Early origin and global colonisation of foot-and-mouth disease virus

Aiewsakun, Pakorn; Pamornchainavakul, Nakarin; Inchaisri, Chaidate

doi:10.1038/s41598-020-72246-6

Cited by 13 publications

(12 citation statements)

References 40 publications

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“…The Southern African Territories (SAT) serotypes can be traced back to the mid-fteenth to mid-sixteenth century (24).…”

Section: Results Of Pooled Prevalencementioning

confidence: 99%

Epidemiology and effectiveness of interventions for Foot and Mouth Disease in Africa: A systematic review and meta-analysis

MWEBE,

Kalinda,

Obuku

et al. 2023

Preprint

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Background Foot and mouth disease (FMD) remains endemic in most African countries despite several interventions that have been instituted for its control. This systematic review and meta-analysis sought to elucidate the epidemiology of FMD and evaluate the effectiveness of the interventions for its control in Africa. Methods We performed a systematic review and meta-analysis to generate evidence on the epidemiology and effectiveness of interventions for the control of foot and mouth disease in Africa. 113 articles were included in the review. Results The overall pooled seroprevalence of FMD in Africa was 16% at 95% CI (4% − 30%). The subgroup analysis showed the following pooled seroprevalence at region: Central Africa at 38%, 95% CI (33% − 43%); Northern Africa at 31%, 95% CI (8% − 57%); Western Africa at 30%, 95% CI (11% − 50%); Eastern Africa at 22% 95% CI (9% − 37%); and Southern Africa at 2%, 95% CI (0% − 9%). Species level: buffaloes at 71%, 95% CI (8% − 100%); goats at 30%, 95% CI (4% − 61%); sheep at 23%, 95% CI (8% − 40%); cattle at 15%, 95%CI (2% − 31%); pigs at 9%, 95% CI (0% − 26%); and other wildlife at 2% (0% − 36%). Diagnostic level: ELISA at 15%, 95% CI (4% − 29%); several tests at 16%, 95% CI (0% − 44%); BTVIA at 29%, 95% CI (14% − 24%); and PCR at 44%, 95% CI (6% − 84%). LFK index of 4.83 indicated publication bias and a high level of heterogeneity. Quarantine and vaccination are the most used control interventions for FMD. Conclusions FMD is prevalent in most Africa in buffaloes and goats, it is mostly diagnosed by ELISA. The disease is mostly controlled by vaccination and quarantine. This review was limited by inadequate data on the effectiveness of interventions. The findings will guide the control of the disease and the use of the PCPFMD. Further research is recommended on the effectiveness of interventions for control. Systematic review registration: The study review was registered in INPLAYS (INPLAYS2022110039. doi:10.337766).

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“…The Southern African Territories (SAT) serotypes can be traced back to the mid-fteenth to mid-sixteenth century (24).…”

Section: Results Of Pooled Prevalencementioning

confidence: 99%

Epidemiology and effectiveness of interventions for Foot and Mouth Disease in Africa: A systematic review and meta-analysis

MWEBE,

Kalinda,

Obuku

et al. 2023

Preprint

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“…Moreover, a new strain–O/ME‐SA/Ind‐2001d was reported in 11 provinces of Thailand in 2016 (WAOH, 2017 ). The co‐infection of FMDVs and intra‐host recombination could increase the genetic diversity of FMDV (Aiewsakun et al., 2020 ). Nevertheless, it is uncertain whether the outbreaks in Thailand result from ongoing transmission or from reintroductions from other locations.…”

Section: Discussionmentioning

confidence: 99%

“…An outbreak is self-limited when the population of susceptible animals in the area is depleted to the point that herd immunity is reached (Estrada et al, 2008). recombination could increase the genetic diversity of FMDV (Aiewsakun et al, 2020). Nevertheless, it is uncertain whether the outbreaks in Thailand result from ongoing transmission or from reintroductions from other locations.…”

Section: Discussionmentioning

confidence: 99%

Epidemiology of foot‐and‐mouth disease outbreaks in Thailand from 2011 to 2018

Chanchaidechachai

Saatkamp

Jong

et al. 2022

Transbounding Emerging Dis

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Foot-and-mouth disease (FMD) is one of the most important animal diseases hindering livestock production in Thailand. In this study, a temporal and spatial analysis at the subdistrict level was performed on FMD outbreak reports in Thailand from 2011 to 2018. Risk factors associated with FMD outbreaks were furthermore investigated using generalized estimating equations. The results showed that the incidence of FMD outbreaks was the highest in 2016 and was affected by season, with a peak in FMD outbreaks occurring in the rainy-winter season, during October to December. FMD outbreaks were mostly distributed in small clusters within a few subdistricts. Some high-risk areas with repeated outbreaks were detected in the central regions.Risk factors, including the increase of subdistrict's size of the dairy population, beef population or pig population, the low percentage of forest area, subdistricts in the provinces adjacent to Malaysia, the presence of a livestock market and the occurrence of an FMD outbreak in a neighbouring subdistrict in the previous month significantly increased the odds of having an FMD outbreak. The increase in proximity to the nearest subdistrict with an FMD outbreak in the previous month decreased the odds of having FMD outbreaks. This study helped to identify high-risk areas and periods of FMD outbreaks in Thailand. Together with the identified risk factors, its results can be used to optimize the FMD control programme in Thailand and in other countries having a similar livestock industry and FMD situation. K E Y W O R D Sfoot-and-mouth disease, risk factors, spatial analysis, temporal analysis, Thailand INTRODUCTIONDriven by domestic consumption and exports of animal products, livestock production in Thailand has been gradually growing since the late 1970s when farming systems in Thailand started to shift from exten-This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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“…A recombination hotspot is defined as a genomic position in which the frequency of putative recombination exceeds neutral expectations (>99% confidence interval of the local density plot created by a permutation test) (29); genomic regions between hotspots are inferred to have low rates of recombination. Thus, the locations of hotspots can be used to subdivide the genome into fragments, where each fragment is relatively free of frequent within-fragment recombination and thus can be used for further phylogenetic analysis (30,31).…”

Section: Recombination Detectionmentioning

confidence: 99%

Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant

et al. 2022

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While the widespread and endemic circulation of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) causes persistent economic losses to the U.S. swine industry, unusual increases of severe cases associated with the emergence of new genetic variants are a major source of concern for pork producers. Between 2020 and 2021, such an event occurred across pig production sites in the Midwestern U.S. The emerging viral clade is referred to as the novel sub-lineage 1C (L1C) 1-4-4 variant. This genetic classification is based on the open reading frame 5 (ORF5) gene. However, although whole genome sequence (WGS) suggested that this variant represented the emergence of a new strain, the true evolutionary history of this variant remains unclear. To better elucidate the variant's evolutionary history, we conducted a recombination detection analysis, time-scaled phylogenetic estimation, and discrete trait analysis on a set of L1C-1-4-4 WGSs (n = 19) alongside other publicly published WGSs (n = 232) collected over a 26-year period (1995–2021). Results from various methodologies consistently suggest that the novel L1C variant was a descendant of a recombinant ancestor characterized by recombination at the ORF1a gene between two segments that would be otherwise classified as L1C and L1A in the ORF5 gene. Based on analysis of different WGS fragments, the L1C-1-4-4 variant descended from an ancestor that existed around late 2018 to early 2019, with relatively high substitution rates in the proximal ORF1a as well as ORF5 regions. Two viruses from 2018 were found to be the closest relatives to the 2020-21 outbreak strain but had different recombination profiles, suggesting that these viruses were not direct ancestors. We also assessed the overall frequency of putative recombination amongst ORF5 and other parts of the genome and found that recombination events which leave detectable numbers of descendants are not common. However, the rapid spread and high virulence of the L1C-1-4-4 recombinant variant demonstrates that inter-sub-lineage recombination occasionally found amongst the U.S. PRRSV-2 might be an evolutionary mechanisms that contributed to this emergence. More generally, recombination amongst PRRSV-2 accelerates genetic change and increases the chance of the emergence of high fitness variants.

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Early origin and global colonisation of foot-and-mouth disease virus

Cited by 13 publications

References 40 publications

Epidemiology and effectiveness of interventions for Foot and Mouth Disease in Africa: A systematic review and meta-analysis

Epidemiology and effectiveness of interventions for Foot and Mouth Disease in Africa: A systematic review and meta-analysis

Epidemiology of foot‐and‐mouth disease outbreaks in Thailand from 2011 to 2018

Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant

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