Current status and molecular epidemiology of rabies virus from different hosts and regions in Malawi.

Although rabies is endemic in Malawi, there have been no studies in which rabies virus was systematically investigated and characterized in multiple animal hosts in that country. In order to provide molecular epidemiological data on rabies virus in Malawi, 683 suspected rabies case reports from 2008 to 2021 were examined, and 46 (dog = 40, cow = 5, and cat = 1) viable rabies-positive brain samples archived at the Central Veterinary Laboratory (CVL), Lilongwe, Malawi, were analyzed genetically. The results showed an increase in the submission of brain samples from 2008 to 2010, with the highest number of submissions observed in 2020. Of the 683 case reports analyzed for the period under review, 38.1% (260/683) (CI: 34.44 - 41.84) were confirmed by direct fluorescent antibody test. Among the confirmed cases, 65.4% (170/260) (CI: 59.23 - 71.09) were canine rabies. Further, phylogenetic analysis revealed that sequences from different animal hosts clustered together within the Africa 1b lineage, suggesting that the strains circulating in livestock are similar to those in domestic dogs. This finding supports the hypothesis that canine rabies is spilling over to livestock and emphasizes the need for further studies to provide data for effective control of rabies in Malawi.

Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi.

Several African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

Spatio-temporal patterns and risk factors of foot-and-mouth disease in Malawi between 1957 and 2019.

Foot-and-mouth disease (FMD) is an important livestock disease causing short-term and long-term production losses and hindering local and international trade. To gain access to lucrative foreign markets and also improve local trade, there is a need to employ effective preventive and control strategies. Although FMD has been present in Malawi for over 60 years, little knowledge is available concerning the dynamics and drivers of FMD in the country. A modelling study based on retrospective data was conducted to establish the spatio-temporal distribution and determine the risk factors associated with FMD in Malawi. A retrospective space-time analysis was performed and a matched case-control study was carried out to investigate risk factors. The number of reported FMD outbreaks has descriptively increased after 2000 and the disease has spread to previously unaffected areas. Two significant spatio-temporal clusters of FMD were identified; one in the southern region and the other in the northern region. An analysis of only index cases (first detected locations) also detected two clusters with one in the northern region and the other in the southern region. Higher beef cattle density (p = 0.023), higher pig density (p = 0.043) and increased distance to wildlife protected areas (p = 0.036) were positively associated with the risk of FMD while increased distances to international borders (p = 0.008) and roads (p = 0.034) were associated with reduced risk of FMD. High FMD risk areas were observed in the southern and northern regions but not in the central region during the early years (1957-1981). The more recent increase in FMD risk at the end of the study period (2019) in the central region might be attributed to increases in livestock density in this region. These findings provide insight into the pattern of FMD occurrence that will promote informed decisions for the progressive control of FMD in the region.