ “This morning someone said to me: — “I just can’t shake this... first a chest infection, and now a urine infection...” Someone else I know (very close) has had three eye infections post-COVID. Another has had a deterioration in their fertility, as compared to their baseline pre- and post-COVID. Measured. It’s almost as if the stuff in the science papers is real. None of them have twigged that COVID might have toasted them yet either. They are all heading into this next wave with no idea how dangerous it might be to abuse their already struggling immune system like this. You know what’s coming next... Multi-drug-resistant bacteria. Many are already here, but this is going to get really out of control. Trying to treat infections in immunodeficient patients is a great way to make loads of drug-resistant bacteria and viruses.” ✾ 📖 (24 Sep 2025 ~ CIDRAP/University of Minnesota) Outpatient antibiotic use in COVID patients linked to 'downstream' antibiotic resistance ➤ 📖 (15 Jul 2025 ~ UKHSA: News story) UTIs [Urinary Tract Infections] cost NHS hospitals over £600m last year ➤ 📖 (26 Jun 2025 ~ Forbes) Cancer Patients Face Silent Crisis From Superbugs, New Research Shows ➤ 📖 (12 Dec 2024 ~ CIDRAP/University of Minnesota) Report describes spread of highly drug-resistant cholera strain ➤ 📖 (1 Nov 2024 ~ China CDC Weekly) Emergence of a New Sublineage of Candida auris Causing Nosocomial Transmissions - Beijing Municipality, China, March-September 2023 ➤ 📖 (17 May 2024 ~ CIDRAP/University of Minnesota) Global Meta-analysis estimates 43% rate of multidrug resistance in COVID patients ➤ 📖 (14 May 2024 ~ Journal of Infection) Global antimicrobial resistance and antibiotic use in COVID-19 patients within health facilities: A systematic review and meta-analysis of aggregated participant data ➤ 📖 (24 May 2023 ~ Current Microbiology) Interaction Between SARS-CoV-2 and Pathogenic Bacteria ➤ 📖 (18 Apr 2023 ~ BMC Infectious Diseases) Fungal infection profile in critically ill COVID-19 patients: a prospective study at a large teaching hospital in a middle-income country ➤ 📖 (29 Mar 2023 ~ Journal of Fungi) Fungal-Bacterial Co-Infections and Super-Infections among Hospitalized COVID-19 Patients: A Systematic Review ➤ 📖 (30 Sep 2021 ~ Business Insider) Drug-resistant infections in the US have risen sharply during the pandemic, and experts warn it's getting worse as COVID patients overwhelm hospital resources ➤
❦ “During my young and ‘indestructible’ days, I did a lot of risky things. I now have a dodgy ankle, and various other aches and pains to remind me... Young people these days will also accumulate their scars of youth... but in my opinion, the COVID scars were unnecessary. We could have made it so much safer to travel and have fun by controlling disease properly. We gave up on them, our youth. We left them last for vaccines, and last for any consideration of their needs. They can’t even date properly without excess risk of long-term health problems because we can’t be bothered to do the work. Dating and finding a partner is a need , by the way. Sure, there are ways around this… but realistically, zero COVID would have been for them. The young. People think it’s to protect the old... but that’s only a small part of the story! Zero COVID would have given our kids safer schools. Parties would be safer. Sport would be safer, and they could excel without fear of COVID ruining their goals. We should have done it for the kids. See what I mean. We have misguided and abandoned them.”
❦ “What are we going to tell young men in twenty years’ time if they discover that they can’t ever have an erection in the usual manner due to repeated childhood COVID infections? Have we thought about using vaccines and therapeutics in children to prevent this? What about protecting children with NPIs ( non-pharmaceutical interventions )? We all worry about kids missing out on fun stuff in this pandemic. What about their sexual health later in life? Is this not fun? Is this not important? Is this not for them ? Let’s not be squeamish. Let’s think this through properly. Our youth are being repeatedly infected with a pathogen that we know affects sexual and reproductive health in a myriad of ways. Due to the fact that I will likely be dead by the time you figure this out, I’m going to take the liberty of saying a few things now. 1) This is unacceptable. 2) I told you so. 3) I’m sorry future adults, I really tried. I hope that solutions come your way.”
❦ “COVID-19 is fighting back by generally depressing the whole adaptive immune system. We are showing narrow resilience to COVID reinfections due to adapting – but we are becoming more vulnerable in general to infections of all kinds. ❦ Worst case scenario A single infection causes on-going and progressive immunodeficiency . ❦ Best case scenario A single infection causes temporary immunosuppression , and we suppress COVID transmission enough to allow recovery. ❦ Most likely scenario, medium-term Immunosuppression that becomes continuous and possibly progressive due to reinfections. Reduced immune function after a viral infection is not unusual. Many viruses do this. The concerning issue is the length and breadth of the immune system dysfunction, coupled with emerging evidence of other pathogens taking advantage .” ✾ ❦ Immunosuppression ~ Suppression of the immune system and its ability to fight infection. ❦ Immunodeficiency ~ A state in which the immune system’s ability to fight infectious diseases and cancer is compromised, or entirely absent.
❦ “I graduated from UCL. It has changed a lot since I was there. The ability to prioritise actions in an emergency is my job. You have to do things in the right order, or none of it works. We need COVID control, so we can free up resources to do other work. I don’t just mean health resources either. Depletion of workers due to sick leave; long-term illness; carer duties; and death – with some jobs becoming frankly undesirable. The expected benefits of ventilation and masks in essential services would be to reduce Reff * and save lives. * Reff , or the effective transmission number , is a measure used to indicate how many people, on average, a single infected person will transmit a disease to. A Reff value above 1 suggests that the infection is spreading , while a value below 1 indicates that the outbreak is declining . How much… you have to do it to find out, because it hasn’t been done before. We have to build this plane while flying. No room for excess baggage. Small case studies (like individual schools, or wards in a hospital ) indicate the benefit might be quite a lot. Even if it’s not as much as hoped, it has to be done, because we are rapidly accumulating long-term sickness. We have to try everything to slow that process.”
❦ “I think it would be good if people stop asking family members of vulnerable people when they will unmask and go on holiday… and what their off-ramp is. Like… is “off-ramp” code for bumping off the vulnerable person in the household? Exit strategy via coffin? The faster everyone accepts that some of us can’t even go to a dentist without a risk-benefit analysis, let alone a dinner party, the happier we will all be. Do I walk around asking you about your personal choice not to mask? What makes you think you can ask me why I do mask? I know that tone says you aren’t actually interested in the answer. Let it go. No, no… I don’t have to learn to “live my life again”. I am living my life the way I have always lived my life. With due respect for myself and others.”
❦ “Let’s play pretend. Pretend we have unlimited resources to staff the hospitals. Unlimited ICU beds. We let COVID-19 take its natural course. COVID-19 would average, what? Two or three infections per person, per year? Let’s be conservative. Let’s say you get COVID-19 once a year. So once a year, a certain proportion of all human beings, except those in countries with good COVID control will: die; have reproductive difficulties like erectile dysfunction; get heart failure; lose the pleasure of the smell and taste of food; have new autoimmune issues; develop new cognitive issues; have vascular problems like strokes; suffer other organ damage, like kidney failure; receive a new diagnosis of diabetes. Etc. Each of these has a percentage prevalence in cases. Some of those numbers are not small. Each time, there will be people that get one or more of these issues. Each of those conditions has their own associated increase in mortality. Then there is the drop in productivity and quality of life. How long do you think it would be before the majority of the population has something not quite right with them due to COVID-19? I don’t think it would take all that long. Ten years maybe? Twenty? How can it possibly be a sane public health strategy to have hospitalisation and ICU capacity preservation as the goal of a nation, when the obvious and massive loss of health (and life) due to circulating COVID can be predicted already? Some years, we will not have a great match between vaccines and circulating strains (such as Omicron); other years we will get it right (maybe if we are fast enough, and we aren’t yet). What does that mean? There will be multiple episodes in the future where vaccine-mediated cover and infection-mediated immunity will not be great. That means the organ damage will be somewhat more severe. Why are public health officials OK with this? Even if we can never get back to zero COVID, why are they OK with having a high frequency of infections per lifetime? Am I in an alternate universe where I can see these studies and they can’t? We have therapeutics coming in, so that will help, but they aren’t 100% magic bullets either. People need a combination of factors to bounce through a COVID infection without noticeable effects (although kidney damage can present late). That combination, to be maintained at all times for an individual is difficult, let alone a population. The strategy of “Living with COVID-19” is fatally flawed. That flaw is the fact that COVID-19 is a rapidly mutating virus that causes irreversible, or slowly reversible damage to the human body. We can’t actually withstand it for our usual natural lifetimes. The government must show the modelling for long-term health outcomes for their “living with the virus” plans. The economic impact of the same. All the colleges of medicine should submit their modelling on how COVID-19 is affecting human health. This is critically important work. How a biohazard was allowed into Australia and allowed to circulate – without modelling its overall impact on human health – is a matter that should be investigated thoroughly. It was a huge decision. There should have been expert discussion and documentation. No… Saying “We didn’t know” is not good enough. If you don’t know… Don’t play with SARS.”
