Aetiology of Acute Febrile Episodes in Children Attending Korogwe District Hospital in North-Eastern Tanzania

Introduction

Although the burden of malaria in many parts of Tanzania has declined, the proportion of children with fever has not changed. This situation underscores the need to explore the possible causes of febrile episodes in patients presenting with symptoms at the Korogwe District Hospital (KDH).

Methods

A hospital based cross-sectional study was conducted at KDH, north-eastern Tanzania. Patients aged 2 to 59 months presenting at the outpatient department with an acute medical condition and fever (measured axillary temperature ≥37.5°C) were enrolled. Blood samples were examined for malaria parasites, human immunodeficiency virus (HIV) and bacterial infections. A urine culture was performed in selected cases to test for bacterial infection and a chest radiograph was requested if pneumonia was suspected. Diagnosis was based on both clinical and laboratory investigations.

Results

A total of 867 patients with a median age of 15.1 months (Interquartile range 8.6–29.9) were enrolled from January 2013 to October 2013. Respiratory tract infections were the leading clinical diagnosis with 406/867 (46.8%) of patients diagnosed with upper respiratory tract infection and 130/867 (15.0%) with pneumonia. Gastroenteritis was diagnosed in 184/867 (21.2%) of patients. Malaria infection was confirmed in 72/867 (8.3%) of patients. Bacterial infection in blood and urine accounted for 26/808 (3.2%) infections in the former, and 66/373 (17.7%) infections in the latter. HIV infection was confirmed in 10/824 (1.2%) of patients. Respiratory tract infections and gastroenteritis were frequent in patients under 36 months of age (87.3% and 91.3% respectively). Co-infections were seen in 221/867 (25.5%) of patients. The cause of fever was not identified in 65/867 (7.5%) of these patients.

Conclusions

The different proportions of infections found among febrile children reflect the causes of fever in the study area. These findings indicate the need to optimise patient management by developing malaria and non-malaria febrile illnesses management protocols.     

Impact of wind farms on soaring bird populations at a migratory bottleneck

Collision with turbines at wind farms is expected to have a greater impact on birds at particular sites where high concentrations of individuals occur, such as migration bottleneck areas. The Strait of Gibraltar (southern Spain) has long been recognized as the most important bottleneck in western Europe for soaring bird migration. Moreover, this area is within one of the most important potential areas for wind energy generation in Spain. Here, we examine monthly migratory soaring bird abundance in relation to long-term avian mortality rates at 21 wind farms located near the Strait of Gibraltar using zero-inflated hurdle negative binomial and gamma models. Best fit models included an effect of season in the collision mortality rates and in the proportion of adult individuals within the total deaths. However, monthly bird abundance was not directly related to the number of fatalities over the year. The accumulated fatalities during autumn migration constitute a small percentage (1%) of the total migrating population size. Moreover, mortality peak during autumn migration is largely attributable to juvenile birds. In contrast, the number of fatalities coinciding with the breeding period constitutes a substantial proportion (6%) of the local population, and it involved substantial losses among adult birds. Our results show that wind farms probably have an individually low impact on the migratory population of soaring birds. On the contrary, annual losses among adult local birds are remarkably high considering the small size of the local populations, and they may have population level effects.     

Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90–0.99) vs. 0.58 (CI = 0.50–0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.     

Identification of Rep-Associated Factors in Herpes Simplex Virus Type 1-Induced Adeno-Associated Virus Type 2 Replication Compartments

Adeno-associated virus (AAV) is a human parvovirus that replicates only in cells coinfected with a helper virus, such as adenovirus or herpes simplex virus type 1 (HSV-1). We previously showed that nine HSV-1 factors are able to support AAV rep gene expression and genome replication. To elucidate the strategy of AAV replication in the presence of HSV-1, we undertook a proteomic analysis of cellular and HSV-1 factors associated with Rep proteins and thus potentially recruited within AAV replication compartments (AAV RCs). This study resulted in the identification of approximately 60 cellular proteins, among which factors involved in DNA and RNA metabolism represented the largest functional categories. Validation analyses indicated that the cellular DNA replication enzymes RPA, RFC, and PCNA were recruited within HSV-1-induced AAV RCs. Polymerase δ was not identified but subsequently was shown to colocalize with Rep within AAV RCs even in the presence of the HSV-1 polymerase complex. In addition, we found that AAV replication is associated with the recruitment of components of the Mre11/Rad50/Nbs1 complex, Ku70 and -86, and the mismatch repair proteins MSH2, -3, and -6. Finally, several HSV-1 factors were also found to be associated with Rep, including UL12. We demonstrated for the first time that this protein plays a role during AAV replication by enhancing the resolution of AAV replicative forms and AAV particle production. Altogether, these analyses provide the basis to understand how AAV adapts its replication strategy to the nuclear environment induced by the helper virus.Adeno-associated virus (AAV) is a human parvovirus that is currently used as a gene transfer vector (14). AAV particles consist of a small icosahedral capsid protecting a single 4.7-kb single-stranded DNA (ssDNA) genome with two open reading frames, rep and cap, surrounded by inverted terminal repeats (ITRs). The ITRs are the only sequences required in cis for genome replication and packaging. The rep gene encodes four nonstructural Rep proteins: Rep78, -68, -52, and -40. The two larger isoforms, Rep78 and -68, have origin binding, helicase, and site-specific endonuclease activities and are involved in AAV gene expression and genome processing, including replication and site-specific integration (39). The two smaller Rep isoforms are not required for AAV DNA replication but are involved in the control of viral gene expression and packaging of viral DNA (30).When wild-type (wt) AAV infects a cell in the absence of a helper virus, it enters latency. Latent AAV genomes persist in cells either as episomes or as integrated genomes, preferentially at a specific locus (named AAVS1) on human chromosome 19. In most instances, no detectable viral gene expression or genome replication occurs unless the cell is co- or superinfected by a helper virus, such as adenovirus, herpes simplex virus type 1 (HSV-1), or HSV-2. Under these conditions, AAV replication and assembly take place in large intranuclear domains called replication compartments (RCs) that frequently colocalize with replication domains formed by the helper virus itself (81). The viral genome replicates by leading-strand synthesis and generates new ssDNA molecules by a strand displacement mechanism that occurs after strand- and site-specific cleavage of viral DNA by Rep78/68 within the ITRs (39).Studies conducted on the relationship between AAV and its helper viruses are important not only to identify helper activities that can be used to produce recombinant AAV vectors but also to understand how AAV adapts its replication strategy to the helper virus and to the nuclear environment in general. Adenovirus helper functions have historically been the first and most extensively studied functions. These studies have shown that adenovirus helps AAV by stimulating viral gene expression and by enhancing AAV genome replication, mostly indirectly (19). Indeed, early studies showed that the adenovirus polymerase (E2b) is dispensable for AAV replication (8) and that the viral DNA-binding protein (DBP), the product of the E2a gene, is able to modestly enhance the processivity of AAV genome replication in vitro (77). More recently, the adenovirus proteins E1b55k and E4orf6 were shown to stimulate AAV genome replication by degrading the cellular Mre11/Rad50/Nbs1 (MRN) complex that restricts AAV genome replication during adenovirus coinfection (32). The concept that AAV genome replication can rely mostly, if not uniquely, on direct help from cellular factors was further strengthened by the demonstration that purified proteins such as replication protein A (RPA), replication factor C (RFC), proliferating cell nuclear antigen (PCNA), minichromosome maintenance (MCM) proteins, and DNA polymerase δ (Pol δ) were sufficient to replicate the AAV genome in vitro in the presence of Rep (40-41, 43). The involvement of these cellular proteins during AAV genome replication was also confirmed by the proteomic analysis of factors associated with Rep proteins during adenovirus-induced AAV replication (42).Interestingly, studies conducted on HSV-1 helper activities suggest that the strategy of AAV replication may vary depending on the helper virus. Indeed, previous studies showed that the HSV-1 helicase-primase (HP) complex (UL5/8/52) and DBP (ICP8) could replicate transfected AAV-2 plasmids (80) and that the helicase activity, but not primase activity, of the HP complex was required for this effect (62, 66). More recently, a comprehensive study of HSV-1 helper activities demonstrated that the HSV-1 immediate-early proteins ICP0, ICP4, and ICP22 could stimulate rep gene expression, probably by diminishing intrinsic antiviral effects (1, 18). In addition, the HSV-1 DNA polymerase encoded by UL30, along with its associated processivity factor (UL42), although not strictly required, was demonstrated to significantly increase AAV replication levels induced in the presence of the HP complex and ICP8. Interestingly, the HSV-1 HP complex, DBP, and polymerase were also shown to be sufficient to replicate AAV DNA in vitro in the presence of Rep proteins without any cellular protein (78). Altogether, these observations indicate that in the context of an HSV-1 coinfection, AAV relies extensively on viral activities provided by the helper that directly participate in AAV genome replication.To further elucidate the strategy of AAV replication in the presence of HSV-1, we undertook a proteomic analysis to identify the cellular and HSV-1 factors associated with Rep proteins and, consequently, potentially recruited within AAV RCs. To analyze Rep-associated proteins in the presence and absence of HSV-1 DNA replication, this analysis was performed using wt HSV-1 and an HSV-1 mutant in which the DNA polymerase encoded by the UL30 gene is absent (HSVΔUL30). This study resulted in the identification of approximately 60 cellular proteins, among which the largest functional categories corresponded to factors involved in DNA and RNA metabolism. Immunofluorescence analyses confirmed that in the presence of HSV-1, a basal set of cellular DNA replication enzymes, including RPA, RFC, and PCNA, was recruited within AAV RCs, with the exception of the MCM helicases. The cellular DNA polymerases, in particular Pol δ, were not identified by this analysis but subsequently were shown to be recruited in AAV RCs even in the presence of the HSV-1 polymerase complex. In addition, our results indicate that AAV replication induced by HSV-1 is associated with the recruitment of DNA repair factors, including components of the MRN complex, the Ku proteins, PARP-1, and factors of the mismatch repair (MMR) pathway. Finally, several HSV-1 proteins, most notably the UL12 protein, were also identified within AAV RCs. Our analyses confirmed the association between UL12 and Rep and demonstrated for the first time that this viral exonuclease plays a critical role during AAV replication by enhancing the formation of discrete AAV replicative forms and the production of AAV particles.Altogether, these results indicate that in the presence of HSV-1, AAV may replicate by using a basal set of cellular DNA replication enzymes but also relies extensively on HSV-1-derived proteins for its replication, including UL12, a newly discovered helper factor. These results suggest that AAV may be able to differentially adapt its replication strategy to the nuclear environment induced by the helper virus.     

The Influence of Prior Learning Experience on Pollinator Choice: An Experiment Using Bumblebees on Two Wild Floral Types of Antirrhinum majus

Understanding how pollinator behavior may influence pollen transmission across floral types is a major challenge, as pollinator decision depends on a complex range of environmental cues and prior experience. Here we report an experiment using the plant Antirrhinum majus and the bumblebee Bombus terrestris to investigate how prior learning experience may affect pollinator preferences between floral types when these are presented together. We trained naive bumblebees to forage freely on flowering individuals of either A. majus pseudomajus (magenta flowers) or A. majus striatum (yellow flowers) in a flight cage. We then used a Y-maze device to expose trained bumblebees to a dual choice between the floral types. We tested the influence of training on their choice, depending on the type of plant signals available (visual signals, olfactory signals, or both). Bumblebees had no innate preference for either subspecies. Bumblebees trained on the yellow-flowered subspecies later preferred the yellow type, even when only visual or only olfactory signals were available, and their preference was not reinforced when both signal types were available. In contrast, bumblebees trained on the magenta-flowered subspecies showed no further preference between floral types and took slightly more time to make their choice. Since pollinator constancy has been observed in wild populations of A. majus with mixed floral types, we suggest that such constancy likely relies on short-term memory rather than acquired preference through long-term memory induced by prior learning.     

Timing vaccination against SARS-CoV-2

Circadian rhythms play an important role in balancing innate and adaptive immune responses.In a recent study in Cell Research,Zhang et al.studied the immunologi...     

Joint estimation of survival and breeding probability in female dolphins and calves with uncertainty in state assignment

While the population growth rate in long‐lived species is highly sensitive to adult survival, reproduction can also significantly drive population dynamics. Reproductive parameters can be challenging to estimate as breeders and nonbreeders may vary in resighting probability and reproductive status may be difficult to assess. We extended capture–recapture (CR) models previously fitted for data on other long‐lived marine mammals to estimate demographic parameters while accounting for detection heterogeneity between individuals and state uncertainty regarding reproductive status. We applied this model to data on 106 adult female bottlenose dolphins observed over 13 years. The detection probability differed depending on breeding status. Concerning state uncertainty, offspring were not always sighted with their mother, and older calves were easier to detect than young‐of‐the‐year (YOY), respectively, 0.79 (95% CI 0.59–0.90) and 0.58 (95% CI 0.46–0.68). This possibly led to inaccurate reproductive status assignment of females. Adult female survival probability was high (0.97 CI 95% 0.96–0.98) and did not differ according to breeding status. Young‐of‐the‐year and 1‐year‐old calves had a significantly higher survival rate than 2‐year‐old (respectively, 0.66 CI 95% 0.50–0.78 and 0.45 CI 95% 0.29–0.61). This reduced survival is probably related to weaning, a period during which young are exposed to more risks since they lose protection and feeding from the mother. The probability of having a new YOY was high for breeding females that had raised a calf to the age of 3 or lost a 2‐year‐old calf (0.71, CI 95% 0.45–0.88). Yet, this probability was much lower for nonbreeding females and breeding females that had lost a YOY or a 1‐year‐old calf (0.33, 95% CI 0.26–0.42). The multievent CR framework we used is highly flexible and could be easily modified for other study questions or taxa (marine or terrestrial) aimed at modeling reproductive parameters.