Serological and phylogenetic characterization of foot and mouth disease viruses from Uganda during cross‐sectional surveillance study in cattle between 2014 and 2017

Abstract

Here, we report the results of a cross-sectional study designed to monitor the circulation and genetic diversity of foot and mouth disease virus (FMDV) in Uganda between 2014 and 2017. In this study, 13,614 sera and 2,068 oral-pharyngeal fluid samples were collected from cattle and analysed to determine FMDV seroprevalence, circulating serotypes and their phylogenetic relationships. Circulation of FMDV was evidenced by the detection of antibodies against non-structural proteins of FMDV or viral isolations in all districts sampled in Uganda. Sequence analysis revealed the presence of FMDV serotypes A, O, SAT 1 and SAT 2. FMDVs belonging to serotype O, isolated from 21 districts, were the most prevalent and were classified into six lineages within two East African topotypes, namely EA-1 and EA-2. Serotype A viruses belonging to the Africa G-I topotype were isolated from two districts. SAT 1 viruses grouped within topotypes I and IV and SAT 2 viruses within topotypes VII, IV and X were isolated from six and four districts respectively. Phylogenetic analysis of SAT 1 and SAT 2 sequences from cattle clustered with historical sequences from African buffalo, indicating possible interspecies transmission at the wildlife-livestock interface. In some cases, Uganda viruses also shared similarities to viral strains recovered from other regions in East Africa. This 3-year study period provides knowledge about the geographical distribution of FMDV serotypes isolated in Uganda and insights into the genetic diversity of the multiple serotypes circulating in the country. Knowledge of circulating FMDV viruses will assist in antigenic matching studies to devise improved FMDV control strategies with vaccination and vaccine strain selection for Uganda. K E Y W O R D Sbuffalo, EA-2, foot and mouth disease, molecular epidemiology, Uganda, vaccine

Phylogeographical and cross‐species transmission dynamics of SAT1 and SAT2 foot‐and‐mouth disease virus in Eastern Africa

“…Thus, the epidemiological situation and transmission dynamics at wildlife–livestock interfaces probably differ in Eastern and Southern Africa. Even if buffalo to cattle transmission occurs equally as often in each region, the relative importance of such wildlife–livestock transmission is overshadowed in Eastern Africa due to widespread and continual waves of FMDV spreading through livestock in the region (Casey‐Bryars et al, ; Mwiine et al, ). Finally, although most outbreaks in cattle result from transmission within and between livestock populations, buffalo may still be a source of novel lineages to which current vaccines are inefficacious.…”

Genetic Diversity of Circulating Foot and Mouth Disease Virus in Uganda Cross-Sectional Study During 2014–2017

“…Supplementary File 1 | Accession Genbank number information form the entire VP1 and P1 sequence dataset collection representing the FMDV genetic diversity in Uganda between 2014 and 2017. Rows colored in green represent unreported sequences, while colored in blue represent sequences used for phylogenetic analysis reported in Mwiine et al (11). Codes for vaccination status are represented by N = non-vaccinated, Y = vaccinated, and U = unknown.…”

“…In terms of genetic diversity, recent reports demonstrate the presence of at least five out of the seven serotypes (A, O, SAT 1, SAT 2, and SAT 3) and multiple topotypes, affecting livestock across the country (4,(7)(8)(9)(10). Historically, FMDV O has been one of the most prevalent serotypes in Uganda, the most recently report indicates the circulation of at least five different lineages (11).…”

“…Information about the genetic diversity and homology at nucleotide and amino acid levels among the sequences within each serotipe contained in this data set is shown in Figures 1A,B, respectively. However, part of the collection (n = 117) was already used for initial phylogenetic analysis, and these sequences were reported elsewhere (11). To avoid possible duplications, here we are reporting the remaining sequences, comprised of 141 previously unpublished VP1 sequences representing serotypes O (n = 102) and SAT 1 (n = 50), as well as a total of 36 P1 sequences including serotypes O (n = 30) and SAT 2 (n = 6).…”

Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus

“…The 2A-coding region is very small and there are several distinct clusters with high conservation within each cluster which do not correlate with serotype (Figure 2d). In this genomic region, A/El-Fayoum/2014 and sample 10 are very closely related, and their nearest relative is a serotype O isolate from Uganda from 2017 (O/AMU_200/Uganda/2017, accession# MH791293, [31]; marked in purple in the figure). This serotype O virus is also the closest known relative to sample 10 in the remainder of the genome downstream of the 2A-coding region (Figures 2e, f and 3; Table 2), in marked contrast to A/El-Fayoum/2014.…”