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Patterns of Rabies Cases in South Africa Between 1993-2019

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Patterns of Rabies Cases in South Africa Between 1993-2019 Patterns of rabies cases in South Africa between 1993-2019, including the role of wildlife Katja Koeppel1, Ockert van Schalkwyk2, and Peter Thompson3 1University of Pretoria Faculty of Veterinary Science 2Government of South Africa 3University of Pretoria February 2, 2021 Abstract Rabies is a global viral zoonosis endemic to South Africa, resulting in fatal encephalitis in warm blooded animals, including humans. The loss of human lives and economic losses in rural areas through loss of livestock are substantial. A review was conducted of all confirmed rabies cases in South Africa from 1993 to 2019, with a total of 11 701 cases identified to species level to assess the wildlife plays in the epidemiology of rabies. A spatiotemporal cluster analysis using a discrete Poisson space-time probability model, accounting for underlying estimated dog and livestock densities, identified 13 significant clusters (p<0.05). These included four long-term clusters lasting more than 8 years in duration and seven short term clusters lasting less than 2 years, with the remaining two clusters being of intermediate length. Outside of these endemic clusters, wildlife outbreaks in the remainder of South Africa were often less than one and a half years in duration most likely due to the rapid decline of wildlife vectors, especially jackals associated with rabies infection. Domestic dogs accounted for 59.8% of cases, with domestic cats (3.2%), livestock (21.1%) and wildlife (15.8%) making up the remainder of the cases. Yellow mongoose (Cynictis penicillate) was the most frequently affected wildlife species, followed by bat-eared fox (Otocyon megalotis), black-backed jackal (Canis mesomelas), meerkat (Suricata suricatta) and aardwolf (Proteles cristatus). Rabies in wildlife species followed different spatial distributions: black-backed jackal cases were more common in the north-western parts of South Africa, yellow mongoose cases more frequent in central South Africa, and bat-eared fox and aardwolf cases were more frequent in southern and western South Africa. Clusters often spanned several provinces, showing the importance of coordinated rabies control campaigns across administrative boundaries, and high-risk areas were highlighted for rabies in South Africa. Hosted file Rabies pattern SA2.pdf available at https://authorea.com/users/393256/articles/506911- patterns-of-rabies-cases-in-south-africa-between-1993-2019-including-the-role-of- wildlife Posted on Authorea 2 Feb 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.161225714.48293578/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 1 Limpopo Total: 835 Mpumalanga Total: 1333 North West Gauteng Total: 758 Total: 216 Free State Total: 1222 Northern Cape Total: 469 KwaZulu−Natal Total: 5198 Eastern Cape Total: 1441 Western Cape Total: 231 Species Companion Livestock Wildlife 800 700 600 Companion 500 animals Livestock 400 Wildlife 300 Total 200 100 Annual Annual laboratories rabies confirmed cases 0 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013 2015 2017 2019 Year Posted on Authorea 2 Feb 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.161225714.48293578/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 2 800 700 600 500 400 Companion animals Livestock 300 Wildlife 200 100 Number of labority confirmed rabies0 cases Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Months Posted on Authorea 2 Feb 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.161225714.48293578/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 3 60 60 30 40 40 20 Cluster 1 Cluster 2 Cluster 3 20 20 10 0 0 0 2004−01 2006−01 2008−01 2010−01 2012−01 2008−01 2010−01 2012−01 2014−01 1995−10 1996−01 12.5 20 30 10.0 15 7.5 20 10 Cluster 4 Cluster 5 Cluster 6 5.0 5 10 2.5 0 0 0.0 2016−01 2016−04 2016−07 2016−10 2000−01 2002−01 2004−01 2006−01 2008−01 2016−01 2016−04 2016−07 2016−10 2017−01 15 20 30 15 10 20 10 Cluster 7 Cluster 8 Cluster 9 5 10 5 0 0 0 2016−01 2016−02 2016−02 2016−03 1994−01 1996−01 1998−01 1994−01 1996−01 1998−01 2000−01 2002−01 2004−01 4 10.0 3 15 Posted on Authorea 2 Feb 2021 | The copyright holder is the author/funder. All7.5 rights reserved. No reuse without permission. | https://doi.org/10.22541/au.161225714.48293578/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 2 10 5.0 Cluster 10 Cluster 11 Cluster 12 5 1 2.5 0 0 0.0 2005−07 2006−01 2006−07 2007−01 2003−07 2004−01 2004−07 2010−01 2015−01 2020−01 10 5 Species Category Dog_Cat Livestock Wildlife Cluster 13 0 2015−05 2015−06 2015−07 2015−08 2015−09 4 60 50 40 30 20 10 No of laboratory confimred rabies cases 0 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 Black-backed jackal Side-striped jackal 80 180 70 160 140 60 120 50 Black-backed jackal 100 40 Aardwolf 80 Bat-eared fox 30 60 Yellow mongoose 20 40 Total wildife 10 20 No of laboratory confirmed rabies cases 0 0 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Months Posted on Authorea 2 Feb 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.161225714.48293578/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 5 Posted on Authorea 2 Feb 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.161225714.48293578/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 6.
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