Viral Co-Infections of Warthogs in Namibia with African Swine Fever Virus and Porcine Parvovirus 1

Six underreported viral diseases of domesticated and wild swine in Africa: Implications and perspectives

Pig production is increasing annually in Africa as it is recognized as a significant source of income, livelihood and food security, particularly in rural communities. Understanding the circulating swine pathogens is crucial for the success of this emerging industry. Although there is extensive data available on the African swine fever virus due to its devastating impact on pig production, knowledge about the presence of other viral swine pathogens on the continent is still extremely limited. This review discusses what is currently known about six swine pathogens in Africa: classical swine fever virus, porcine reproductive and respiratory syndrome virus, porcine circovirus-2, porcine circovirus-3, porcine parvovirus-1, and pseudorabies virus. Gaps in our knowledge are identified and topics of future focus discussed.

First detection and molecular characterization of porcine reproductive and respiratory syndrome virus in Namibia, Africa

Introduction

The swine sector in Africa plays an important role in local economies, contributing to poverty alleviation and community subsistence. In addition, intensive farming is progressively becoming more important in the region. Therefore, any disease affecting swine populations can have detrimental effects on local communities. Porcine Reproductive and Respiratory Syndrome (PRRS) is among the most important infectious diseases affecting swine worldwide, but information on its epidemiology in Africa is extremely limited.

Material and methods

In the present study, 147 healthy butchered pigs, originating from 15 Namibian intensive and rural farms were tested by RT-PCR and the ORF7 genes of positive samples were sequenced for further genetic characterization and phylogenetic analysis. Additionally, 55 warthogs were also evaluated using the same approach.

Results

Overall, 7 out of 147 pigs (4.76%) tested positive, all originating from 3 rural farms (with a within-herd detection frequency higher than 14%) characterized by strong epidemiological links. All industrial pig and warthog samples were negative. Sequence analysis revealed that all strains belonged to the Betaarterivirus suid1 species, previously known as PRRSV type I, and were likely imported from Europe at least 6 years ago, evolving independently thereafter. When and how the first introduction occurred could not be determined due to the absence of other African sequences for comparison.

Discussion

The present work provides the first detection and characterization of PRRSV molecular epidemiology in Namibia. Based on the present findings, the presence of the PPRSV appears marginal and limited to backyard farms. While biosecurity measures applied in industrial farms appear to be effective in preventing viral introduction, PRRSV circulation in rural settings still represents a potential threat, and considering the socio-economical implication of livestock diseases decreasing animal performances in rural areas, active monitoring should be encouraged to promptly act against emerging menaces and guarantee the welfare of local pig populations.

High detection frequency and genetic diversity of porcine circovirus 3 (PCV-3) in Namibian backyard farms and warthogs

Since its first identification in 2015, porcine circovirus 3 (PCV-3) has been reported worldwide with a high frequency and in the presence of several clinical conditions, although its impact on pig health and productivity is still debated. Data on the presence of PCV-3 in Africa are, however, limited. A previous study performed on commercial pigs in Namibia failed to identify the pathogen. In the present study, the viral circulation in backyard farms, characterised by lower biosecurity measures and frequent animal exchange between farms, was assessed. The susceptibility of warthogs to PCV-3 infection and their potential epidemiological role were also evaluated. Tonsils from 77 pigs from backyard piggeries and 55 warthogs were collected in different regions of Namibia and tested by PCR. Positive samples were sequenced and compared to PCV-3 strains circulating globally. Forty-two out of 77 pigs (54.54 %) and 12 out of 55 warthogs (21.82 %) tested positive, demonstrating the presence of PCV-3 in the country and suggesting that the high biosecurity measures implemented in the commercial farms that previously tested negative for PCV-3 probably prevented viral introduction. The partial ORF2 gene was successfully sequenced in samples from 27 pigs and 6 warthogs. Genetically, the identified strains were part of 3 distinct groups which included both backyard pigs and warthogs from different regions of Namibia. There is also evidence for the occurrence of multiple introduction events most likely from Asian countries, either directly into Namibia or through other African countries. Considering the strict Namibian regulations on live animal importation, understanding the source of viral introduction is challenging, although semen importation or the habit of feeding backyard pigs with human food waste might have played a role. Pig exchanges between farms for breeding purposes or wildlife movements could also have been involved in PCV-3 dispersal within Namibia. Despite the significant advances in the field, further studies should be undertaken to properly understand PCV-3 epidemiology in Namibia and its impact on pig productivity and wildlife health.

An Updated Review of Ornithodoros Ticks as Reservoirs of African Swine Fever in Sub-Saharan Africa and Madagascar

This updated review provides an overview of the available information on Ornithodoros ticks as reservoirs and biological vectors of the ASF virus in Africa and Indian Ocean islands in order to update the current knowledge in this field, inclusive of an overview of available methods to investigate the presence of ticks in the natural environment and in domestic pig premises. In addition, it highlights the major areas of research that require attention in order to guide future investigations and fill knowledge gaps. The available information suggests that current knowledge is clearly insufficient to develop risk-based control and prevention strategies, which should be based on a sound understanding of genotype distribution and the potential for spillover from the source population. Studies on tick biology in the natural and domestic cycle, including genetics and systematics, represent another important knowledge gap. Considering the rapidly changing dynamics affecting the African continent (demographic growth, agricultural expansion, habitat transformation), anthropogenic factors influencing tick population distribution and ASF virus (ASFV) evolution in Africa are anticipated and have been recorded in southern Africa. This dynamic context, together with the current global trends of ASFV dissemination, highlights the need to prioritize further investigation on the acarological aspects linked with ASF ecology and evolution.

A Phylogeographic Analysis of Porcine Parvovirus 1 in Africa

Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as the virulent 27a strain, for which lower protection induced by vaccines has been demonstrated, is of increasing concern. Even though constant monitoring of PPV1 using molecular epidemiological approaches is of pivotal importance, viral sequence data are scarce especially in low-income countries. To fill this gap, a collection of 71 partial VP2 sequences originating from eight African countries (Burkina Faso, Côte d'Ivoire, Kenya, Mozambique, Namibia, Nigeria, Senegal, and Tanzania) during the period 2011-2021 were analyzed within the context of global PPV1 variability. The observed pattern largely reflected what has been observed in high-income regions, i.e., 27a-like strains were more frequently detected than less virulent NADL-8-like strains. A phylogeographic analysis supported this observation, highlighting that the African scenario has been largely shaped by multiple PPV1 importation events from other continents, especially Europe and Asia. The existence of such an international movement coupled with the circulation of potential vaccine-escape variants requires the careful evaluation of the control strategies to prevent new strain introduction and persistence.