Multiple origins of foot-and-mouth disease virus serotype Asia 1 outbreaks, 2003-2007

Complete coding region sequence analyses and antigenic characterization of emerging lineage G-IX of foot- and-mouth disease virus serotype Asia1

Foot-and-mouth disease Virus (FMDV) serotype Asia1 is prevalent in the Indian subcontinent, with only G-III and G-VIII reported in India until 2020. However, in 2019, a novel genetic group within serotype Asia1, designated as G-IX, emerged in Bangladesh, followed by its detection in India in 2020. This report presents analyses of the complete coding region sequences of the G-IX lineage isolates. The length of the open reading frame (ORF) of the two G-IX isolates was 6990 nucleotides without any deletion or insertion. The G-IX isolates showed the highest sequence similarity with an isolate of G-III at the ORF, L, P2, and P3 regions, and with an isolate of G-VIII at the P1 region. Phylogenetic analysis based on the capsid region (P1) supports the hypothesis that G-VIII and G-IX originated from a common ancestor, as speculated earlier. Further, VP1 region-based phylogenetic analyses revealed the re-emergence of G-VIII after a gap of 3 years. One isolate of G-VIII collected during 2023 revealed a codon insertion in the G-H loop of VP1. The vaccine matching studies support the suitability of the currently used Indian vaccine strain IND63/1972 to contain outbreaks due to viruses belonging to G-IX.

Foot-and-mouth disease virus strains isolated in Vietnam during 2010-2019: genetic characterization and antigenic relatedness to the Euro SA vaccine

Foot-and-mouth disease is a highly contagious disease that affects cloven-hoofed animals. It has an important socio-economic impact on the livestock industry because it produces a drastic decrease of productivity. The disease has been successfully eradicated from some regions, including North America and Western Europe, but it is still endemic in developing countries. Agriculture plays an important role in the national economy of Vietnam, to which animal production contributes a great proportion. The concurrent circulation of foot-and-mouth disease virus (FMDV) serotypes O, A, and Asia 1 has been detected in recent years, but serotype O remains the most prevalent and is responsible for the highest numbers of outbreaks. Appropriate vaccine strain selection is an important element in the control of FMD and is necessary for the application of vaccination programs in FMD-affected regions. Here, we present updated information about the genetic and antigenic characteristics of circulating strains, collected from endemic outbreaks involving types O and A, between 2010 and 2019. Neutralizing assays showed a good in vitro match between type O strains and the monovalent O1 Campos vaccine strain. High r1 values were obtained (above 0.7) when testing a swine serum pool collected 21 days after vaccination, but the O/VTN/2/2019 strain was an exception. An EPP estimation resulted in a median neutralizing titre of about 1.65 log10, indicating that good protection could be achieved. For type A Asia SEA 97 lineage strains, acceptable individual neutralizing titres were obtained with estimated EPP values over 80% for different combinations of vaccine strains. Taking into account that the r1 value is one tool of a battery of tests that should be considered for estimating the cross-protection of a field strain against a vaccine strain, an in vivo challenge experiment was also performed, yielding a PD50 value of 8.0. The results indicate that South American strains could be potentially used for controlling outbreaks involving these lineages. This study demonstrates the importance of considering strain characteristics when choosing vaccine strains and controls.

Emergence of a novel genetic lineage 'A/ASIA/G-18/2019' of foot and mouth disease virus serotype A in India: A challenge to reckon with

Foot and mouth disease (FMD) has engendered large scale socioeconomic crises on numerous occasions owing to its extreme contagiousness, transboundary nature, complicated epidemiology, negative impact on productivity, trade embargo, and need for intensive surveillance and expensive control measures. Emerging FMD virus variants have been predicted to have originated and spread from endemic Pool 2, native to South Asia, to other parts of the globe. In this study, 26 Indian serotype A isolates sampled between the year 2015 and 2022 were sequenced for the VP1 region. BLAST and maximum likelihood phylogeny suggest emergence of a novel genetic group within genotype 18, named here as 'A/ASIA/G-18/2019' lineage, that is restricted so far only to India and its eastern neighbour, Bangladesh. The lineage subsequent to its first appearance in 2019 seems to have displaced all other prevalent strains, in support of the phenomenon of 'genotype/lineage turnover'. It has diversified into two distinct sub-clusters, reflecting a phase of active evolution. The rate of evolution of the VP1 region for the Indian serotype A dataset was estimated to be 6.747 × 10-3 substitutions/site/year. India is implementing a vaccination centric FMD control programme. The novel lineage showed good antigenic match with the proposed vaccine candidate A IND 27/2011 when tested in virus neutralization test, while the existing vaccine strain A IND 40/2000 showed homology with only 31% of the isolates. Therefore, in order to combat this challenge of antigenic divergence, A IND 27/2011 could be the preferred strain in the Indian vaccine formulations.

A Vaccine Based on Asia1 Shamir of the Foot-and-Mouth Disease Virus Offers Low Levels of Protection to Pigs against Asia1/MOG/05, Circulating in East Asia

Foot-and-mouth disease (FMD) is one of the most contagious diseases in cloven hoof animals. Vaccination can prevent or control FMD, and vaccine antigens should be matched against circulating viruses. According to phylogenetic analyses, field isolates in this region belonged to genotype V and showed low genetic similarity with the Asia1 Shamir vaccine, the OIE-recommended vaccine strain. In this study, we investigated whether pigs vaccinated with the Asia1 Shamir vaccine could be protected from challenges with the Asia1/MOG/05 virus, one of the genotype V field isolates. Eight pigs were divided into either vaccinated or nonvaccinated control groups. After two vaccinations with Asia1 Shamir, both groups of pigs were challenged with the Asia1/MOG/05 field isolate at 2 weeks after the second vaccination. In the control group, symptoms appeared at 2 days post-infection (dpi). The clinical sign score peaked at 4 dpi, and this coincided with virus shedding through nasal discharge. Neutralizing antibody titers peaked at 17 dpi. In the vaccinated group, clinical signs were delayed compared with the control group, and the highest score was shown at 10 dpi accompanied with virus nasal shedding, which peaked at 11 dpi. Neutralizing antibodies were induced 2 weeks after the second vaccination and peaked at 17 dpi. In conclusion, Asia1 Shamir vaccination in pigs provided partial protection from Asia1/MOG/05 virus infection.

Did Climate Change Influence the Emergence, Transmission, and Expression of the COVID-19 Pandemic?

The human race has survived many epidemics and pandemics that have emerged and reemerged throughout history. The novel coronavirus Severe Acute Respiratory Syndrome SARS-CoV-2/COVID-19 is the latest pandemic and this has caused major health and socioeconomic problems in almost all communities of the world. The origin of the virus is still in dispute but most likely, the virus emerged from the bats and also may involve an intermediate host before affecting humans. Several other factors also may have affected the emergence and outcome of the infection but in this review, we make a case for a possible role of climate change. The rise in industrialization-related human activities has created a marked imbalance in the homeostasis of environmental factors such as temperature and other weather and these might even have imposed conditions for the emergence of future coronavirus cycles. An attempt is made in this review to explore the effect of ongoing climate changes and discuss if these changes had a role in facilitating the emergence, transmission, and even the expression of the COVID-19 pandemic. We surmise that pandemics will be more frequent in the future and more severely impactful unless climate changes are mitigated.

Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages

Livestock farming across the world is constantly threatened by the evolutionary turnover of foot-and-mouth disease virus (FMDV) strains in endemic systems, the underlying dynamics of which remain to be elucidated. Here, we map the eco-evolutionary landscape of cocirculating FMDV lineages within an important endemic virus pool encompassing Western, Central, and parts of Southern Asia, reconstructing the evolutionary history and spatial dynamics over the last 20 years that shape the current epidemiological situation. We demonstrate that new FMDV variants periodically emerge from Southern Asia, precipitating waves of virus incursions that systematically travel in a westerly direction. We evidence how metapopulation dynamics drive the emergence and extinction of spatially structured virus populations, and how transmission in different host species regulates the evolutionary space of virus serotypes. Our work provides the first integrative framework that defines coevolutionary signatures of FMDV in regional contexts to help understand the complex interplay between virus phenotypes, host characteristics, and key epidemiological determinants of transmission that drive FMDV evolution in endemic settings.

Host selection pattern and flavivirus screening of mosquitoes in a disturbed Colombian rainforest

Studies on the feeding behavior of hematophagous insects, particularly those of medical importance, are relevant for tracking possible pathogen transmission routes and identifying biases in the choice of vertebrates. We evaluated host selection of blood-feeding mosquitoes in a disturbed forest in the Magdalena Medio valley in Colombia from March 2017 to April 2018, after the introduction of Zika virus to the Americas from the 2015-2016 outbreak. We estimated vertebrate diversity and collected blood-engorged female mosquitoes. Genomic DNA/RNA was extracted from the mosquito's abdomen for vertebrate host identification and pathogen detection. We performed conventional PCR and sequencing, using universal primers targeting vertebrate regions of the eukaryotic mitochondrial genome to determine bloodmeal host. Additionally, we tested for the presence of flaviviruses in all mosquito samples with RT-PCR. Based on the identity and quantity of detected bloodmeals, we performed mosquito-vertebrate interaction network analysis and estimated topology metrics. In total, we collected 292 engorged female mosquitoes representing 20 different species. Bloodmeal analyses identified 26 vertebrate species, the majority of which were mammals (N = 16; 61.5%). No flaviviruses of medical importance were detected from the samples. Although feeding patterns varied, network analyses showed a high degree of specialization by mosquitoes and revealed ecological and phylogenetic relationships among the host community. We conclude that host selection or preference by mosquitoes is species specific.

Morphometric Patterns and Blood Biochemistry of Capybaras (Hydrochoerus hydrochaeris) from Human-Modified Landscapes and Natural Landscapes in Brazil

The capybara, Hydrochoerus hydrochaeris, is the largest extant rodent of the world. To better understand the correlation between size and body mass, and biochemical parameters of capybaras from areas with different degrees of anthropization (i.e., different food supplies), we sampled free-ranging capybaras from areas of natural landscapes (NLs) and human-modified landscapes (HMLs) in Brazil. Analyses of biometrical and biochemical parameters of capybaras showed that animals from HMLs were heavier (higher body mass) than those from NL, a condition possibly related to fat deposit rather than body length, as indicated by Body Condition Index (BCI) analyses. Biochemical parameters indicated higher serum levels of albumin, creatine kinase, cholesterol, fructosamine and total protein among capybaras from HMLs than from NLs; however, when all adult capybaras were analyzed together only cholesterol and triglycerides were positively correlated with body mass. We propose that the biochemical profile differences between HMLs and NLs are related to the obesity condition of capybaras among HMLs. Considering that heavier animals might live longer and reproduce more often, our results could have important implications in the population dynamics of capybaras among HMLs, where this rodent species is frequently represented by overgrowth populations that generate several levels of conflicts with human beings.

Risk assessment and integrated surveillance of foot-and-mouth disease outbreaks in Russia based on Monte Carlo simulation

Background

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock worldwide. Russia is a big agricultural country with a wide geographical area where FMD outbreaks have become an obstacle for the development of the animal and animal products trade. In this study, we aimed to assess the export risk of FMD from Russia.

Results

After simulation by Monte Carlo, the results showed that the probability of cattle infected with FMD in the surveillance zone (Surrounding the areas where no epidemic disease has occurred within the prescribed time limit, the construction of buffer areas is called surveillance zone.) of Russia was 1.29 × 10^− 6. The probability that at least one FMD positive case was exported from Russia per year in the surveillance zone was 6 %. The predicted number of positive cattle of the 39,530 - 50,576 exported from Russia per year was 0.06. A key node in the impact model was the probability of occurrence of FMD outbreaks in the Russian surveillance zone. By semi-quantitative model calculation, the risk probability of FMD defense system defects was 1.84 × 10^− 5, indicating that there was a potential risk in the prevention and control measures of FMD in Russia. The spatial time scan model found that the most likely FMD cluster (P < 0.01) was in the Eastern and Siberian Central regions.

Conclusions

There was a risk of FMDV among cattle exported from Russia, and the infection rate of cattle in the monitored area was the key factor. Understanding the export risk of FMD in Russia and relevant epidemic prevention measures will help policymakers to develop targeted surveillance plans.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02967-x.

Host infection and community composition predict vector burden

Lyme disease is the most prevalent vector-borne disease in the United States, yet critical gaps remain in our understanding of tick and host interactions that shape disease dynamics. Rodents such as deer mice (Peromyscus spp.) and dusky-footed woodrats (Neotoma fuscipes) are key reservoirs for Borrelia burgdorferi, the etiological bacterium of Lyme disease, and can vary greatly in abundance between habitats. The aggregation of Ixodes pacificus, the western black-legged tick, on rodent hosts is often assumed to be constant across various habitats and not dependent on the rodent or predator communities; however, this is rarely tested. The factors that determine tick burdens on key reservoir hosts are important in estimating Lyme disease risk because larger tick burdens can amplify pathogen transmission. This study is the first to empirically measure I. pacificus larval burdens on competent reservoir hosts as a function of community factors such as rodent diversity, predator diversity, and questing tick abundance. Rodents were live trapped at oak woodland sites to collect tick burdens and tissue samples to test for infection with Borrelia burgdorferi sensu lato. We found that N. fuscipes tick burdens were negatively correlated with predator diversity, but positively correlated with questing I. pacificus larvae. In addition, rodent hosts that were infected with B. burgdorferi sensu lato tend to have higher burdens of larval ticks. These results demonstrate that tick burdens can be shaped by variability between individuals, species, and the broader host community with consequences for transmission and prevalence of tick-borne pathogens.

Efficient protection against Asia1 type foot-and-mouth disease using a chimeric vaccine strain suitable for East Asia

The type Asia1 genetic group(G)-V lineage foot-and-mouth disease (FMD) virus was identified in the East-Asian region in 2009. To date, only Shamir has been used as a standard vaccine strain worldwide for type Asia1. To prevent type Asia1 FMD in eastern Asia, two vaccine strains (ASM-R: G-V and ASM-SM: G-V/Shamir fusion) were developed and tested against type Asia1 virus strains. After immunization with the two experimental vaccines, the ASM-SM strain showed a higher level of protection against Shamir virus in mice. Additional immunogenicity tests were carried out in cattle and pigs, revealing sufficient antibody production capable of protecting the animals against the viral challenge. In cattle, the immune response started just 2 weeks after vaccination. Immunogenicity was lower in pigs, but antibody production was greatly increased to a high level after a second vaccination round. In particular, herein, 60 % and 100 % of the vaccinated pigs challenged with the Asia1 Shamir virus were determined to be clinically protected after one and two vaccination rounds with ASM-R, respectively. Pigs vaccinated twice produced sufficient antibody titers with low virus shedding for short time. Moreover, ASM-SM single-vaccinated pigs showed 100 % protection when challenged with the Asia1 Shamir virus. In summary, the vaccine strain ASM-SM designed for the defense of the Asian region efficiently granted protection to pigs against the typical Asia1 virus, Shamir.

Polymerase Fidelity Contributes to Foot-and-Mouth Disease Virus Pathogenicity and Transmissibility In Vivo

The low fidelity of foot-and-mouth disease virus (FMDV) RNA-dependent RNA polymerase allows FMDV to exhibit high genetic diversity. Previously, we showed that the genetic diversity of FMDV plays an important role in virulence in suckling mice. Here, we mutated the amino acid residue Phe257, located in the finger domain of FMDV polymerase and conserved across FMDV serotypes, to a cysteine (F257C) to study the relationship between viral genetic diversity, virulence, and transmissibility in natural hosts. The single amino acid substitution in FMDV polymerase resulted in a high-fidelity virus variant, rF257C, with growth kinetics indistinguishable from those of wild-type (WT) virus in cell culture, but it displayed smaller plaques and impaired fitness in direct competition assays. Furthermore, we found that rF257C was attenuated in vivo in both suckling mice and pigs (one of its natural hosts). Importantly, contact exposure experiments showed that the rF257C virus exhibited reduced transmissibility compared to that of wild-type FMDV in the porcine model. This study provides evidence that FMDV genetic diversity is important for viral virulence and transmissibility in susceptible animals. Given that type O FMDV exhibits the highest genetic diversity among all seven serotypes of FMDV, we propose that the lower polymerase fidelity of the type O FMDV could contribute to its dominance worldwide.IMPORTANCE Among the seven serotypes of FMDV, serotype O FMDV have the broadest distribution worldwide, which could be due to their high virulence and transmissibility induced by high genetic diversity. In this paper, we generated a single amino acid substitution FMDV variant with a high-fidelity polymerase associated with viral fitness, virulence, and transmissibility in a natural host. The results highlight that maintenance of viral population diversity is essential for interhost viral spread. This study provides evidence that higher genetic diversity of type O FMDV could increase both virulence and transmissibility, thus leading to their dominance in the global epidemic.

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

Introduction

Three strains of the FMD virus (A, O, and SAT 2) were recognised as causes of the FMD circulating in Egypt. The aims of this study were to trace the FMDV isolates from outbreaks in Egypt to understand their epidemiology and evolution and to understand the situation of the vaccine strains compared with the circulating serotypes.

Material and Methods

A meta-analysis was carried out by using the data available for FMD outbreaks in Egypt from GenBank and the World Reference Laboratory for Foot-and-Mouth Disease (WRLFMD); a comparison was done with both data sets for the three serotypes. MEGA-X was used for the evolution analysis, through constructions of phylogenetic trees for all sequences recorded in GenBank for each serotype in different Egyptian outbreaks in different years and also within the same year. Additionally, nucleotide substitution rate, molecular clock, and mean evolutionary rates were estimated for the three serotypes to understand and compare their evolution.

Results

Absence of some records of certain serotype outbreaks from the WRLFMD database was noted as were subsequent missing appropriate vaccine programmes. Genetic variation was recorded among the virus isolates within the same years and also the vaccine strain was associated with up to 26 amino acid substitutions. The evolution rate of the SAT2 strain was the highest of the circulating strains. SAT2 had high amino acid substitution per year at an important immunogenic site (130–170), serotype A had less, and serotype O the least.

Conclusion

The need for different strategies for vaccine serotype selection is indicated.

Emergence of foot-and-mouth disease virus serotype Asia1 group IX in India

Foot-and-mouth disease virus (FMDV) serotype Asia1 is prevalent in India and is responsible for a minor proportion of FMD outbreaks. Globally, serotype Asia1 is grouped into nine different groups (GI-IX) based on genetic analysis. In India, only Asia1/G-III and Asia1/G-VIII have been documented so far. Phylogenetic analysis of recent serotype Asia1 isolates from India revealed the emergence of Asia1/G-IX. The Asia1/G-IX lineage shares recent common ancestry with Asia1/G-VIII dating to 2016. The root state posterior probabilities of Asia1/G-VIII are inclusive and there may have been either an incursion of the virus from Bangladesh, where it was first identified, or in situ evolution of the virus within India, which is an intriguing possibility.

Antigenic properties of a novel vaccine strain for type Asia1 foot-and-mouth disease in pigs

Newly developed vaccine strains to prevent foot-and-mouth disease caused by the emerging serotype Asia1 virus were evaluated. To protect against the group (G)-VIII strain, which occurred recently, we produced an infectious cDNA clone of Asia1 Shamir cDNA (Asia1 Shamir-R). In addition, by adding a site 1 epitope of VP1 of the G-VIII lineage virus to this virus, we produced a new virus (Sham GVIII- EPI), and another virus(Sham GVIII-VP1) was replaced with that of G-VIII lineage in the VP1 region of Shamir. Test vaccines were produced using these three types of vaccine virus, and their immunogenicity and protection capabilities were evaluated in mice. Immunized mice were challenged with the Asia1 Shamir or G-VIII virus, and the results show that all the vaccines have similar protective effects. As they showed similar antigenicity, we chose the Shamir-R vaccine. Pigs maintained relatively high neutralizing antibody levels against homologous viruses of the Shamir and G-VII or G-VIII lineage three to four weeks after immunization. However, they formed relatively low levels of antibodies to G-IV and G-V viruses. In conclusion, we produced a vaccine candidate capable of protection against the G-VIII virus in the vaccine experiment for the type Asia1 serotype vaccine. This Shamir-R vaccine virus was found to protect against the viruses of the Asia1 genotype G-VII and G-VIII lineages, which occurred recently in Asia.

A history of FMD research and control programmes in Southeast Asia: lessons from the past informing the future

Foot and mouth disease (FMD) is a major animal health problem within Southeast Asia (SEA). Although Indonesia and more recently the Philippines have achieved freedom from FMD, the disease remains endemic on continental SEA. Control of FMD within SEA would increase access to markets in more developed economies and reduce lost productivity in smallholder and emerging commercial farmer settings. However, despite many years of vaccination by individual countries, numerous factors have prevented the successful control of FMD within the region, including unregulated ‘informal’ transboundary movement of livestock and their products, difficulties implementing vaccination programmes, emergence of new virus topotypes and lineages, low-level technical capacity and biosecurity at national levels, limited farmer knowledge on FMD disease recognition, failure of timely outbreak reporting and response, and limitations in national and international FMD control programmes. This paper examines the published research of FMD in the SEA region, reviewing the history, virology, epidemiology and control programmes and identifies future opportunities for FMD research aimed at the eventual eradication of FMD from the region.

The first full genome characterization of an Iranian foot and mouth disease virus

High transmissibility of FMDV and drop in productivity following infection, make FMD an important economically disease of livestock. According to the endemic nature of the disease in Iran, vaccines have been routinely applied, but not able to prevent frequent outbreaks. Circulation of different FMDV types in Iran along with unrestricted animal movements complicates epidemiological situations. The relatively short length of VP1 does not provide high resolution molecular epidemiological data, therefore FMDV full genome sequencing has been employed. Outbreaks of FMD occurred in Qom province, Iran during 2017. A 8190 nucleotide-long FMDV complete genome was sequenced. Phylogenetic analysis clustered the virus into Asia 1 serotype. Complete genome analysis revealed a high level of homology of the virus to Asia 1 viruses previously detected in Turkey, India, Israel, and Pakistan. The data suggest that Asia 1/Shimi/2017 probably originated from India, have circulating in Iran since the last couple of years and reached Turkey in 2013. The results highlight the role of Iran in westward spreading of FMDV among South-central Asia, hinting the urgent need for an effective vaccine against Asia 1 type FMDV and also applying restriction rules on animal movements.

Towards common ground in the biodiversity-disease debate

The disease ecology community has struggled to come to consensus on whether biodiversity reduces or increases infectious disease risk, a question that directly affects policy decisions for biodiversity conservation and public health. Here, we summarize the primary points of contention regarding biodiversity–disease relationships and suggest that vector-borne, generalist wildlife and zoonotic pathogens are the types of parasites most likely to be affected by changes to biodiversity. One synthesis on this topic revealed a positive correlation between biodiversity and human disease burden across countries, but as biodiversity changed over time within these countries, this correlation became weaker and more variable. Another synthesis—a meta-analysis of generally smaller-scale experimental and field studies—revealed a negative correlation between biodiversity and infectious diseases (a dilution effect) in various host taxa. These results raise the question of whether biodiversity–disease relationships are more negative at smaller spatial scales. If so, biodiversity conservation at the appropriate scales might prevent wildlife and zoonotic diseases from increasing in prevalence or becoming problematic (general proactive approaches). Further, protecting natural areas from human incursion should reduce zoonotic disease spillover. By contrast, for some infectious diseases, managing particular species or habitats and targeted biomedical approaches (targeted reactive approaches) might outperform biodiversity conservation as a tool for disease control. Importantly, biodiversity conservation and management need to be considered alongside other disease management options. These suggested guiding principles should provide common ground that can enhance scientific and policy clarity for those interested in simultaneously improving wildlife and human health.

There has been intense debate as to whether biodiversity increases or reduces the risk of infectious disease. This Review is the result of researchers from both sides of the debate attempting to reach a consensus.

Hantavirus infection and biodiversity in the Americas

Species diversity has been proposed to decrease prevalence of disease in a wide variety of host-pathogen systems, in a phenomenon labeled the dilution effect. This phenomenon was first proposed and tested for vector-borne diseases but was later extended to directly transmitted parasite systems such as hantavirus. Though there seems to be clear evidence for the dilution effect in some hantavirus/rodent systems, the generality of this hypothesis remains debated. In the present meta-analysis, we examined the evidence supporting the dilution effect for hantavirus/rodent systems in the Americas. General linear models employed on data from 56 field studies identified the abundance of the reservoir rodent species and its relative proportion in the community as the only relevant variables explaining the prevalence of antibodies against hantavirus in the reservoir. Thus, we found no clear support for the dilution effect hypothesis for hantavirus/rodent systems in the Americas.

Detection of possible spillover of a novel hantavirus in a Natal mastomys from Guinea

To date, only two rodent-borne hantaviruses have been detected in sub-Saharan Africa. Here, we report the detection of a yet unknown hantavirus in a Natal mastomys (Mastomys natalensis) in Méliandou, Guinea, in 2014. The phylogenetic placement of this virus suggests that it might represent a cross-order spillover event from an unknown bat or eulipotyphlan host.

Emergence of novel lineage of foot-and-mouth disease virus serotype Asia1 BD-18 (G-IX) in Bangladesh

Foot-and-mouth disease virus (FMDV) is a highly evolutionary divergent pathogen causing great economic havoc in many countries. Among its seven existing serotypes, Asia1 is the least divergent with a single topotype both genetically and antigenically. It is reported sporadically in Indian subcontinent and was classified under lineage G-VIII. In 2018, serotype Asia1 re-emerged in Bangladesh after 2013, along with circulation of a novel serotype Asia1 BD-18 (G-IX) lineage. VP1 phylogeny and sequence variation clearly demonstrated the novel strains which was estimated to have at least >5% nucleotide divergence with distinct clade formation. Also, the Bayesian phylogeographic inferences traced back to the origin time of lineage G-IX in early 2017 and a possible origin in Bangladesh. Mutational analysis considering established eight lineages revealed that the virus strains belonged to lineage G-IX contained a unique mutation at 44 position in the B-C loop region of VP1. Inappropriate vaccination and inefficient outbreak surveillance possibly contributed to the current episode of emergence. Therefore, active surveillance and continued vigilance are essential to assess and timely detect the occurrence, extent and distribution of this novel Asia1 strains in Bangladesh and the neighbouring countries.

History and epidemiology of foot-and-mouth disease in Afghanistan: a retrospective study

BACKGROUND

Foot and mouth disease (FMD) is endemic in Afghanistan with serotypes O, A and Asia 1 being prevalent. A retrospective study of data collected through passive surveillance of outbreaks of FMD in Afghanistan from 1995 to 2016 was undertaken to determine the temporal and spatial distribution of FMD in the country.

RESULTS

A total of 4171 outbreaks were reported between 1995 and 2008 with a strong correlation between the number of outbreaks and the number of provinces (r = 0.85, s = 68.2, p < 0.001); and between the number of outbreaks and the number of districts containing infected animals (r = 0.68, s = 147.8, p = 0.008). Of 7558 samples collected from livestock originating from 34 provinces in 2009, 2011 and 2013-2015, 54.1% were test positive (FMDV 3ABC-trapping ELISA) and the prevalence varied significantly between years (χ2 = 263.98, df = 4, P < 0.001). Clinically suspected cases were reported in 2016 with a substantial positive correlation (r = 0.70, P < 0.001) between the number of districts with cases and the number of reported cases. Serotype O was the predominant serotype detected during the study period, although serotypes A and Asia1 were also detected. Cattle were involved in all outbreaks in the study period and infections were detected in all years of the study in Hirat province in the north-west (bordering Iran), Nangarhar province in the east (bordering Pakistan) and Kabul province in the centre of the country.

CONCLUSIONS

The current paper was the first analysis of existing data focusing on the spatiotemporal distribution of FMD in Afghanistan. The findings from this study provide valuable direction for further research to understand the epidemiology of FMD and its control in Afghanistan.

Estimating the protection afforded by foot-and-mouth disease vaccines in the laboratory

Foot-and-mouth disease (FMD) vaccines must be carefully selected and their application closely monitored to optimise their effectiveness. This review covers serological techniques for FMD vaccine quality control, including potency testing, vaccine matching and post-vaccination monitoring. It also discusses alternative laboratory procedures, such as antigen quantification and nucleotide sequencing, and briefly compares the approaches for FMD with those for measuring protection against influenza virus, where humoral immunity is also important. Serology is widely used to predict the protection afforded by vaccines and has great practical utility but also limitations. Animals differ in their responses to vaccines and in the protective mechanisms that they develop. Antibodies have a variety of properties and tests differ in what they measure. Antibody-virus interactions may vary between virus serotypes and strains and protection may be affected by the vaccination regime and the nature and timing of field virus challenge. Finally, tests employing biological reagents are difficult to standardise, whilst cross-protection data needed for test calibration and validation are scarce. All of this is difficult to reconcile with the desire for simple and universal criteria and thresholds for evaluating vaccines and vaccination responses and means that oversimplification of test procedures and their interpretation can lead to poor predictions. A holistic approach is therefore recommended, considering multiple sources of field, experimental and laboratory data. New antibody avidity and isotype tests seem promising alternatives to evaluate cross-protective, post-vaccination serological responses, taking account of vaccine potency as well as match. After choosing appropriate serological tests or test combinations and cut-offs, results should be interpreted cautiously and in context. Since opportunities for experimental challenge studies of cross-protection are limited and the approaches incompletely reflect real life, more field studies are needed to quantify cross-protection and its correlation to in vitro measurements.

The Ecology and Phylogeny of Hosts Drive the Enzootic Infection Cycles of Hantaviruses

Hantaviruses (Family: Hantaviridae; genus: Orthohantavirus) and their associated human diseases occur globally and differ according to their geographic distribution. The structure of small mammal assemblages and phylogenetic relatedness among host species are suggested as strong drivers for the maintenance and spread of hantavirus infections in small mammals. We developed predictive models for hantavirus infection prevalence in rodent assemblages using defined ecological correlates from our current knowledge of hantavirus-host distributions to provide predictive models at the global and continental scale. We utilized data from published research between 1971–2014 and determined the biological and ecological characteristics of small mammal assemblages to predict the prevalence of hantavirus infections. These models are useful in predicting hantavirus disease outbreaks based on environmental and biological information obtained through the surveillance of rodents.

Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America

Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching, and reassortment. Jemez Springs virus (JMSV), an orthohantavirus harbored by the dusky shrew (Sorex monticola) and five close relatives distributed widely in western North America, was used to test this hypothesis. Total RNAs, extracted from liver or lung tissue from 164 shrews collected from western North America during 1983–2007, were analyzed for orthohantavirus RNA by reverse transcription polymerase chain reaction (RT-PCR). Phylogenies inferred from the L-, M-, and S-segment sequences of 30 JMSV strains were compared with host mitochondrial cytochrome b. Viral clades largely corresponded to host clades, which were primarily structured by geography and were consistent with hypothesized post-glacial expansion. Despite an overall congruence between host and viral gene phylogenies at deeper scales, phylogenetic signals were recovered that also suggested a complex pattern of host switching and at least one reassortment event in the evolutionary history of JMSV. A fundamental understanding of how orthohantaviruses respond to periods of host population expansion, contraction, and secondary host contact is the key to establishing a framework for both more comprehensive understanding of orthohantavirus evolutionary dynamics and broader insights into host–pathogen systems.

The ecological dynamics of hantavirus diseases: From environmental variability to disease prevention largely based on data from China

Hantaviruses can cause hantavirus pulmonary syndrome (HPS) in the Americas and hemorrhagic fever with renal syndrome (HFRS) in Eurasia. In recent decades, repeated outbreaks of hantavirus disease have led to public concern and have created a global public health burden. Hantavirus spillover from natural hosts into human populations could be considered an ecological process, in which environmental forces, behavioral determinants of exposure, and dynamics at the human–animal interface affect human susceptibility and the epidemiology of the disease. In this review, we summarize the progress made in understanding hantavirus epidemiology and rodent reservoir population biology. We mainly focus on three species of rodent hosts with longitudinal studies of sufficient scale: the striped field mouse (Apodemus agrarius, the main reservoir host for Hantaan virus [HTNV], which causes HFRS) in Asia, the deer mouse (Peromyscus maniculatus, the main reservoir host for Sin Nombre virus [SNV], which causes HPS) in North America, and the bank vole (Myodes glareolus, the main reservoir host for Puumala virus [PUUV], which causes HFRS) in Europe. Moreover, we discuss the influence of ecological factors on human hantavirus disease outbreaks and provide an overview of research perspectives.

Foot-and-mouth disease virus O/ME-SA/Ind 2001 lineage outbreak in vaccinated Holstein Friesian cattle in Saudi Arabia in 2016

Background: Foot-and-mouth disease virus (FMDV) is a highly contagious viral infection of large ruminants. Despite the massive application of vaccines against FMDV, several outbreaks are still being reported in Africa and Asia.

Aim: To perform molecular characterization of FMDV in an outbreak among a cattle herd Saudi Arabia in 2016. This herd had been vaccinated with a polyvalent FMDV vaccine.

Methods: To investigate this outbreak, we collected specimens from 77 animals showing typical clinical signs of FMDV. Specimens including sera, nasal swabs, and tissues (tongue, coronary bands, hooves, and hearts) were collected. We tested the collected cattle sera for the presence of FMDV antibodies with commercial ELISA kits. In addition, we tested the swabs for the presence of the most common FMDV strains (O, A, Asia-1 and SAT-2) with RT-PCR using serotype-specific oligonucleotides.

Results: Serology showed that 22% of the tested sera were positive. Molecular testing of the examined swabs confirmed that 24% of the tested animals were positive. Our sequencing analysis confirmed that the circulating strains of FMDV belonged to FMDV serotype O. The phylogenetic tree based on the FMDV-VP-1 gene revealed high nucleotide identity between the circulating strains and the Bangladesh strain (99%). These strains were distinct (shared 89% nucleotide identity) from the FMDV-O strains used for the preparation of the vaccine administered to the animals in this herd. Moreover, they had 7% nucleotide difference between the FMDV-O strains reported in Saudi Arabian in 2013.

Conclusion: More in-depth molecular characterization of these FMDV strains is warranted.

Foot-and-mouth disease outbreaks due to an exotic serotype Asia 1 virus in Myanmar in 2017

In January 2017, two villages located in Rakhine State of Myanmar reported clinical signs in cattle suggestive of foot-and-mouth disease virus (FMDV) infection. Laboratory analysis identified the outbreak virus as FMDV serotype Asia 1, which represented the first detection of this serotype in Myanmar since 2005 and in the region of South-East Asia (SEA) since 2007. Genetic analysis revealed that the outbreak virus was different from historical viruses from Myanmar and was more closely related to viruses circulating in Bangladesh and India during 2012-2013, indicating that a novel viral introduction had occurred. The precise origin of the outbreaks was not clear, but frequent informal livestock trade with South Asia was reported. Responses to the outbreaks involved disinfection, quarantine and animal movement restrictions; no further outbreaks were detected under the present passive surveillance system. Detection of serotype Asia 1 highlights the complex and dynamic nature of FMDV in SEA. Active surveillance is needed to assess the extent and distribution of this exotic Asia 1 strain and continued vigilance to timely detect the occurrence of emerging and re-emerging FMDV strains is essential.

Generation of monoclonal antibodies against foot-and-mouth disease virus SAT 2 and the development of a lateral flow strip test for virus detection

Foot-and-mouth disease (FMD) remains a major economic concern for the livestock productivity in many developing countries and a continued threat to countries that are disease free because of its potential devastating impact on agricultural, food chain and tourism sectors. FMD virus (FMDV) is recognized as having seven serotypes: O, A, C, Asia 1, South African Territories (SAT) 1, 2, 3 and multiple subtypes within each serotype. FMD outbreaks due to SAT 2 have been reported in many African countries. The development of a rapid and easily performed test for FMD detection is critical for controlling FMD outbreaks and containing its spread. The present project developed a lateral flow immunochromatographic (LFI) strip test for the rapid detection of FMDV SAT 2. A panel of monoclonal antibodies (mAbs) against FMDV serotype SAT 2 was produced and characterized. One mAb (#10) was selected as the capture mAb because it reacted to all 23 SAT 2 isolates archived at the National Center for Foreign Animal Disease. The LFI strip test was developed using biotin-conjugated mAb #10, and the colloid gold-conjugated FMDV serotype-independent mAb as the detection mAb. A generic Rapid Assay Device (gRAD) with one test line and a control line was used for the test. The LFI strip test detected all 23 tested SAT 2 isolates and recent outbreak strains. The results indicated that the diagnostic specificity and sensitivity of the LFI strip test were greater than the double antibody sandwich (DAS) DAS ELISA. The ability of the LFI strip test to produce rapid diagnostic results will be useful for early on-site diagnosis during FMD outbreaks.

Habitat, species richness and hantaviruses of sigmodontine rodents within the Interior Atlantic Forest, Paraguay

Four of the nine sigmodontine tribes have species that serve as reservoirs of rodent-borne hantaviruses (RBO-HV), few have been studied in any depth. Several viruses have been associated with human cases of hantavirus pulmonary syndrome often through peridomestic exposure. Jabora (JABV) and Juquitiba (JUQV), harbored by Akodon montensis and Oligoryzomys nigripes, respectively, are endemic and sympatric in the Reserva Natural de Bosque Mbaracayú (RNBM), Paraguay, a protected area of the Interior Atlantic Forest. Rodent communities were surveyed along a 30 km stretch of the RNBM in eight vegetation classifications (Low, High, Bamboo, Riparian and Liana Forests, Bamboo Understory, Cerrado, and Meadow/Grasslands). We collected 417 rodents from which 11 species were identified; Akodon montensis was the predominant species (72%; 95%CI: 64.7%-76.3%), followed by Hylaeamys megacephalus (15% (11.2%-18.2%)) and Oligoryzomys nigripes (9% (6.6%-12.4%)). We examined the statistical associations among habitat (vegetation class) type, rodent species diversity, population structure (age, sex, and weight), and prevalence of RBO-HV antibody and/or viral RNA (Ab/RNA) or characteristic Leishmania tail lesions. Ab/RNA positive rodents were not observed in Cerrado and Low Forest. A. montensis had an overall Ab/RNA prevalence of 7.7% (4.9%-11.3%) and O. nigripes had an overall prevalence of 8.6% (1.8%-23.1%). For A. montensis, the odds of being Ab/RNA positive in High Forest was 3.73 times of the other habitats combined. There was no significant difference among age classes in the proportion of Ab/RNA positive rodents overall (p = 0.66), however, all 11 RNA-positive individuals were adult. Sex and habitat had independent prognostic value for hantaviral Ab/RNA in the study population; age, presence of tail scar/lesion (19% of the rodents) and weight did not. Adjusting for habitat, female rodents had less risk of becoming infected. Importantly, these data suggest habitat preferences of two sympatric rodent reservoirs for two endemic hantaviruses and the importance of including habitat in models of species diversity and habitat fragmentation.

Species diversity concurrently dilutes and amplifies transmission in a zoonotic host-pathogen system through competing mechanisms

In this era of unprecedented biodiversity loss and increased zoonotic disease emergence, it is imperative to understand the effects of biodiversity on zoonotic pathogen dynamics in wildlife. Whether increasing biodiversity should lead to a decrease or increase in infection prevalence, termed the dilution and amplification effects, respectively, has been hotly debated in disease ecology. Sin Nombre hantavirus, which has an ∼35% mortality rate when it spills over into humans, occurs at a lower prevalence in the reservoir host, the North American deermouse, in areas with higher small mammal diversity-a dilution effect. However, the mechanism driving this relationship is not understood. Using a mechanistic mathematical model of infection dynamics and a unique long-term, high-resolution, multisite dataset, it appears that the observed dilution effect is a result of increasing small-mammal diversity leading to decreased deermouse population density and, subsequently, prevalence (a result of density-dependent transmission). However, once density is taken into account, there is an increase in the transmission rate at sites with higher diversity-a component amplification effect. Therefore, dilution and amplification are occurring at the same time in the same host-pathogen system; there is a component amplification effect (increase in transmission rate), but overall a net dilution because the effect of diversity on reservoir host population density is stronger. These results suggest we should focus on how biodiversity affects individual mechanisms that drive prevalence and their relative strengths if we want to make generalizable predictions across host-pathogen systems.

A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversification, spread, and emergence of new variants with enhanced fitness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specific viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at different breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

Molecular epidemiology, evolution and phylogeny of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) is responsible for one of the most economically important infectious diseases of livestock. The virus spreads very easily and continues to affect many countries (mainly in Africa and Asia). The risks associated with the introduction of FMDV result in major barriers to trade in animals and their products. Seven antigenically distinct forms of the virus are known, called serotypes, but serotype C has not been detected anywhere for many years and may now be extinct. The serotypes have been further divided into topotypes (except for serotype Asia-1 viruses, which comprise a single topotype), genotypes, lineages and sub-lineages, which are usually restricted to specific geographical regions. However, sometimes, trans-regional spread of some strains occurs. Due to the error-prone replication of the RNA genome, the virus continuously evolves and new strains frequently arise (e.g. with modified antigenicity). Using nucleotide sequencing technologies, this rapid evolution of the viral genome can be followed. This allows the tracing of virus transmission pathways within an outbreak of disease if (near) full-length genome sequences can be generated. Furthermore, the movement of distinct virus lineages, from one country to another can be analyzed. Some important examples of the spread of new strains of FMD virus are described.

Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts

Foot-and-mouth disease (FMD) is a severe infection caused by a picornavirus that affects livestock and wildlife. Persistence in ruminants is a well-documented feature of Foot-and-mouth disease virus (FMDV) pathogenesis and a major concern for disease control. Persistently infected animals harbor virus for extended periods, providing a unique opportunity to study within-host virus evolution. This study investigated the genetic dynamics of FMDV during persistent infections of naturally infected Asian buffalo. Using next-generation sequencing (NGS) we obtained 21 near complete FMDV genome sequences from 12 sub-clinically infected buffalo over a period of one year. Four animals yielded only one virus isolate and one yielded two isolates of different serotype suggesting a serial infection. Seven persistently infected animals yielded more than one virus of the same serotype showing a long-term intra-host viral genetic divergence at the consensus level of less than 2.5%. Quasi-species analysis showed few nucleotide variants and non-synonymous substitutions of progeny virus despite intra-host persistence of up to 152 days. Phylogenetic analyses of serotype Asia-1 VP1 sequences clustered all viruses from persistent animals with Group VII viruses circulating in Pakistan in 2011, but distinct from those circulating on 2008–2009. Furthermore, signature amino acid (aa) substitutions were found in the antigenically relevant VP1 of persistent viruses compared with viruses from 2008–2009. Intra-host purifying selective pressure was observed, with few codons in structural proteins undergoing positive selection. However, FMD persistent viruses did not show a clear pattern of antigenic selection. Our findings provide insight into the evolutionary dynamics of FMDV populations within naturally occurring subclinical and persistent infections that may have implications to vaccination strategies in the region.

Emergence of an exotic strain of serotype O foot-and-mouth disease virus O/ME-SA/Ind-2001d in South-East Asia in 2015

The O/Middle East-South Asia (ME-SA)/Ind-2001 lineage of foot-and-mouth disease virus (FMDV) is endemic in the Indian subcontinent and has been reported in the Middle East and North Africa, but it had not been detected in South-East Asia (SEA) before 2015. This study reports the recent incursions of this viral lineage into SEA, which caused outbreaks in Vientiane Capital of Lao People's Democratic Republic (PDR) in April 2015, in Dak Nong, Dak Lak and Ninh Thuan Provinces of Vietnam from May to October 2015, and in Rakhine State of Myanmar in October 2015. Disease investigations were conducted during the outbreaks and followed up after laboratory results confirmed the involvement of FMDV O/ME-SA/Ind-2001 sublineage d (O/ME-SA/Ind-2001d). Affected host species included cattle, buffalo and pig, and all the outbreaks resolved within 2 months. Animals with clinical signs were separated, and affected premises were disinfected. However, strict movement restrictions were not enforced, and emergency vaccinations were only implemented in Vientiane Capital of Lao PDR and Dak Nong and Ninh Thuan Provinces of Vietnam. Clinical samples were collected from each outbreak and examined by nucleotide sequencing of the FMDV viral protein 1 coding region. Sequence analysis revealed that the O/ME-SA/Ind-2001d isolates from Lao PDR and Vietnam were closely related to each other and similar to viruses previously circulating in India in 2013. Viruses collected from Myanmar were divergent from viruses of the same sublineage recovered from Lao PDR and Vietnam but were closely related to viruses present in Bangladesh in 2015. These findings imply that at least two independent introductions of O/ME-SA/Ind-2001d into SEA have occurred. Our study highlights the transboundary nature of foot-and-mouth disease (FMD) and reinforces the importance of improved FMD surveillance and promotion of safer cross-border trade in SEA to control the risk of introduction and spread of exotic FMDV strains.

Null expectations for disease dynamics in shrinking habitat: dilution or amplification?

As biodiversity declines with anthropogenic land-use change, it is increasingly important to understand how changing biodiversity affects infectious disease risk. The dilution effect hypothesis, which points to decreases in biodiversity as critical to an increase in infection risk, has received considerable attention due to the allure of a win-win scenario for conservation and human well-being. Yet some empirical data suggest that the dilution effect is not a generalizable phenomenon. We explore the response of pathogen transmission dynamics to changes in biodiversity that are driven by habitat loss using an allometrically scaled multi-host model. With this model, we show that declining habitat, and thus declining biodiversity, can lead to either increasing or decreasing infectious-disease risk, measured as endemic prevalence. Whether larger habitats, and thus greater biodiversity, lead to a decrease (dilution effect) or increase (amplification effect) in infection prevalence depends upon the pathogen transmission mode and how host competence scales with body size. Dilution effects were detected for most frequency-transmitted pathogens and amplification effects were detected for density-dependent pathogens. Amplification effects were also observed over a particular range of habitat loss in frequency-dependent pathogens when we assumed that host competence was greatest in large-bodied species. By contrast, only amplification effects were observed for density-dependent pathogens; host competency only affected the magnitude of the effect. These models can be used to guide future empirical studies of biodiversity-disease relationships across gradients of habitat loss. The type of transmission, the relationship between host competence and community assembly, the identity of hosts contributing to transmission, and how transmission scales with area are essential factors to consider when elucidating the mechanisms driving disease risk in shrinking habitat.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

Conservation of biodiversity as a strategy for improving human health and well-being

The Earth's ecosystems have been altered by anthropogenic processes, including land use, harvesting populations, species introductions and climate change. These anthropogenic processes greatly alter plant and animal communities, thereby changing transmission of the zoonotic pathogens they carry. Biodiversity conservation may be a potential win-win strategy for maintaining ecosystem health and protecting public health, yet the causal evidence to support this strategy is limited. Evaluating conservation as a viable public health intervention requires answering four questions: (i) Is there a general and causal relationship between biodiversity and pathogen transmission, and if so, which direction is it in? (ii) Does increased pathogen diversity with increased host biodiversity result in an increase in total disease burden? (iii) Do the net benefits of biodiversity conservation to human well-being outweigh the benefits that biodiversity-degrading activities, such as agriculture and resource utilization, provide? (iv) Are biodiversity conservation interventions cost-effective when compared to other options employed in standard public health approaches? Here, we summarize current knowledge on biodiversity-zoonotic disease relationships and outline a research plan to address the gaps in our understanding for each of these four questions. Developing practical and self-sustaining biodiversity conservation interventions will require significant investment in disease ecology research to determine when and where they will be effective.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

Hantaviruses and a neglected environmental determinant

Most human pathogenic hantaviruses cause severe hemorrhagic fevers with a high rate of fatalities, such as occurs due to the genotypes causing hantavirus cardiopulmonary syndrome carried by the New World Sigmodontinae and Neotominae rodents. An increasing number of outbreaks and the possibility of cases spreading over international borders have led to greater interest in these viruses and the environmental determinants that facilitate their transmission. Rodents, shrews, moles and bats act as reservoir hosts of hantaviruses, and within the hantavirus transmission flow, the prevalence and distribution of infection in reservoir hosts is influenced by a range of factors. Climate change and landscape alteration affect hantavirus transmission, but the outcomes can differ among different hantaviruses and for the same virus in differentbiomes. However, it is evident that the underlying mechanisms that mediate hantavirus transmission are largely unknown, so that much work remains to be done regarding the transmission dynamics of hantaviruses. Overall, our review highlights the importance of examining interactions over several trophic levels and the underlying mechanisms (density and trait-mediated indirect effects) linking predation risk and hantavirus transmission, to develop an ecological framework to understand disease in natural, preserved and degraded systems.

Dynamics of widespread foot-and-mouth disease virus serotypes A, O and Asia-1 in southern Asia: A Bayesian phylogenetic perspective

Foot-and-mouth disease (FMD) is, arguably, the animal disease with the most devastating global economic impact owing in part, to the severe trade restrictions imposed upon affected countries and regions. South Asia is one of the regions where widespread lineages of the FMDV virus (FMDV) have emerged. Here, we performed an integrative phylogenetic analysis of all FMDV serotypes (A, O and Asia-1) circulating in southern Asia, including viral sequences collected until 2013. Our results describe the occurrence of FMD caused by different serotypes and lineages, focusing in the cycles where a specific lineage predominates within a region for a protracted period and then are rapidly or progressively replaced by an emergent or re-emergent strain that is introduced from an adjacent region. Transmission between the two main regions in southern Asia (the Indian subcontinent and the region comprised by Afghanistan, Iran and Pakistan) has been limited. Results of time divergence estimation of lineages that currently circulate in this region indicate that the most recent common ancestor of endemic lineages are: 1992 [1989-1995] for lineage O/PanAsia; 1997 [1995-1999] for PanAsia2; 2001 [1998-2004] for O/Ind2001; 2001 [2000-2002] for A/Iran-05; 1990 [1988-1991] for A/G-18 (G-VII); 2003 [2000-2006] for Asia-1 Sindh08 and 2002 [1999-2004] for Asia-1 G-VIII. We estimated the mean of the overall substitution rate of the VP1 coding region (substitution/site/year) for serotype O (5.95 × 10^-3 ), serotype A (1.19 × 10^-2 ) and serotype Asia-1 (3.08 × 10^-3 ). The potential factors driving the lineage turnover are discussed. Our results provide insights into the ecological and evolutionary factors driving the emergence of FMDV.

Species Identity Supersedes the Dilution Effect Concerning Hantavirus Prevalence at Sites across Texas and México

Recent models suggest a relationship exists between community diversity and pathogen prevalence, the proportion of individuals in a population that are infected by a pathogen, with most inferences tied to assemblage structure. Two contrasting outcomes of this relationship have been proposed: the "dilution effect" and the "amplification effect." Small mammal assemblage structure in disturbed habitats often differs from assemblages in sylvan environments, and hantavirus prevalence is often negatively correlated with habitats containing high species diversity via dilution effect dynamics. As species richness increases, prevalence of infection often is decreased. However, anthropogenic changes to sylvan landscapes have been shown to decrease species richness and/or increase phylogenetic similarities within assemblages. Between January 2011 and January 2016, we captured and tested 2406 individual small mammals for hantavirus antibodies at 20 sites across Texas and México and compared differences in hantavirus seroprevalence, species composition, and assemblage structure between sylvan and disturbed habitats. We found 313 small mammals positive for antibodies against hantaviruses, evincing an overall prevalence of 9.7% across all sites. In total, 40 species of small mammals were identified comprising 2 taxonomic orders (Rodentia and Eulipotyphla). By sampling both habitat types concurrently, we were able to make real-world inferences into the efficacy of dilution effect theory in terms of hantavirus ecology. Our hypothesis predicting greater species richness higher in sylvan habitats compared to disturbed areas was not supported, suggesting the characteristics of assemblage structure do not adhere to current conceptions of species richness negatively influencing prevalence via a dilution effect.

Dampening of population cycles in voles affects small mammal community structure, decreases diversity, and increases prevalence of a zoonotic disease

Long-term decline and depression of density in cyclic small rodents is a recent widespread phenomenon. These observed changes at the population level might have cascading effects at the ecosystem level. Here, we assessed relationships between changing boreal landscapes and biodiversity changes of small mammal communities. We also inferred potential effects of observed community changes for increased transmission risk of Puumala virus (PUUV) spread, causing the zoonotic disease nephropatica epidemica in humans. Analyses were based on long-term (1971-2013) monitoring data of shrews and voles representing 58 time series in northern Sweden. We calculated richness, diversity, and evenness at alpha, beta, and gamma level, partitioned beta diversity into turnover (species replacement) and nestedness (species addition/removal), used similarity percentages (SIMPER) analysis to assess community structure, and calculated the cumulated number of PUUV-infected bank voles and average PUUV prevalence (percentage of infected bank voles) per vole cycle. Alpha, beta, and gamma richness and diversity of voles, but not shrews, showed long-term trends that varied spatially. The observed patterns were associated with an increase in community contribution of bank vole (Myodes glareolus), a decrease of gray-sided vole (M. rufocanus) and field vole (Microtus agrestis) and a hump-shaped variation in contribution of common shrew (Sorex araneus). Long-term biodiversity changes were largely related to changes in forest landscape structure. Number of PUUV-infected bank voles in spring was negatively related to beta and gamma diversity, and positively related to turnover of shrews (replaced by voles) and to community contribution of bank voles. The latter was also positively related to average PUUV prevalence in spring. We showed that long-term changes in the boreal landscape contributed to explain the decrease in biodiversity and the change in structure of small mammal communities. In addition, our results suggest decrease in small mammal diversity to have knock-on effects on dynamics of infectious diseases among small mammals with potential implications for disease transmission to humans.

Outbreak of foot and mouth disease and peste des petits ruminants in sheep flock imported for immediate slaughter in Riyadh

Aim:

To detect and identify the causative agent or agents of the following clinical symptoms which were fever, lack of appetite, salivation, vesiculation, erosions of the buccal mucosa, nose, and feet. The signs vary from mild to severe. The mortality rate of the disease is high. The morbidity rate reaches up to 100%. Sheep also show bloody diarrhea and rapid respiration. Sheep flock resident in El-Kharje Governorate.

Materials and Methods:

A total of 50 serum samples and 50 buffy coat samples were collected from Marino sheep flock suffered from high mortalities, fever, lameness, diarrhea, stomatitis, and respiratory distress. PrioCHECK^® foot and mouth disease virus (FMDV) nonstructural (NS) (marketable enzyme-linked immunosorbent assay [ELISA] kit) was used for revealing of the NS antibodies and liquid phase blocking enzyme immunoassay (LPBE) for identifying the FMD serotype and examined by competitive ELISA (cELISA) for detection of peste des petits ruminants (PPR) antibodies. The buffy coat samples were examined by immunocapture ELISA (Ic ELISA) for detection of PPR antigen.

Results:

Using PrioCHECK^® FMDV NS: Commercial ELISA kit: 38/50 (76%) of the serum samples were positive for the presence of FMD NS viral proteins. In addition, using LPBE the positive samples were identified as FMD serotype O. Examination of the serum sample by cELISA for detection of PPR antibodies gave positive results in 32/50 (64%). While the Ic ELISA identified 32 (64%) positive reactors for PPR antigen.

Conclusion:

This study reflected high susceptibility of the imported sheep flocks to the infection with FMD and PPR viruses, which are endemic in the Kingdom of Saudi Arabia (KSA). Hence, the imported flocks that prepared for slaughter must be vaccinated with the used vaccine in KSA in the quarantine for the control of FMD especially when importation occurs from counters that are free from these diseases.

Community perceptions of health and rodent-borne diseases along the Inter-Oceanic Highway in Madre de Dios, Peru

Background

Madre de Dios is located in the southeastern Amazonian region of Peru. Rodents have been estimated to be the reservoirs for up to 50 % of emerging zoonotic pathogens, including a host of viruses, bacteria, and parasites. As part of a larger study involving both human and animal research, this study serves to obtain a broader understanding of the key challenges and concerns related to health and rodent-borne illnesses from the perspective of the people living in these communities.

Methods

We used a mixed methods approach, which comprised of 12 focus group discussions, 34 key informant interviews and the application of a survey (n = 522) in four communities along the Inter-Oceanic Highway (IOH) in Madre de Dios, Peru over a two-year period.

Results

Although 90 % of survey respondents answered that rodents can transmit diseases and had seen rodents in their homes and immediate surroundings, most could not name specific rodent-borne diseases and, when probed, described rodents as pests or nuisance animals, but were not concerned about acquiring illnesses from them. Key informant interview data suggests that there has been a perceived increase in the amount of rodents in the communities since the construction of the IOH, however this potential increase was not coupled with increased knowledge about diseases or perceived risks among these key informants. Health providers also mentioned a lack of diagnostic tools specific for rodent-borne illnesses. This may be related to the fact that although a common rodent-borne disease like leptospirosis is frequently detected in the region, it is not routinely and readily diagnosed, therefore the real burden of the disease and exposure risk can be underestimated. If rodent-borne diseases are not on the radar of health professionals, they may not consider presumptive treatment, which could result in unnecessary morbidity and mortality.

Conclusion

Awareness of rodent-borne diseases is still lacking in the area, even among health care professionals within the communities, despite the known burden of diseases like leptospirosis. We expect to report further findings as we obtain more information from all the study components.

Large-scale production of foot-and-mouth disease virus (serotype Asia1) VLP vaccine in Escherichia coli and protection potency evaluation in cattle

BACKGROUND

Foot-and-mouth disease (FMD) is an acute, highly contagious disease that infects cloven-hoofed animals. Vaccination is an effective means of preventing and controlling FMD. Compared to conventional inactivated FMDV vaccines, the format of FMDV virus-like particles (VLPs) as a non-replicating particulate vaccine candidate is a promising alternative.

RESULTS

In this study, we have developed a co-expression system in E. coli, which drove the expression of FMDV capsid proteins (VP0, VP1, and VP3) in tandem by a single plasmid. The co-expressed FMDV capsid proteins (VP0, VP1, and VP3) were produced in large scale by fermentation at 10 L scale and the chromatographic purified capsid proteins were auto-assembled as VLPs in vitro. Cattle vaccinated with a single dose of the subunit vaccine, comprising in vitro assembled FMDV VLP and adjuvant, developed FMDV-specific antibody response (ELISA antibodies and neutralizing antibodies) with the persistent period of 6 months. Moreover, cattle vaccinated with the subunit vaccine showed the high protection potency with the 50 % bovine protective dose (PD50) reaching 11.75 PD50 per dose.

CONCLUSIONS

Our data strongly suggest that in vitro assembled recombinant FMDV VLPs produced from E. coli could function as a potent FMDV vaccine candidate against FMDV Asia1 infection. Furthermore, the robust protein expression and purification approaches described here could lead to the development of industrial level large-scale production of E. coli-based VLPs against FMDV infections with different serotypes.

Aerosol transmission of foot-and-mouth disease virus Asia-1 under experimental conditions

Foot-and-mouth disease virus (FMDV) control measures rely on understanding of virus transmission mechanisms. Direct contact between naïve and infected animals or spread by contaminated fomites is prevented by quarantines and rigorous decontamination procedures during outbreaks. Transmission of FMDV by aerosol may not be prevented by these control measures and this route of transmission may allow infection of animals at distance from the infection source. Understanding the potential for aerosol spread of specific FMDV strains is important for informing control strategies in an outbreak. Here, the potential for transmission of an FMDV Asia 1 strain between pigs and cattle by indirect aerosol exposure was evaluated in an experimental setting. Four naïve calves were exposed to aerosols emitted from three infected pigs in an adjacent room for a 10h period. Direct contact between pigs and cattle and fomite transfer between rooms was prevented. Viral titres in aerosols emitted by the infected pigs were measured to estimate the dose that calves were exposed to. One of the calves developed clinical signs of FMD, whilst there was serological evidence for spread to cattle by aerosol transmission in the remaining three calves. This highlights the possibility that this FMDV Asia 1 strain could be spread by aerosol transmission given appropriate environmental conditions should an outbreak occur in pigs. Our estimates suggest the exposure dose required for aerosol transmission was higher than has been previously quantified for other serotypes, implying that aerosols are less likely to play a significant role in transmission and spread of this FMDV strain.

Behavioural differences: a link between biodiversity and pathogen transmission

Biodiversity often serves to reduce zoonotic pathogens, such that prevalence is lower in communities of greater diversity. This phenomenon is termed the dilution effect, and although it has been reported for several pathogens (e.g. Sin Nombre virus, SNV), the mechanism is largely unknown. We investigated a putative mechanism, by testing the hypothesis that higher biodiversity alters behaviours important in pathogen transmission. Using deer mice (Peromyscus maniculatus) and SNV as our host-pathogen system, and a novel surveillance system, we compared host behaviours between high- and low-diversity communities. Behaviours were observed on foraging trays equipped with infrared cameras and passive integrated transponder (PIT) tag readers. Deer mice inhabiting the more diverse site spent less time in behaviours related to SNV transmission compared to deer mice from the less diverse site. The differences were attributed to the composition of behavioural phenotypes ('bold' versus 'shy') on the sites. Bold deer mice were 4.6 times more numerous on the less diverse site and three times more likely to be infected with SNV than shy deer mice. Our findings suggest that biodiversity affects pathogen transmission by altering the presence of different behavioural phenotypes. These findings have implications for human health and conservation.

Atmospheric dispersion modelling of bioaerosols that are pathogenic to humans and livestock - A review to inform risk assessment studies

In this review we discuss studies that applied atmospheric dispersion models (ADM) to bioaerosols that are pathogenic to humans and livestock in the context of risk assessment studies. Traditionally, ADMs have been developed to describe the atmospheric transport of chemical pollutants, radioactive matter, dust, and particulate matter. However, they have also enabled researchers to simulate bioaerosol dispersion. To inform risk assessment, the aims of this review were fourfold, namely (1) to describe the most important physical processes related to ADMs and pathogen transport, (2) to discuss studies that focused on the application of ADMs to pathogenic bioaerosols, (3) to discuss emission and inactivation rate parameterisations, and (4) to discuss methods for conversion of concentrations to infection probabilities (concerning quantitative microbial risk assessment). The studies included human, livestock, and industrial sources. Important factors for dispersion included wind speed, atmospheric stability, topographic effects, and deposition. Inactivation was mainly governed by humidity, temperature, and ultraviolet radiation. A majority of the reviewed studies, however, lacked quantitative analyses and application of full quantitative microbial risk assessments (QMRA). Qualitative conclusions based on geographical dispersion maps and threshold doses were encountered frequently. Thus, to improve risk assessment for future outbreaks and releases, we recommended determining well-quantified emission and inactivation rates and applying dosimetry and dose-response models to estimate infection probabilities in the population at risk.

Frontiers in research on biodiversity and disease

Global losses of biodiversity have galvanised efforts to understand how changes to communities affect ecological processes, including transmission of infectious pathogens. Here, we review recent research on diversity-disease relationships and identify future priorities. Growing evidence from experimental, observational and modelling studies indicates that biodiversity changes alter infection for a range of pathogens and through diverse mechanisms. Drawing upon lessons from the community ecology of free-living organisms, we illustrate how recent advances from biodiversity research generally can provide necessary theoretical foundations, inform experimental designs, and guide future research at the interface between infectious disease risk and changing ecological communities. Dilution effects are expected when ecological communities are nested and interactions between the pathogen and the most competent host group(s) persist or increase as biodiversity declines. To move beyond polarising debates about the generality of diversity effects and develop a predictive framework, we emphasise the need to identify how the effects of diversity vary with temporal and spatial scale, to explore how realistic patterns of community assembly affect transmission, and to use experimental studies to consider mechanisms beyond simple changes in host richness, including shifts in trophic structure, functional diversity and symbiont composition.