Spillover of pH1N1 to swine in Cameroon: an investigation of risk factors.

BACKGROUND: The 2009 pH1N1 influenza pandemic resulted in at least 18,500 deaths worldwide. While pH1N1 is now considered to be in a post-pandemic stage in humans it has nevertheless spilled back into swine in at least 20 countries. Understanding the factors that increase the risk of spillover events between swine and humans is essential to predicting and preventing future outbreaks. We assessed risk factors that may have led to spillover of pH1N1 from humans to swine in Cameroon, Central Africa. We sampled swine, domestic poultry and wild birds for influenza A virus at twelve sites in Cameroon from December 2009 while the pandemic was ongoing, to August 2012. At the same time we conducted point-count surveys to assess the abundance of domestic livestock and wild birds and assess interspecific contact rates. Random forest models were used to assess which variables were the best predictors of influenza in swine. RESULTS: We found swine with either active pH1N1 infections or positive for influenza A at four of our 12 sites. Only one swine tested positive by competitive ELISA in 2011-2012. To date we have found pH1N1 only in the North and Extreme North regions of Cameroon (regions in Cameroon are administrative units similar to provinces), though half of our sites are in the Central and Western regions. Swine husbandry practices differ between the North and Extreme North regions where it is common practice in to let swine roam freely, and the Central and Western regions where swine are typically confined to pens. Random forest analyses revealed that the three best predictors of the presence of pH1N1 in swine were contact rates between free-ranging swine and domestic ducks, contact rates between free-ranging swine and wild Columbiformes, and contact rates between humans and ducks. Sites in which swine were allowed to range freely had closer contact with other species than did sites in which swine were kept penned. CONCLUSIONS: Results suggest that the practice of allowing swine to roam freely is a significant risk factor for spillover of influenza from humans into swine populations.

Predicting hotspots for influenza virus reassortment.

The 1957 and 1968 influenza pandemics, each of which killed ≈1 million persons, arose through reassortment events. Influenza virus in humans and domestic animals could reassort and cause another pandemic. To identify geographic areas where agricultural production systems are conducive to reassortment, we fitted multivariate regression models to surveillance data on influenza A virus subtype H5N1 among poultry in China and Egypt and subtype H3N2 among humans. We then applied the models across Asia and Egypt to predict where subtype H3N2 from humans and subtype H5N1 from birds overlap; this overlap serves as a proxy for co-infection and in vivo reassortment. For Asia, we refined the prioritization by identifying areas that also have high swine density. Potential geographic foci of reassortment include the northern plains of India, coastal and central provinces of China, the western Korean Peninsula and southwestern Japan in Asia, and the Nile Delta in Egypt.

Coquillettidia (Culicidae, Diptera) mosquitoes are natural vectors of avian malaria in Africa.

BACKGROUND: The mosquito vectors of Plasmodium spp. have largely been overlooked in studies of ecology and evolution of avian malaria and other vertebrates in wildlife. METHODS: Plasmodium DNA from wild-caught Coquillettidia spp. collected from lowland forests in Cameroon was isolated and sequenced using nested PCR. Female Coquillettidia aurites were also dissected and salivary glands were isolated and microscopically examined for the presence of sporozoites. RESULTS: In total, 33% (85/256) of mosquito pools tested positive for avian Plasmodium spp., harbouring at least eight distinct parasite lineages. Sporozoites of Plasmodium spp. were recorded in salivary glands of C. aurites supporting the PCR data that the parasites complete development in these mosquitoes. Results suggest C. aurites, Coquillettidia pseudoconopas and Coquillettidia metallica as new and important vectors of avian malaria in Africa. All parasite lineages recovered clustered with parasites formerly identified from several bird species and suggest the vectors capability of infecting birds from different families. CONCLUSION: Identifying the major vectors of avian Plasmodium spp. will assist in understanding the epizootiology of avian malaria, including differences in this disease distribution between pristine and disturbed landscapes.

A Dynamical and Zero-Inflated Negative Binomial Regression Modelling of Malaria Incidence in Limpopo Province, South Africa.

Recent studies have considered the connections between malaria incidence and climate variables using mathematical and statistical models. Some of the statistical models focused on time series approach based on Box-Jenkins methodology or on dynamic model. The latter approach allows for covariates different from its original lagged values, while the Box-Jenkins does not. In real situations, malaria incidence counts may turn up with many zero terms in the time series. Fitting time series model based on the Box-Jenkins approach and ARIMA may be spurious. In this study, a zero-inflated negative binomial regression model was formulated for fitting malaria incidence in Mopani and Vhembe-two of the epidemic district municipalities in Limpopo, South Africa. In particular, a zero-inflated negative binomial regression model was formulated for daily malaria counts as a function of some climate variables, with the aim of identifying the model that best predicts reported malaria cases. Results from this study show that daily rainfall amount and the average temperature at various lags have a significant influence on malaria incidence in the study areas. The significance of zero inflation on the malaria count was examined using the Vuong test and the result shows that zero-inflated negative binomial regression model fits the data better. A dynamical climate-based model was further used to investigate the population dynamics of mosquitoes over the two regions. Findings highlight the significant roles of Anopheles arabiensis on malaria transmission over the regions and suggest that vector control activities should be intense to eradicate malaria in Mopani and Vhembe districts. Although An. arabiensis has been identified as the major vector over these regions, our findings further suggest the presence of additional vectors transmitting malaria in the study regions. The findings from this study offer insight into climate-malaria incidence linkages over Limpopo province of South Africa.

Phylogeny, biogeography and taxonomy of the African wattle-eyes (Aves: Passeriformes: Platysteiridae).

The African wattle-eyes (genera Platysteira and Dyaphorophyia) comprise 10 species endemic to Africa. We analyzed both mitochondrial and nuclear DNA sequence data to test the monophyly of this group and its two genera, provide a preliminary assessment of species limits, and gain insight into the phylogeographic history of the wattle-eye radiation. Analyses based on mitochondrial ND2 sequences failed to recover wattle-eye monophyly, but the alternatives were not well-supported. In contrast, analyses of two nuclear introns (myoglobin intron-2 and beta-fibrinogen intron-5) recovered wattle-eye monophyly, as did combined analyses of mitochondrial and nuclear data. These analyses, however, did not support reciprocal monophyly of the two wattle-eye genera typically recognized, suggesting instead that Platysteira is nested within a paraphyletic Dyaphorophyia. The diversification of most wattle-eye species and many subspecies occurred through the divergence of allopatric populations well before the Pleistocene. Species and subspecies with disjunct distributions are typically characterized by deep genetic divergences, suggesting that many of these populations are evolutionary independent and could be recognized as additional phylogenetic species. In D. castanea and D. chalybea, for example, divergent haplotypes from geographically disjunct populations were paraphyletic with respect to those of D. tonsa and D. jamesoni, respectively. Similarly, Platysteira laticincta is highly divergent from its sister taxon P. peltata ( approximately 9.5% ND2 sequence divergence), consistent with species level recognition of this endangered species. In contrast, more broadly distributed taxa inhabiting a greater diversity of habitats (e.g., P. peltata and P. cyannea) show evidence of gene flow and connectivity among regions, suggesting that previously isolated populations expanded and fused into one another. Our study provides a framework for additional analyses of intraspecific phylogeography and species limits in these colorful birds.

Exploring the Influence of Daily Climate Variables on Malaria Transmission and Abundance of Anopheles arabiensis over Nkomazi Local Municipality, Mpumalanga Province, South Africa.

The recent resurgence of malaria incidence across epidemic regions in South Africa has been linked to climatic and environmental factors. An in-depth investigation of the impact of climate variability and mosquito abundance on malaria parasite incidence may therefore offer useful insight towards the control of this life-threatening disease. In this study, we investigate the influence of climatic factors on malaria transmission over Nkomazi Municipality. The variability and interconnectedness between the variables were analyzed using wavelet coherence analysis. Time-series analyses revealed that malaria cases significantly declined after the outbreak in early 2000, but with a slight increase from 2015. Furthermore, the wavelet coherence and time-lagged correlation analyses identified rainfall and abundance of Anopheles arabiensis as the major variables responsible for malaria transmission over the study region. The analysis further highlights a high malaria intensity with the variables from 1998-2002, 2004-2006, and 2010-2013 and a noticeable periodicity value of 256-512 days. Also, malaria transmission shows a time lag between one month and three months with respect to mosquito abundance and the different climatic variables. The findings from this study offer a better understanding of the importance of climatic factors on the transmission of malaria. The study further highlights the significant roles of An. arabiensis on malaria occurrence over Nkomazi. Implementing the mosquito model to predict mosquito abundance could provide more insight into malaria elimination or control in Africa.

Climate warming causes declines in crop yields and lowers school attendance rates in Central Africa.

Although a number of recent studies suggest that climate associated shifts in agriculture are affecting social and economic systems, there have been relatively few studies of these effects in Africa. Such studies would be particularly useful in Central Africa, where the impacts of climate warming are predicted to be high but coincide with an area with low adaptive capacity. Focusing on plantain (Musa paradisiaca), we assess whether recent climate change has led to reduced yields. Analysis of annual temperature between 1950 and 2013 indicated a 0.8°C temperature increase over this 63-year period - a trend that is also observed in monthly temperatures in the last twenty years. From 1991 to 2011, there was a 43% decrease in plantain productivity in Central Africa, which was explained by shifts in temperature (R2=0.68). This decline may have reduced rural household wealth and decreased parental investment in education. Over the past two decades, there was a six month decrease in the duration of school attendance, and the decline was tightly linked to plantain yield (R2=0.82). By 2080, mean annual temperature is expected to increase at least 2°C in Central Africa, and our models predict a concomitant decrease of 39% in plantain yields and 51% in education outcomes, relative to the 1991 baseline. These predictions should be seen as a call-to-action for policy interventions such as farmer training programs to enhance the adaptive capacity of food production systems to mitigate impacts on rural income and education.

Putative human and avian risk factors for avian influenza virus infections in backyard poultry in Egypt.

Highly pathogenic influenza A virus subtype H5N1 causes significant poultry mortality in the six countries where it is endemic and can also infect humans. Egypt has reported the third highest number of poultry outbreaks (n=1084) globally. The objective of this cross-sectional study was to identify putative risk factors for H5N1 infections in backyard poultry in 16 villages in Damietta, El Gharbia, Fayoum, and Menofia governorates from 2010-2012. Cloacal and tracheal swabs and serum samples from domestic (n=1242) and wild birds (n=807) were tested for H5N1 via RT-PCR and hemagglutination inhibition, respectively. We measured poultry rearing practices with questionnaires (n=306 households) and contact rates among domestic and wild bird species with scan sampling. Domestic birds (chickens, ducks, and geese, n=51) in three governorates tested positive for H5N1 by PCR or serology. A regression model identified a significant correlation between H5N1 in poultry and the practice of disposing of dead poultry and poultry feces in the garbage (F=15.7, p<0.0001). In addition, contact between domestic and wild birds was more frequent in villages where we detected H5N1 in backyard flocks (F=29.5, p<0.0001).

Pandemic A/H1N1/2009 influenza virus in swine, Cameroon, 2010.

Although swine origin A/H1N1/2009 influenza virus (hereafter "pH1N1″) has been detected in swine in 20 countries, there has been no published surveillance of the virus in African livestock. The objective of this study was to assess the circulation of influenza A viruses, including pH1N1 in swine in Cameroon, Central Africa. We collected 108 nasal swabs and 98 sera samples from domestic pigs randomly sampled at 11 herds in villages and farms in Cameroon. pH1N1 was isolated from two swine sampled in northern Cameroon in January 2010. Sera from 28% of these herds were positive for influenza A by competitive ELISA and 92.6% of these swine showed cross reactivity with pandemic A/H1N1/2009 influenza virus isolated from humans. These results provide the first evidence of this virus in the animal population in Africa. In light of the significant role of swine in the ecology of influenza viruses, our results call for greater monitoring and study in Central Africa.