Geospatial Tracking of a Rabies Outbreak in the Eastern Cape Province, South Africa, Using Molecular Data

Area of Science:

• Veterinary epidemiology
• Molecular epidemiology of zoonotic diseases
• Public health surveillance

Background:

• Rabies remains a significant neglected zoonotic disease, causing fatalities globally, particularly in resource-limited regions.
• South Africa faces rabies challenges with both domestic and wildlife reservoirs, leading to frequent cross-species transmission.
• A notable dog rabies outbreak occurred in the Eastern Cape (EC) province, South Africa, between 2020 and 2024.

Purpose of the Study:

• To investigate the origin and spread of a prominent dog rabies outbreak in the Nelson Mandela Bay Municipality (NMBM) and the wider EC province.
• To analyze epidemiological data and rabies virus (RABV) genetic sequences to understand transmission dynamics.
• To identify potential factors contributing to the outbreak, such as vaccination status.

Main Methods:

• Retrospective analysis of epidemiological data from 2596 reported rabies cases (November 2020–December 2024).
• Partial glycoprotein gene sequence analysis of RABVs from various hosts, including dogs (n=102), humans (n=4), cats (n=3), and livestock (n=5).
• Descriptive epidemiology and phylogenetic analysis to delineate viral clusters and identify origins.

Main Results:

• Dogs were the most frequently infected hosts (n=705) during the Eastern Cape outbreak, underscoring their role in rabies epizootiology.
• RABVs from the outbreak exhibited high sequence homology (99% mean identity), suggesting a common progenitor.
• Phylogenetic analysis revealed three distinct RABV clusters, with most samples in DD-I and DD-II, and one in BEF-II, indicating at least three independent introductions into the NMBM dog population.

Conclusions:

• The study suggests multiple independent introductions of RABV into the NMBM dog population between 2021 and 2024, with DD-II subgroup C being dominant.
• High sequence homology supports a historical introduction of rabies into South Africa.
• Lapsed dog vaccinations during the outbreak period may have complicated the introduction and spread of rabies in the study area.