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Page 24 Jaswant et al. One Health Implement Res 2024;4:15-37 https://dx.doi.org/10.20517/ohir.2023.61

Asian subclades [118,119] .

Studies examined reservoir dynamics, investigating new variants and quantifying transmission within and
between species. For example, an Israeli study showed emergence of a dog-related clade that was distinct
from fox-associated clades that were predominant before fox-targeted oral rabies vaccination began. The
emerging dog-related clade might have indicated a host shift, but sequence similarity to Turkish dog isolates
[120]
suggested cross-border introduction as the cause of the clade emergence . Bayesian phylogenetic inference
from WGS of samples from Turkey spanning from 1999 to 2015 was used to refine the date of a host shift
[121]
that did occur from dogs to foxes to ~1997 . A European red fox-associated variant reported from hyenas
in Tanzania , was concluded to stem from laboratory contamination as other studies found that sequences
[122]
from both wildlife and dogs all belonged to typical and closely-related dog-mediated variants belonging to
[9]
clade AF1b . Further analysis confirmed the central role of domestic dogs in maintaining circulation of
AF1b in this region . In the same setting, sequencing an African civet cat case that was presumed to be
[123]
spillover of dog-mediated rabies, also unexpectedly identified a novel highly divergent lyssavirus , and no
[124]
cases of this variant have been found in dogs. The majority of spillover examples identified were from dogs
into wildlife, but a limited number of publications reported spillover from wildlife to dogs or other animals,
for example, from Coyote into dogs in Mexico .
[56]

Human rabies
In total 24 studies (16 from Asia, 6 from Africa, and 2 from Latin America) reported sequences from human
rabies cases, with a total of 219 human samples sequenced. Most of these studies (n = 19) identified human
cases to be the result of dog-mediated rabies only. Three studies reported wildlife exposure only including 1
[126]
[125]
[66]
raccoon exposure from Nepal and 2 fox exposures, one from India and one from Mexico . The
report of raccoon exposure in Nepal may be a misidentification, as raccoons are not native to the country.
It’s possible that the biting animal was a red panda, which is indigenous to Nepal. Both species share
similarities in head features, dentition, and ringed tails . A longitudinal study from South Africa reported
[127]
a majority of human cases from dog-mediated rabies as well as three cases spread from mongoose (AF3) .
[128]
One of the Latin American publications reported a veterinarian who became infected while handling rabid
livestock that was determined through genetic analysis to be vampire bat rabies .
[129]
Several of the human cases occurred in rabies-free countries and were resolved through phylogenetic
analysis. Eight were traced to immigrants with exposure histories in countries with endemic dog-mediated
rabies where PEP was not received before travel to the (rabies-free) country of diagnosis. Analysis of the
patient isolates revealed similarity with cases in postulated countries of origin, including a case in the UK
imported from Nigeria and a case in France imported from Mali , two unrelated cases in Qatar both
[130]
[131]
[134]
[133]
[132]
imported from Nepal , and cases imported from the Philippines to the UK , Japan and Finland , as
[66]
well one that likely originated from insectivorous bats involving a Mexican immigrant who was bitten by a
fox, and who died in California . Similarly a sequence from a patient in France, with recent travel history
[126]
to Mali but no known exposure, belonged to AF2 subclade that circulates in West Africa .
[131]
Human cases with prolonged incubation periods were also identified (normal incubation periods range
from 1 week to 8 months). One human case in rabies-free Australia was traced to exposure before
relocation. The 10-year-old of Vietnamese origin had stayed in Hong Kong before immigrating to Australia
5 years prior to symptoms onset. Phylogenetic analysis revealed the isolate’s distinctness from Australian
Bat Lyssavirus and Vietnamese RABV lineages; instead grouping with a China-associated lineage,
[135]
suggesting acquisition in Hong Kong and prolonged incubation . Two human cases imported to Japan
also had incubation periods exceeding 8 months . Most human cases resulted from bites, with two
[133]