Viral Reactivation

This is the most overlooked danger in chronic illness recovery, and it is not where you think it is. The popular fear is that fasting itself reactivates dormant viruses like herpes (HSV-1, HSV-2), shingles (VZV), Epstein-Barr (EBV), and the HHV-6/7 family. The truth is the opposite. The dry fast is the safest period your immune system experiences all year. The danger window opens the moment you break it.

For someone with Long Covid, ME/CFS, post-mono fatigue, or unexplained chronic illness, this single insight separates a successful recovery from a setback that can last months. The protocol must be built around the vulnerability window, not just the fast itself.

The Counterintuitive Truth, In One Sentence

During the dry fast, your body becomes biologically hostile to viral replication. The moment you refeed, that hostility collapses faster than your immune system can rebuild. Any virus you have spent the fast suppressing now has a multi-day window to replicate, refill eradicated reservoirs, and infect entirely new nerve cells before you have any defence in place.

The full reactivation cascade. The fasted state is safe. The refeed window is where everything can come apart if the natural antiviral stack is not in place before the first calorie returns and valacyclovir does not follow on refeed day 3.

Why You Are Almost Untouchable During the Dry Fast

Picture a fortified city under siege. The food stores are locked, the wells are dry, the gates are sealed, and patrols sweep every street. That is what your body looks like to a virus on Day 3 of a dry fast. Four overlapping systems make viral replication mechanically and metabolically near-impossible during the fasted state.

The Four Layers of Anti-Viral Defence That Activate During a Dry Fast

1. Autophagy clears infected cells from the inside outAutophagy is your body’s “self-eating” recycling program. Viruses hide inside cells precisely because immune cells can’t see them there. Autophagy bypasses that. It identifies damaged or virus-occupied cellular machinery and digests it. Beth Levine’s landmark work established autophagy as a primary innate antiviral defence (Levine et al., 2011, Nature). Dry fasting drives autophagy harder than any other intervention because it removes both the food signal and the water signal at the same time, sending a maximal “clean house” instruction to every cell. Latent HSV, EBV, and HHV-6 sitting inside ganglion and immune cells are physically removed in this state.
2. Ketones starve viruses of the metabolism they needBy Day 2 your body has switched from burning glucose to burning ketones (β-hydroxybutyrate). Most pathogenic viruses are obligate glucose users; their replication enzymes depend on the glycolytic pathway. Ketone metabolism doesn’t feed them. β-hydroxybutyrate also has direct signalling effects: it inhibits the NLRP3 inflammasome (Youm et al., 2015, Nature Medicine) and shifts the cellular environment in ways that suppress viral protein synthesis. The deeper the ketosis, the more hostile the territory.
3. mTOR shutdown removes the growth signal viruses depend onThis is the most underappreciated mechanism. Viruses don’t make their own protein synthesis machinery. They hijack yours. The master switch for protein synthesis is a pathway called mTOR. Fasting (especially dry fasting) suppresses mTOR profoundly. Without mTOR activation, cap-dependent translation stops, and viral proteins cannot be assembled efficiently. This is why rapamycin (a drug that blocks mTOR) has well-documented antiviral properties. A dry fast is a free, total-body rapamycin signal.
4. Natural Killer (NK) cells get activated and stem cells regenerate the immune systemCheng et al. (2014, Cell Stem Cell) showed that prolonged fasting triggers haematopoietic stem cell self-renewal: the body starts rebuilding the immune system from scratch. NK cells, the first-line patrol that destroys virus-infected cells before adaptive immunity is even involved, become more active relative to the ambient viral load. Your immune system isn’t weakened during the fast in the way most people think. It’s being restructured and concentrated where it matters.

On top of all four mechanisms, dehydration itself concentrates antimicrobial peptides in tissue and blood. Less water means higher local concentrations of the molecules that kill pathogens. The protective barrier is multi-layered, redundant, and active in every compartment of the body simultaneously. This is why most people get through a dry fast with no viral flare even when they’ve had monthly outbreaks for years.

The Refeed: When the Walls Come Down All at Once

Now picture that fortified city, but every defence drops in the same hour the supply caravan arrives at the gates. Food, water, fuel: everything pours back in. The patrols haven’t restocked. The wells haven’t been re-secured. And anything that survived inside the walls now has all the resources it needs to expand.

The dry fast suppressed the virus. The refeed un-suppresses it, catastrophically and quickly, while the immune system is still rebuilding. Five things happen in parallel during the first 24–72 hours after breaking the fast, and each of them, on its own, would be a viral reactivation risk. Together they create a window of near-zero antiviral capacity.

The Five Vulnerability Mechanisms in the Refeed Window

1. mTOR roars back on within hoursThe first calories (even kompot or coconut water) send an insulin and amino acid signal that switches mTOR back on. Cap-dependent translation resumes. Cellular protein synthesis resumes. And so does viral protein synthesis, on the same machinery, at the same time. Any virus that was sitting dormant during the fast now has the green light to replicate. This is why mTOR-active states (post-meal, post-exercise, glucose-fed) are the moments viruses prefer.
2. Autophagy shuts off as soon as you eatThe signal that drove autophagy was nutrient absence. The moment calories return, autophagy is downregulated within hours. The house-cleaning crew clocks out. Any newly emerging viral particles are no longer being mopped up at the cellular level.
3. Circulating immune cells haven’t returned to the bloodstream yetNagai et al. (2019, Immunity) demonstrated that fasting relocates memory T cells out of circulation and into the bone marrow. CD8+ T cells (the patrols that contain herpes virus reactivation in healthy people within 12–24 hours) take days to fully redistribute back into the blood after refeeding starts. During that lag, the surveillance system is physically not where it needs to be.
4. Cortisol is still elevated and is the canonical herpes triggerCortisol peaks late in a dry fast and stays elevated for days into the refeed. Padgett et al. (1998, PNAS) showed in mice that the only requirement to trigger HSV-1 reactivation was a glucocorticoid spike. Adrenalectomy abolished the effect, proving cortisol was the trigger. Sainz et al. (2001, Journal of Medical Virology) showed the same effect with synthetic glucocorticoids in neuronal culture. The exact stress signal that tells latent herpesviruses to wake up is at peak intensity in the refeed window.
5. T3 has crashed and antiviral immune signalling is bluntedFree T3 drops about 25% by Day 3 of an absolute fast (Khoroshilov fasting study). Reverse T3 rises 56%. T3 directly potentiates Type I interferon signalling and NK cell killing capacity (De Vito et al., 2011, Thyroid). The interferon response is the immune arm that controls latent viruses specifically, and it depends on T3 to run at full strength. Low T3 = blunted antiviral response, exactly when you need it most.

Why a Reactivation in the Refeed Window Is Worse Than a Normal Outbreak

Most people have had a cold sore. Most people don’t panic about them because in a healthy person the immune system contains the outbreak in 12–24 hours, the lesion stays small, and the viral pool in the ganglion gets topped back up but doesn’t expand. What happens during a refeed reactivation is fundamentally different, and much more dangerous in a chronically ill body.

What Actually Happens When a Virus Reactivates in the Refeed Window

The dry fast eradicated the virus from many of its hiding placesAutophagy reaches latent reservoirs that drug therapy cannot. Many ganglion cells, immune cells, and tissue niches that previously carried latent virus have been cleared. This is the upside of the fast.
The remaining virus, now liberated, has a multi-day open roadThe cells the virus was hiding in have died (autophagic clearance). The viral particles that were inside those cells have been released. In a normal state, immune surveillance would mop them up. In the refeed window, surveillance is physically absent. Those particles have hours to find new host cells.
The virus refills cleared reservoirs AND seeds new onesThis is the part most clinicians miss. Without immune containment, the virus doesn’t just return to its old territory. It can enter ganglia and tissue regions it never previously occupied. A patient who entered the protocol with HSV-1 in the trigeminal ganglion can finish a reckless refeed with HSV-1 also seeded in spinal ganglia, sacral ganglia, or peripheral nerves. The fast made the patient cleaner; the unprotected refeed made them more broadly infected than when they started. This is the worst-case outcome and it is preventable.
In Long Covid / ME-CFS this becomes catastrophicGold et al. (2021, Pathogens) found 66% of Long Covid patients show active EBV reactivation, correlating with physiological stress events. The Long Covid patient is starting the refeed with a higher baseline viral load than a healthy person, a weaker baseline antiviral immune system, and (often) spike protein persistence in vascular and nerve tissue (Rong et al., 2024). The refeed vulnerability window is exponentially more dangerous in this population. A botched refeed can produce a 6-month crash that wipes out everything the fast achieved.

The Bridge Strategy: Dry Fast → Water Fast → Protected Refeed

The Scorch Protocol does not exit the dry fast directly into eating. It bridges through a water fast specifically to close the vulnerability window before food returns. This is the single most important structural decision in the protocol and the reason it differs from every recreational fasting program online.

What the Water Fast Bridge Accomplishes

Rehydrates organs while keeping you in ketosisPlain water rehydrates the kidneys, liver, brain, and intestines so they can metabolise oral medications and supplements. But because there are still no calories, mTOR stays suppressed, autophagy stays active, and ketones stay elevated. You are still in the protective siege state. You just have working organs again.
Lets L-lysine return before food does, and extends the fastYou cannot safely take oral acyclovir, valacyclovir, or L-lysine during a dry fast. Without renal water flow, the dosing window and clearance kinetics are wrong, and you risk concentrated toxicity. The water bridge rehydrates the organs, extends the protective fasting state, and lets L-lysine come back on water day 1. What it does not do is clear the way for prescription antivirals. Water fasting still purges water through the kidneys, so the body stays systemically dehydrated even on the water days, and electrolytes help without fixing it. Valacyclovir waits for the refeed: day 3 at the earliest, after two days of eating with heavy rehydration. (T3 is not part of this bridge either. It is held back until after Day 7 of the refeed.)
Gives the immune system several days to start redistributing back to circulationT-cells and monocytes begin returning to the bloodstream during the water fast phase, before food signals trigger mTOR. By the time you take your first calories, baseline immune surveillance is materially better than it would have been on a hard refeed.
Cortisol begins to descendWater intake reduces the perceived stress signal compared to dry fasting. Cortisol begins its descent from peak. The herpes reactivation trigger weakens before the refeed even starts.

The Pharmacological Stack for the Refeed Vulnerability Window

Nothing oral runs during the dry fast itself. Without renal water flow, dosing and clearance kinetics are wrong and concentrated toxicity becomes a real risk. The water fast bridge rehydrates the organs and lets L-lysine return on water day 1, but it does not clear the way for a renally cleared drug: water fasting still purges water through the kidneys, so the body stays systemically dehydrated on the water days too, and electrolytes help without fixing that. So you build your defensive walls in stages and keep them standing through the whole refeed, not just on day one. The first wall is antiviral pressure, and it goes up in two steps: L-lysine from water day 1, monolaurin and olive leaf with the first meal, then valacyclovir as the standing backbone from refeed day 3 at the earliest, after at least two days of eating with heavy rehydration, held through the calorie ramp, into maintenance and through the months between fasts, and never during the fast in either form. Ivermectin runs alongside it as a supportive antiviral (it calms the nervous system and inflammation and may mildly inhibit viral entry) and, more importantly, as the primary antiparasitic, working in synergy with the fast itself. The second wall is active immune rebuilding via thymic peptides (Thymalin early in the refeed; Thymus Alpha-1 has been retired from the protocol, see the note below). Through the first seven days of refeeding you also add a case-by-case metabolic layer, methylene blue and in selected cases ethyl pyruvate, to support the mitochondria while food scales back in. T3 is deliberately held until you have scaled food for a full seven days: the antiviral stack, not T3, is what closes the vulnerability window. This stack is not optional for anyone with Long Covid, ME/CFS, recurring herpesvirus history, or unexplained chronic illness. Each component blocks, rebuilds, or supports a different stage of the cascade.

AgentWhen to StartWhat It Does Mechanistically
L-LysineRefeed Day 1, continued through the refeedCompetes with arginine for the amino acid transporter herpes viruses depend on. Griffith et al. (1987, Dermatologica) showed lysine supplementation reduces HSV outbreak frequency. Critical because muscle protein breakdown during the fast has already mobilised arginine, tilting the ratio in the virus’s favour.
MonolaurinRefeed Day 1, continued through the refeedDisrupts the lipid envelope of all herpesviruses (HSV-1, HSV-2, VZV, EBV, CMV, HHV-6, HHV-7, HHV-8). A virus with a damaged envelope cannot enter new cells. This is the “containment wall” component.
Ivermectin (supportive antiviral + antiparasitic)Started at the water fast bridge, continued through the entire refeedBlocks importin α/β nuclear transport, which herpesviruses depend on to replicate inside the host cell nucleus ([1] [2]). Ivermectin runs in the second seat here, alongside the standing valacyclovir course, chosen for its gentler gut profile and its double duty as an antiparasitic. Treat it as a supportive antiviral (it calms the nervous system and inflammation and may mildly inhibit viral entry) rather than a standalone virus-killer. The combination of ivermectin and dry fasting clears most parasitic load, with supportive antiviral coverage riding along on top. Coverage does not stop at the 24 to 72 hour vulnerability window: it runs across the full refeed, bridging the gap until T3 begins after Day 7.
Acyclovir or Valacyclovir (standing antiviral backbone)Off for the whole fast, dry and water (a water fast still leaves the body dehydrated); standing course starts refeed day 3 at the earliest, after two days of eating with heavy rehydration, and is held through the calorie ramp, into maintenance and through the months between fasts. On handbefore the fast ends.Inhibits viral DNA polymerase. Covers HSV-1, HSV-2, VZV completely; partial coverage of EBV and CMV. This is now the standing backbone of the antiviral layer: never run during the fast in either form, since a water fast still purges water through the kidneys and the dosing and clearance kinetics stay wrong, but started on refeed day 3 at the earliest and then run daily to lower the burden of reactivated EBV, HSV and shingles through the months of refeeding and regeneration. A prodrome loading dose, the tingling, itching, or burning at a previous outbreak site that signals an oncoming HSV reactivation, is layered on top of that standing course as an escalation, not a substitute for it, only once the course is running, and can abort the outbreak before lesions form. Ivermectin runs alongside the standing course in the second seat, for its antiparasitic and supportive antiviral role.
Methylene blue (mitochondrial support)First 7 days of the refeedActs as an alternative electron carrier for the mitochondria. Coming out of the fast the cell is loaded with NADH from fat-burning, a reductive stress, and if the electron transport chain cannot clear it that NADH backs up and stalls energy production. Methylene blue accepts electrons from the backed-up NADH and passes them down the chain, restoring the NAD+ to NADH balance so the mitochondria can make energy again while food is scaling back in and before T3 begins. It is added case by case, matched to the individual. No dose is published here: it is set with you directly in the consult, in keeping with the Fasting Detective approach.
Ethyl pyruvate (metabolic support, selected cases)First 7 days of the refeed, selected casesA metabolic and anti-inflammatory support option considered alongside methylene blue for some individuals during the early refeed. Used only when it fits the case, and only as decided in the consult. As with methylene blue, no dose is published here.
Thymalin (immune rebuild: early)Early refeedThymic peptide used clinically in Russia and Eastern Europe as an immunomodulator. Strengthens the thymus, body peptides, and overall immune system after the fasting demolition. Pairs with BPC-157 in the broader rebuild phase (see the T3 Therapy page).
Thymus Alpha-1 (Tα1) (retired)No longer usedRetired from the protocol. Through my own research and experiments, I found that Tα1 hypersensitizes immune cells and can backfire, driving new allergies instead of balancing the immune system. Working theory: the wave of benzyl alcohol allergies people keep developing traces back to reconstituting Tα1 with bacteriostatic water, which is preserved with benzyl alcohol. Thymalin is now the only thymus peptide in the protocol.
Avoid arginine-rich foodsRefeed Day 1 through Week 2Nuts, seeds, chocolate, peanut butter. These spike free arginine and undo the work lysine is doing. Especially critical in the first week.

Doses for this stack, including the valacyclovir standing course and its prodrome escalation, are intentionally not published on this page. They are highly patient-specific (dependent on weight, prior viral load, baseline immune status, comorbidities, and current symptom pattern). Generalised public dosing would contradict the “Fasting Detective” clinical-individualisation approach that the protocol is built around. Dose-level work for these individualised levers belongs to the members portal and direct clinical assessment. This applies with particular force to the metabolic supports: methylene blue and ethyl pyruvate are dosed strictly per individual, and no amount for them is published on this page.

The Scorch Protocol runs four parallel layers, not a single linear protocol. Pathogen targeting (antiviral, antifungal, antiparasitic) and immune rebuild (thymic peptides) all run alongside the core fasting + T3 + hGH work.

My deeper breakdown of ivermectin’s antiviral mechanism, from @DryFastingClub on X:

Stop Signals: How to Know Reactivation Is Happening

Even with the full bridge protocol, reactivation can break through, especially in cycle 1 or 2 when baseline viral load is highest. Catch it early. The earliest signs are the most subtle and almost always missed if you don’t know what you’re looking for. The signs below are scoped to the refeed window, when the standing antiviral course is running or about to start. A prodrome that arrives during the fast itself, dry or water, is a different call, and it is covered directly after them.

Early Reactivation Warning Signs in the Refeed Window

Tingling, burning, or itching at a previous outbreak siteThe prodrome: a viral particle has reached a nerve ending and replication has started. This is the moment to escalate antivirals, not after the lesion appears. A loading dose of valacyclovir, layered on top of the standing course once that course is running, can abort an outbreak entirely at the prodrome. On refeed day 1 or 2, before the course has started, it is your decision: if you feel rehydrated you can start early, knowing why the drug is not advised while water fasting.
Sudden return of pre-protocol fatigue, brain fog, or post-exertional malaiseEspecially in Long Covid / ME-CFS patients, this often signals EBV or HHV-6 reactivation rather than refeeding-syndrome fatigue. The quality is different: heavier, more “flu-like,” with lymph node tenderness or sore throat that wasn’t present before the fast.
Lymph node swelling, low-grade fever, sore throat without infectionClassic EBV/CMV reactivation pattern. Pull bloodwork (EBV early antigen IgG, viral capsid IgM) to confirm. Reinforce the standing valacyclovir course (running by this point, or due to start on refeed day 3), even though coverage of EBV is partial. Combined with T3 and monolaurin, it provides meaningful pressure.
New pain in nerve territories that weren’t previously affectedThis is the most concerning sign. It suggests the virus has spread beyond its original ganglion to new nerve tissue, exactly the worst-case scenario described above. Stop the refeed advancement, maximise antiviral coverage, and reinforce the ivermectin support already running alongside the standing valacyclovir course.

If a Prodrome Hits During the Fast Itself

Everything above assumes the standing antiviral course is running or about to start. During the fast it is not, and it cannot be. Valacyclovir is renally cleared. A dry-fasted body has no renal water flow to clear it with, and a water-fasted body is not much better: water fasting still purges water through the kidneys, so the body stays systemically dehydrated on the water days, electrolytes or not. Dosing kinetics go wrong, concentration builds, and you risk a kidney injury on top of the outbreak you were trying to stop. This is the same boundary that holds the standing course back until refeed day 3, and it does not bend because a tingle showed up early.

So the answer is not to push a rescue dose into a dehydrated body, and it is not to grit your teeth and finish the fast. In my clinical judgement, a prodrome during the fast is the signal that ends the fast, in a set order.

Prodrome During the Fast: The Sequence

1. Convert to water, with electrolytesIf you are in the dry phase, this is the first move. It is not a refeed: water comes back, food does not, so ketosis holds, mTOR stays suppressed, and autophagy keeps working while the organs start to rehydrate. Put electrolytes in the water from the first glass. If the prodrome arrives on the water days, you are already at this step.
2. L-lysine at onceL-lysine goes in the moment water does. It is gentle enough for a fasting gut, it does not carry valacyclovir’s renal problem, and it starts tilting the arginine ratio away from replication immediately.
3. Break the fast once you are rehydrated, and how long that takes depends on how deep the dry fast wasA prodrome caught early in the dry phase rehydrates relatively quickly, and the fast can be broken soon after. A prodrome deep into a long dry fast is a different body: the deficit is larger, it is not water alone, and it calls for a substantially longer stretch of aggressive rehydration with electrolytes before the first calories. The specific length, and where the line between a shallow and a deep dry fast sits for you, are per-case calls and are deliberately not published here. Do not estimate them. Ask me for the modified protocol, and keep rehydrating while you wait for the answer, because rehydrating is the part that is safe to start without one.
4. Monolaurin and olive leaf with the first calories, valacyclovir on the standing ruleWhen you break the fast, monolaurin and olive leaf come in with the first calories. Valacyclovir then follows the same rule as a planned refeed: day 3 at the earliest, after two days of eating with heavy rehydration, with the prodrome loading dose layered on top once the course is running. If the prodrome is still active on refeed day 1 or 2, starting early is your decision, made knowing why the drug waits. Monolaurin before food is a different matter: because it is a fat, adding it to a water fast converts it into what I call a fat-water fast, a deliberate variant with its own rules, handled case by case rather than published as a recipe.
5. If it keeps happening, the fast itself is the wrong shapeA prodrome that returns cycle after cycle is not telling you the rescue was too small. It is telling you the sequence is wrong for your viral load. In that situation I invert the order: the cycle opens with a water-first lead-in, and the dry phase only begins once the fast’s own protective mechanisms are established and the natural stack has had time to do its work. That lead-in has one condition: at least 3 L of water a day with electrolytes, a pinch of normal salt plus potassium salt, while the drug is held, because valacyclovir does not run on the water days either. The restructure is built per patient and is not a public template.

None of this comes from a trial. There is no published literature on managing a herpes prodrome inside a dry fast, because almost nobody outside this protocol runs fasts deep enough to create the situation. What is above is my clinical judgement from running the protocol with patients, and the reasoning is set out so you can recognise the situation rather than improvise inside it.

Medical caveat: converting a fast, rehydrating a deeply dry-fasted body, and starting a prescription antiviral are decisions to make with a physician who knows your renal function and your history.

The parts deliberately left out above (how long to rehydrate, where your own shallow-to-deep line falls, how a fat-water fast is run, and how a water-first lead-in transitions into the dry fast) are the parts that move with the patient. Getting them wrong from a guess is how a recoverable prodrome becomes a lost cycle. If a prodrome has interrupted one of your fasts, or keeps interrupting them, that is the modified protocol to ask me for rather than assemble yourself.

Ask Yannick for the modified protocol →

Why This Becomes Easier With Each Cycle

Reactivation is most likely in the first one or two protocol cycles when total body viral load is at its highest. Each completed cycle, if managed correctly, reduces the reservoir. By cycle three or four, most patients report dramatically reduced reactivation symptoms even with a less aggressive antiviral stack. By cycle five or six, the herpes pattern that ran their lives for years is often gone entirely. This is the long-term goal and it is achievable.

The non-negotiable rule: do not chase faster cycles in pursuit of faster recovery. Each refeed must be fully protected. A reckless refeed in cycle 2 can re-seed reservoirs the cycle 1 fast cleared and set you back a year. This is the mistake that ends most chronic illness recoveries before they finish.

The T3 Cycle Off-Ramp Is the Other High-Risk Window

Reactivation risk does not end with the refeed. When you taper off a T3 cycle, your metabolic rate temporarily dips while the thyroid re-establishes its own production. This dip recreates the energetic trough that triggers reactivation during the fast-to-refeed transition. Continue antiviral coverage through any T3 wind-down until your waking body temperature has been at your pre-T3 baseline for 5–7 consecutive days.

Bottom Line for Anyone With Chronic Illness

The Mental Model to Carry Through the Whole Protocol

The dry fast is the safest period your immune system experiences all year. The refeed is the most dangerous. Your job is not to fear the fast. It is to fear the transition. The Scorch Protocol’s structure (dry fast → water fast bridge → controlled refeed with the antiviral stack already on board and running straight through it) exists specifically to close the vulnerability window before food can open it. T3 comes later, after a full seven days of refeeding. Honour that structure and viral reactivation becomes manageable. Skip it and you can undo every gain the fast produced, ending up more broadly infected than when you started.

For deeper context on the refeed itself, see the Phase 3: The Refeed page. For T3 dosing, see T3 Therapy. For protocol entry decisions based on baseline temperature and viral history, see the Decision Logic Tree.

Once this window has closed and you are in the long gap before the next cycle, the standing daily stack that holds the ground the fast took is on the Between Fasts page.

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The information on this site describes a personal health protocol and is provided for educational purposes only. It is not medical advice. Consult a qualified physician before modifying your diet, fasting practice, or any medication regimen.