The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa

Abstract

Foot-and-mouth disease (FMD) is a major livestock disease with direct clinical impacts as well as indirect trade implications. Control through vaccination and stamping-out has successfully reduced or eradicated the disease from Europe and large parts of South America. However, sub-Saharan Africa remains endemically affected with 5/7 serotypes currently known to be circulating across the continent. This has significant implications both locally for livestock production and poverty reduction but also globally as it represents a major reservoir of viruses, which could spark new epidemics in disease free countries or vaccination zones. This paper describes the phylodynamics of serotypes A and SAT2 in Africa including recent isolates from Cameroon in Central Africa. We estimated the most recent common ancestor for serotype A was an East African virus from the 1930s compared to SAT2 which has a much older common ancestor from the early 1700s. Detailed analysis of the different clades shows clearly that different clades are evolving and diffusing across the landscape at different rates with both serotypes having a particularly recent clade that is evolving and spreading more rapidly than other clades within their serotype. However, the lack of detailed sequence data available for Africa seriously limits our understanding of FMD epidemiology across the continent. A comprehensive view of the evolutionary history and dynamics of FMD viruses is essential to understand many basic epidemiological aspects of FMD in Africa such as the scale of persistence and the role of wildlife and thus the opportunities and scale at which vaccination and other controls could be applied. Finally we ask endemic countries to join the OIE/FAO supported regional networks and take advantage of new cheap technologies being rolled out to collect isolates and submit them to the World Reference Laboratory. 2/169/16

Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States

“…absence of coinfections) and factors related with on‐farm biosecurity (i.e. presence of a line of separation, cleaning and disinfection station) (Altizer, Bartel, & Han, 2011; Lycett et al., 2019; Rappole et al., 2006). Thus, further studies are needed to evaluate how biosecurity practices and overall pig health may contribute in slowing or accelerating PRRSV spread, results of these assessments can be used to predict the most effective biosecurity measures and optimize control strategies that go beyond PRRSV (Silva et al., 2019), not to mention current diseases that pose large‐scale biosecurity threats to the U.S swine health such as African Swine Fever.…”

Meta-analysis of genetic diversity of the VP1 gene among the circulating O, A, and SAT2 serotypes and vaccine strains of FMD virus in Egypt

“…In our study, SAT2 has the highest amino acid substitution per year at this site, serotype A having less, and serotype O the least. Similarly, Lycett et al (21) demonstrated genetic diversity between the topotype clades of SAT2 in sub-Saharan African isolates indicated by a large number of amino acid substitutions and large average pairwise distances between sequences from one topotype to another. Ullah et al (37) suggested that eight amino acid substitutions in the G-H loop of VP1 of the locally circulating FMDV Asia1 serotype may be a cause of vaccination failure.…”

“…The study of the evolutionary history and dynamics of FMD viruses along boundaries, in different countries or at continent level is important for better understanding of the basic epidemiological aspects of the virus and the geographical basis of the functional divergence of the virus serotypes (3,14,17,18,21,35,36). However, with recovery of live virus 28 days after acute infection and the persistence of FMDV in cattle in the oropharynx for years (3,26), local strains of the viruses evolve with different immunological identity.…”

Phylogeographic analysis of foot‐and‐mouth disease virus serotype O dispersal and associated drivers in East Africa

“…For example, Dellicour et al (2018) demonstrated that major urban areas were crucial in dissemination of the 2014–2015 West Africa Ebola virus outbreak, Lu et al (2017) identified geographic hot spots for diffusion of avian influenza virus in China, and Streicker et al (2016) predicted invasion routes of vampire bat rabies in South America. As sequencing technologies become more accessible, opportunities for constructing a more comprehensive view of the epidemiology of viruses, including FMDV, are becoming more abundant (Knight‐Jones et al, 2016b; Lycett et al, 2019).…”