Rabies — Questions

Histological feature: Negri bodies: eosinophilic cytoplasmic inclusions of viral nucleoprotein in Purkinje cells, hippocampal and brainstem neurons. Pathognomonic but not fully sensitive; absence does not exclude rabies.

Virus: Rabies virus (genus Lyssavirus, family Rhabdoviridae): a bullet-shaped, enveloped, negative-sense RNA virus (Baltimore class V), ~12 kb genome encoding N, P, M, G and L.

Pre-exposure prophylaxis (PrEP): vaccine on days 0 and 7 (intramuscular or intradermal) for high-risk groups (laboratory, veterinary and animal workers, bat handlers, and travellers to endemic areas with poor PEP access). Immunocompromised patients receive a third dose at day 21 to 28.

Post-exposure prophylaxis (PEP), Category III exposure: wash the wound for 15 minutes, antibiotics/tetanus vaccine as indicated, vaccine on days 0, 3, 7 and 14 to 28 plus rabies immunoglobulin (20 IU/kg HRIG or 40 IU/kg ERIG) infiltrated into the wound within 7 days of the first dose. Previously vaccinated patients: two doses (days 0 and 3), no RIG.

Routine rabies post-exposure prophylaxis is not indicated here, for two reasons:

1. The animal. Rodents and small terrestrial mammals (moles, rats, mice, squirrels, hamsters, rabbits) are not known rabies reservoirs anywhere. South African rabies cycles are maintained in domestic dogs, black-backed jackals, yellow mongoose, bat-eared fox and bats, not moles.

2. The region. Cape Town and the Western Cape are not high-risk for rabies. The canid cycle is concentrated in KwaZulu-Natal, Eastern Cape, Mpumalanga, Free State and Limpopo. A bat-eared fox cycle is recognised in parts of the Western and Northern Cape, but not in urban gardens.

Practical advice:

• Wound care: wash thoroughly with soap and running water for several minutes; disinfect with chlorhexidine or povidone-iodine.
• Tetanus prophylaxis should be reviewed and updated if needed; this is a puncture wound.
• Antibiotics: consider amoxicillin-clavulanate prophylactically for a clearly contaminated bite.
• No rabies vaccine, no RIG.
• Counsel the patient about the very low risk and document the discussion.
• Atypical caveat: if the mole was behaving abnormally (aggressive, paralysed, diurnal in a normally nocturnal species), submit the carcass for laboratory testing; otherwise observation is not feasible for wild rodents.

a. The greatest concern is rabies, a uniformly fatal lyssavirus encephalitis once symptomatic. Bat teeth are tiny and a bite can leave no visible wound, so the absence of a recollected bite does not exclude exposure. Also to consider are the African bat lyssaviruses (Duvenhage, Lagos bat and Mokola viruses), which cause a clinically identical disease.

b. Treat this as a Category III exposure, because plausible bat contact with a sleeping or otherwise incapacitated person is managed as high-risk even without a demonstrable wound. Wash any potentially exposed skin thoroughly with soap and water; give full post-exposure prophylaxis, meaning rabies vaccine plus rabies immunoglobulin infiltrated around the exposure site; and capture the bat for testing only if it is safe to do so.

c. Efficacy is threatened by the frequent unavailability of rabies immunoglobulin in rural and resource-limited settings, by delay in reaching a facility that can provide it, and by the possibility that the agent is an African bat lyssavirus against which the standard vaccine offers uncertain or no cross-protection.

This is a WHO Category III exposure in a high-endemicity region: the Eastern Cape is one of South Africa’s primary rabies-endemic provinces. The stray dog cannot be observed and must be assumed rabid. Full post-exposure prophylaxis is indicated without delay.

1. Wound care (immediate). Wash all wounds with soap and running water for 15 minutes; flush with copious water; disinfect with chlorhexidine 0.05% or povidone-iodine 10%. Avoid suturing unless required for haemostasis. Avoid local anaesthetic infiltration at the wound (risk of forcing virus into deeper tissues). Tetanus booster and consider antibiotic prophylaxis (amoxicillin-clavulanate) for a contaminated bite wound.

2. Rabies vaccine. 4-dose IM schedule on days 0, 3, 7, and one day between 14 and 28. In a child under 2 years, give in the anterolateral thigh (not deltoid, not gluteal). Identical adult dose (one full vial per administration).

3. Rabies immunoglobulin (RIG). 20 IU/kg HRIG (or 40 IU/kg ERIG if HRIG unavailable). Infiltrate the entire calculated dose into and around the wounds. Do not give the remainder at a distant intramuscular site (this is the current SA practice, a change from older guidance). Dilute with saline if wounds are multiple or small. Never mix RIG into the same syringe as the vaccine.

4. Source-animal action. Notify Veterinary Services. The stray dog should be captured if safe; if euthanised, the whole brain is submitted to the NICD in 50% glycerol-saline for fluorescent-antibody testing. PEP continues regardless while awaiting the result.

5. Follow-up. Document the visit and the schedule. Review on each vaccine day. Ensure the child completes all 4 doses. Confirm tetanus cover and monitor the wound for infection. Notify the local public-health authority.

6. Counsel the family on the rationale (without scaring them): rabies is invariably fatal once symptoms begin; full and timely PEP is essentially 100% effective.

Five lyssaviruses besides classical rabies virus (RABV) have been detected in South Africa:

• Duvenhage virus (DUVV): Phylogroup 1; insectivorous bats; rare fatal human encephalitis.
• Mokola virus (MOKV): Phylogroup 2; not cross-protected by vaccine or RIG.
• Lagos bat virus (LBV): Phylogroup 2; African fruit bats; no human cases.
• Matlo bat lyssavirus (MBLV): recently described, highly divergent.
• Phala bat lyssavirus (PBLV): recently described in a Schlieffen’s bat.

Standard vaccine and RIG cross-protect only within Phylogroup 1, so any bat contact is managed as Category III regardless.

No single specimen is sensitive at every stage, so a panel is submitted.

Ante-mortem:

• Saliva: at least 500 μL, one specimen daily on 3 consecutive days, collected by syringe or suction (not sputum); RT-PCR.
• CSF: at least 500 μL in an untreated sterile tube; RT-PCR, plus anti-rabies neutralising antibody in an unvaccinated patient.
• Nuchal skin biopsy: 5 to 6 mm wide and 5 to 7 mm deep, including hair follicles and the nerves at their base; on saline-moistened gauze with no fixative; DFA or RT-PCR.

Post-mortem:

• Brain tissue: 2 cm cubes from the cerebellum and cerebrum, in 50% glycerol-saline and never formalin; DFA is the gold standard.

All samples go to the NICD, leak-proof and marked “suspected rabies”. A single negative does not exclude rabies; repeat sampling is essential.

RIG window. RIG must be given on day 0 with the first vaccine dose, or as soon as possible thereafter. After day 7 from the first vaccine dose, RIG is no longer indicated: endogenous neutralising antibody has begun to develop, and adding passive antibody at that point will reduce the patient’s own vaccine response.

If RIG is unavailable on day 0, source it urgently and give it as soon as possible within the 7-day window. Never inject RIG into the same anatomical site or the same syringe as the vaccine, because they neutralise each other.

A complete answer follows the virus from the bite to the brain and out to the saliva, stressing that spread is neural and that there is no viraemia.

Local replication. After inoculation in saliva, rabies virus replicates in striated muscle near the neuromuscular junction.

Neural entry. It binds the nicotinic acetylcholine receptor at the motor end-plate (NCAM and p75NTR also implicated) and enters peripheral nerve terminals.

Centripetal transport. Virus travels by retrograde fast axonal transport to the spinal cord and brain. There is no viraemia, so it is shielded from circulating antibody, which is why post-exposure prophylaxis works.

CNS injury. The virus causes neuronal dysfunction rather than destruction, with a striking paucity of histological damage; eosinophilic cytoplasmic Negri bodies are pathognomonic, and the P protein blunts interferon signalling.

Centrifugal spread. From the CNS the virus passes outward along autonomic and sensory nerves to the salivary glands (high-titre shedding closes the transmission cycle) and skin. Once symptomatic, disease is effectively 100% fatal.

The 10-day observation rule applies only to domestic dogs, cats and ferrets, which shed rabies virus in saliva only within the 10 days preceding clinical signs. A bite from one of these animals carries no risk if the animal remains healthy at 10 days.

The practical algorithm:

• Start PEP immediately if there is any reasonable risk.
• Quarantine and observe the dog/cat/ferret for 10 days under veterinary supervision.
• If the animal remains clinically healthy at day 10, PEP may be stopped.
• If the animal develops signs of rabies or dies during observation, complete PEP and submit brain tissue for testing.

The rule does not extend to wild animals, stray dogs that cannot be reliably observed, or any other species.

The WHO categories stratify exposure by skin breach:

• Category I: no skin breach (touching, feeding a healthy-appearing animal, licks on intact skin). No PEP; wash the area.
• Category II: nibbling of uncovered skin, minor scratches or abrasions without bleeding. Vaccine alone (full schedule), no RIG.
• Category III: single or multiple transdermal bites or scratches, mucosal contact (eyes, nose, mouth), licks on broken skin, any contact with a bat. Vaccine + RIG at full schedule.

The “any contact with a bat = Category III” rule reflects the bat-bite paradox: bat teeth are tiny and bites may leave no visible wound.

Bat teeth are tiny and bat bites can leave no visible wound. Documented rabies fatalities have followed unrecognised bat exposures: the patient denies any bite and no wound is found, yet the virus is transmitted nonetheless. Any direct bat contact is treated as Category III when there is plausible exposure (bat in a room with a sleeping or otherwise incapacitated person, with a child, or any contact with bare skin or hair).

Management:

• Wash any potentially exposed areas with soap and water.
• Capture the bat if safe to do so, for laboratory testing.
• Offer full PEP: vaccine + RIG.
• PEP may be stopped if the bat tests negative.

A previously vaccinated person needs only two further vaccine doses and no rabies immunoglobulin. This is the main practical value of pre-exposure vaccination, because immunoglobulin is scarce across much of the endemic world.

Immunoglobulin and the four-dose course are reserved for those never previously vaccinated; wound cleansing is always required.

After CNS replication, rabies virus spreads centrifugally along sensory and autonomic nerves to multiple peripheral tissues, including the heart, adrenal medulla, gastrointestinal tract and skin.

The most clinically important destination is the salivary glands, where the virus replicates to high titres and is shed in saliva. This is the basis for bite transmission to the next host, closing the zoonotic cycle. Centrifugal spread to skin underlies the diagnostic value of the nuchal skin biopsy (virus in nerve fibres around hair follicles).

A previously-vaccinated patient (prior PrEP or prior PEP) is given an abridged 2-dose schedule on days 0 and 3 with no RIG. Endogenous immunity is rapidly boosted by the vaccine, and providing RIG would unnecessarily suppress the patient’s own response.

The full 4-dose-plus-RIG schedule is reserved for unvaccinated patients. If the exposure occurs within 3 months of completing a previous PEP course, no further PEP is needed at all.

A patient with HIV who is on effective ART, clinically well and virologically suppressed is not considered immunocompromised for the purposes of rabies vaccination. The standard 2-dose IM PrEP schedule on days 0 and 7 applies, with normal expected seroconversion.

The extended 3-dose schedule (days 0, 7, 21–28) is reserved for genuinely immunocompromised patients: symptomatic HIV with low CD4 counts, active cancer chemotherapy, high-dose corticosteroids (≥20 mg/day prednisone for ≥2 weeks), or transplant immunosuppression. Inactivated rabies vaccine is safe at any CD4 count.

Rabies virus binds the nicotinic acetylcholine receptor (nAChR) at the postsynaptic membrane of the neuromuscular junction. Two additional neuronal receptors, neural cell adhesion molecule (NCAM) and p75 neurotrophin receptor (p75NTR), are also implicated in cell-to-cell spread within the nervous system.

The glycoprotein G is the viral attachment protein and mediates pH-dependent fusion after endocytosis. Entry is the rate-limiting step at the periphery; once the virus has entered an axon and begun retrograde transport, it is no longer accessible to neutralising antibody.

The NICD-recommended nuchal biopsy is 5–6 mm in diameter and 5–7 mm deep, taken from the nape of the neck at the hairline. It must include hair follicles and the cutaneous nerves at the base of the follicles, the structures in which rabies virus is detected by direct fluorescent antibody (DFA) or RT-PCR.

The biopsy is placed on sterile gauze moistened with saline or water and covered to prevent drying. No fixative is used, because formalin destroys the virus and renders the specimen unsuitable for DFA and RT-PCR.

Rabies is a Category 1 Notifiable Medical Condition in South Africa, requiring immediate notification through the NICD NMC system.

This is more urgent than the Category 2 framework that applies to viral hepatitis (which allows seven days for written or electronic notification). Animal rabies is separately notifiable under the Animal Diseases Act, 1984 (Act No. 35 of 1984) through state Veterinary Services, with surveillance coordinated by the NICD and DALRRD under a One-Health framework.

Negri bodies are eosinophilic cytoplasmic inclusion bodies composed predominantly of rabies viral nucleoprotein (N). They are classically described in the cytoplasm of Purkinje cells of the cerebellum, hippocampal pyramidal neurons, and brainstem neurons.

They are pathognomonic for rabies when present, but not 100% sensitive: their absence does not exclude infection. Direct fluorescent antibody (DFA) testing on brain tissue is more sensitive and is the post-mortem gold standard.

The preferred handling for post-mortem rabies-suspect brain tissue is 2 cm × 2 cm cubes from both the cerebellum and the cerebrum, submerged in 50% glycerol-saline (half glycerol, half PBS) in a screw-top container, never glass, and transported as soon as possible.

Critically, the tissue must not be fixed in formalin: formalin destroys viral antigen and renders DFA testing impossible. If 50% glycerol-saline is unavailable, fresh-frozen tissue sent without delay is the alternative. The Forensic Pathologist usually collects the specimen.

Rabies is notifiable on both axes:

• Human cases through the Notifiable Medical Conditions (NMC) framework, reported to the Department of Health (typically via the NICD NMC App).
• Animal cases under the Animal Diseases Act, 1984 (Act No. 35 of 1984), reported to state Veterinary Services (Department of Agriculture, Land Reform and Rural Development).

Surveillance is coordinated under a One-Health framework, with laboratory confirmation centralised at the NICD reference laboratory. Both suspected and confirmed cases must be reported; notification is not conditional on laboratory confirmation.

The immunoglobulin provides instant passive protection in the first days, bridging the gap until the vaccine generates the patient’s own lasting antibody. It is infiltrated into the wound and gives no added benefit once the vaccine response has begun.

It does not prolong the vaccine, lower cost, or replace wound care.

Rabies virus is the type species of the genus Lyssavirus, family Rhabdoviridae, order Mononegavirales. The genus name derives from the Greek lyssa, “frenzy”.

Other Rhabdoviridae genera include Vesiculovirus (vesicular stomatitis virus, mostly veterinary) and several plant and invertebrate viruses; Lyssavirus is the genus of medical importance, containing classical rabies virus and the rabies-related lyssaviruses (Duvenhage, Mokola, Australian bat lyssavirus and others).

Rabies is the prototype of neuronal spread. The virus replicates at the inoculation site, binds acetylcholine receptors to enter peripheral nerve endings, and travels by axonal transport to the brainstem and limbic system, shielded from circulating immunity. Spread along the olfactory route (option E) is a feature of herpes simplex virus, not rabies, and rabies does not depend on a viraemia (option A).

After inoculation, rabies virus binds receptors at neuromuscular junctions (nicotinic acetylcholine receptor, NCAM, p75NTR) and undergoes retrograde fast axonal transport along peripheral nerves to the spinal cord and brain. There is no detectable viraemia during the incubation period, so the virus is sequestered in muscle and nerve.

This is why post-exposure prophylaxis works: while the virus is still on its way to the CNS, neutralising antibody (vaccine-induced or passive RIG) can reach it and neutralise it. Once the virus enters the CNS, antibody is excluded by the blood-brain barrier and PEP is too late.

The genus Lyssavirus is split into three antigenic phylogroups. Standard rabies vaccines and RIG cross-protect within Phylogroup 1, which includes the classical rabies virus, Duvenhage virus (SA-relevant), Australian bat lyssavirus, European bat lyssaviruses 1 and 2, and Irkut, Aravan and Khujand viruses.

Phylogroup 2 (Mokola, Lagos bat, Shimoni bat) is antigenically distinct, and current vaccines provide no reliable cross-protection. Phylogroup 3 (West Caucasian bat, Ikoma, Matlo bat) is similarly poorly protected.

Standard PEP works for dog rabies and most bat lyssavirus exposures, but provides no proven protection against Mokola virus.

Pre-exposure rabies vaccination is now a two-dose schedule given on days 0 and 7. It does not remove the need for care after a bite, but it simplifies it.

The older three-dose regimen has been superseded, and the four-dose course is a post-exposure schedule for the previously unvaccinated.

Classical RABV in South Africa is maintained in two main terrestrial cycles:

• Canid cycle: domestic dogs (the principal source of human exposure) plus black-backed jackals in the wild. Dominant in KwaZulu-Natal, the Eastern Cape, Mpumalanga, Free State and Limpopo.
• Mongoose (herpestid) cycle: yellow mongoose (Cynictis penicillata) on the central plateau; rarer human exposures.

A separate bat-eared fox cycle is recognised in the Western and Northern Cape, the western Free State, Eastern Cape and North West.

Approximately 10 laboratory-confirmed human cases are recorded annually in SA (with 16 in 2018), concentrated in the eastern provinces.

Approximately 59,000 human deaths from rabies occur each year, almost certainly an underestimate given limited surveillance in endemic settings. Over 99% of cases are caused by domestic dog exposure. Asia and Africa carry the largest share of the burden.

The WHO’s stated target is zero human dog-mediated rabies deaths by 2030, pursued through mass dog vaccination and improved access to post-exposure prophylaxis. Bat-mediated rabies is the dominant terrestrial cycle in the Americas but is a much smaller contributor to global mortality.

Louis Pasteur administered the first successful rabies vaccine on 6 July 1885 to Joseph Meister, a nine-year-old severely bitten by a rabid dog. Pasteur had developed an attenuated preparation through serial passage of rabies virus in rabbit spinal cord. Meister survived. The achievement is regarded as opening the modern era of vaccinology, predating any understanding of viruses or even the germ theory in its mature form.

Modern rabies vaccines (HDCV, PCEC, Verorab) are inactivated whole-virus preparations grown in cell culture rather than animal nervous tissue, with dramatically improved safety and efficacy.

The direct fluorescent antibody (DFA) test on brain tissue is the gold-standard post-mortem diagnostic. Performed on smears or impressions of brain tissue (typically brainstem and cerebellum), it has greater than 99% sensitivity and specificity and produces results within hours.

RT-PCR on the same tissue is a complementary molecular test. Histology for Negri bodies is supportive but less sensitive than DFA. In South Africa, post-mortem rabies confirmation is centralised at the NICD reference laboratory; whole brain is submitted in 50% glycerol-saline.

The Milwaukee protocol was the regimen used in the 2004 Wisconsin survivor (Jeanna Giese, bat-virus exposure, no prior vaccine). Subsequent attempts have failed in over 30 documented cases, with no proven viral clearance, no neuroprotection at autopsy in treated patients, and ketamine has been shown to be ineffective in cultured rabies-infected neurons. The Milwaukee protocol has no role in current management.

Symptomatic rabies remains effectively 100% fatal in the unvaccinated. Care is palliative. The handful of true survivors (mostly with prior partial vaccination, mostly with bat-variant exposure) reflects a less neurovirulent virus and pre-existing immunity, not the intervention.

Rabies virus is Baltimore class V: a non-segmented, negative-sense single-stranded RNA virus of approximately 12 kb. The genome is organised 3’-N-P-M-G-L-5’ and encodes five proteins:

• N: nucleoprotein
• P: phosphoprotein (polymerase cofactor; also blunts innate immunity)
• M: matrix protein
• G: glycoprotein (the major neutralising antigen and the target of all current vaccines)
• L: large polymerase (the RNA-dependent RNA polymerase)

This non-segmented negative-sense architecture is characteristic of the order Mononegavirales, shared with the paramyxoviruses, filoviruses and bornaviruses.

The current standard PrEP schedule is 2 doses IM on days 0 and 7. This replaced the older 3-dose schedule (days 0, 7, 21–28). Equivalent intradermal options (2 sites per visit on days 0 and 7) provide a dose-sparing alternative.

Immunocompromised patients require the extended 3-dose schedule on days 0, 7 and 21–28, IM (single site) or ID (2 sites).

Boosters are guided by neutralising antibody titres, typically every 2 years for ongoing high-risk exposure (veterinarians, lab workers).

The typical incubation period is 1 to 3 months, but the range is very wide, from a few days to over a year, with rare documented cases at six years or more.

Incubation length depends on:

• Distance from inoculation to the central nervous system (proximal head and face bites are shortest).
• Inoculum size (larger viral dose, shorter incubation).
• Innervation of the bite site (richly innervated sites are shorter).

Post-exposure prophylaxis is effective if started promptly after exposure, because the long incubation gives vaccine-induced immunity time to develop before the virus reaches the CNS.

Approximately 80% of human cases present as the furious (encephalitic) form: episodes of hyperexcitability, agitation, aggression, hallucinations and confusion separated by lucid intervals, with autonomic dysfunction (hypersalivation, sweating, arrhythmias).

Hydrophobia, painful spasms of the diaphragm and inspiratory muscles triggered by swallowing or even the sight or mention of water, is pathognomonic but more common with canine than bat exposure. Aerophobia, the same spasms triggered by air movement, is equally characteristic.

The remaining 20% present as paralytic (dumb) rabies: ascending flaccid paralysis from the bitten limb, sphincter involvement, slower progression, hydrophobia rare. Both forms progress to coma and death.

The current ICTV-ratified species name is Lyssavirus rabies, under the binomial mandate that requires every virus species to be named “genus name + a single-word epithet”.

The previous name was Rabies lyssavirus (a “common-name first” format that has now been retired in favour of the genus-first binomial). The everyday name “rabies virus” remains correct and unaffected in clinical and laboratory practice.

The NICD Specimen Collection Guide recommends at least 500 μL of saliva per specimen collected by syringe or suction device, with one specimen submitted daily on three consecutive days.

Sputum is not acceptable as a substitute. The serial-day strategy maximises diagnostic yield because saliva shedding is intermittent, and starting as soon as rabies enters the differential is important, because patients often present late in disease and the testing window may be brief.

Current practice is to infiltrate the entire calculated dose into and around the wound(s), a change from older guidance that split the dose between local infiltration and a distant IM site. If the wound is small and the full volume cannot be accommodated, dilute with normal saline rather than diverting the remainder to a distant site.

Doses:

• HRIG (human): 20 IU/kg
• ERIG (equine): 40 IU/kg

Critical rules: never mix RIG with the vaccine in the same syringe; never inject RIG into the same anatomical site as the vaccine, because they neutralise each other. RIG must be given within 7 days of the first vaccine dose; after day 7, endogenous antibody is present and RIG is no longer indicated.