Advances in understanding bat infection dynamics across biological scales

Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.

Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony: considerations for spillover

Novel coronavirus species of public health and veterinary importance have emerged in the first two decades of the twenty-first century, with bats identified as natural hosts for progenitors of many coronaviruses. Targeted wildlife surveillance is needed to identify the factors involved in viral perpetuation within natural host populations, and drivers of interspecies transmission. We monitored a natural colony of Egyptian rousette bats at monthly intervals across two years to identify circulating coronaviruses, and to investigate shedding dynamics and viral maintenance within the colony. Three distinct lineages were detected, with different seasonal temporal excretion dynamics. For two lineages, the highest periods of coronavirus shedding were at the start of the year, when large numbers of bats were found in the colony. Highest peaks for a third lineage were observed towards the middle of the year. Among individual bat-level factors (age, sex, reproductive status, and forearm mass index), only reproductive status showed significant effects on excretion probability, with reproductive adults having lower rates of detection, though factors were highly interdependent. Analysis of recaptured bats suggests that viral clearance may occur within one month. These findings may be implemented in the development of risk reduction strategies for potential zoonotic coronavirus transmission.

Development of a Pan-Filoviridae SYBR Green qPCR Assay for Biosurveillance Studies in Bats

Recent studies have indicated that bats are hosts to diverse filoviruses. Currently, no pan-filovirus molecular assays are available that have been evaluated for the detection of all mammalian filoviruses. In this study, a two-step pan-filovirus SYBR Green real-time PCR assay targeting the nucleoprotein gene was developed for filovirus surveillance in bats. Synthetic constructs were designed as representatives of nine filovirus species and used to evaluate the assay. This assay detected all synthetic constructs included with an analytical sensitivity of 3-31.7 copies/reaction and was evaluated against the field collected samples. The assay's performance was similar to a previously published probe based assay for detecting Ebola- and Marburgvirus. The developed pan-filovirus SYBR Green assay will allow for more affordable and sensitive detection of mammalian filoviruses in bat samples.

Seasonal shedding patterns of diverse henipavirus-related paramyxoviruses in Egyptian rousette bats

Bat-borne viruses in the Henipavirus genus have been associated with zoonotic diseases of high morbidity and mortality in Asia and Australia. In Africa, the Egyptian rousette bat species (Rousettus aegyptiacus) is an important viral host in which Henipavirus-related viral sequences have previously been identified. We expanded these findings by assessing the viral dynamics in a southern African bat population. A longitudinal study of henipavirus diversity and excretion dynamics identified 18 putative viral species circulating in a local population, three with differing seasonal dynamics, and the winter and spring periods posing a higher risk of virus spillover and transmission. The annual peaks in virus excretion are most likely driven by subadults and may be linked to the waning of maternal immunity and recolonization of the roost in early spring. These results provide insightful information into the bat-host relationship that can be extrapolated to other populations across Africa and be communicated to at-risk communities as a part of evidence-based public health education and prevention measures against pathogen spillover threats.

Bat-borne viruses in Africa: a critical review

In Africa, bat‐borne zoonoses emerged in the past few decades resulting in large outbreaks or just sporadic spillovers. In addition, hundreds of more viruses are described without any information on zoonotic potential. We discuss important characteristics of bats including bat biology, evolution, distribution and ecology that not only make them unique among most mammals but also contribute to their potential as viral reservoirs. The detection of a virus in bats does not imply that spillover will occur and several biological, ecological and anthropogenic factors play a role in such an event. We summarize and critically analyse the current knowledge on African bats as reservoirs for corona‐, filo‐, paramyxo‐ and lyssaviruses. We highlight that important information on epidemiology, bat biology and ecology is often not available to make informed decisions on zoonotic spillover potential. Even if knowledge gaps exist, it is still important to recognize the role of bats in zoonotic disease outbreaks and implement mitigation strategies to prevent exposure to infectious agents including working safely with bats. Equally important is the crucial role of bats in various ecosystem services. This necessitates a multidisciplinary One Health approach to close knowledge gaps and ensure the development of responsible mitigation strategies to not only minimize risk of infection but also ensure conservation of the species.

Paramyxo- and Coronaviruses in Rwandan Bats

A high diversity of corona- and paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of corona- and paramyxoviral RNA using reverse transcription PCR assays. Positive results were further characterized by DNA sequencing and phylogenetic analysis. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species. We detected a novel Betacoronavirus in two Geoffroy’s horseshoe bats (Rhinolophus clivosus) bats. We also detected several different paramyxoviral species from various insectivorous bats. One of these viral species was found to be homologous to the genomes of viruses belonging to the Jeilongvirus genus. Additionally, a Henipavirus-related sequence was detected in an Egyptian rousette fruit bat (Rousettus aegyptiacus). These results expand on the known diversity of corona- and paramyxoviruses and their geographical distribution in Africa.

Co-Circulation and Excretion Dynamics of Diverse Rubula- and Related Viruses in Egyptian Rousette Bats from South Africa

The Egyptian rousette bat (Rousettus aegyptiacus) has previously been implicated as the natural host of a zoonotic rubulavirus; however, its association with rubulaviruses has been studied to a limited extent. Urine, spleen, and other organs collected from the R. aegyptiacus population within South Africa were tested with a hemi-nested RT-PCR assay targeting a partial polymerase gene region of viruses from the Avula- and Rubulavirus genera. Urine was collected over a 14-month period to study the temporal dynamics of viral excretion. Diverse rubulaviruses, including viruses related to human mumps and parainfluenza virus 2, were detected. Active excretion was identified during two peak periods coinciding with the host reproductive cycle. Analysis of additional organs indicated co-infection of individual bats with a number of different putative rubulaviruses, highlighting the limitations of using a single sample type when determining viral presence and diversity. Our findings suggest that R. aegyptiacus can harbor a range of Rubula- and related viruses, some of which are related to known human pathogens. The observed peaks in viral excretion represents potential periods of a higher risk of virus transmission and zoonotic disease spill-over.

Novel Paramyxoviruses in Bats from Sub-Saharan Africa, 2007-2012

As part of a larger survey for detection of pathogens among wildlife in sub-Saharan Africa conducted during 2007–2012, multiple diverse paramyxovirus sequences were detected in renal tissues of bats. Phylogenetic analysis supports the presence of at least 2 major viral lineages and suggests that paramyxoviruses are strongly associated with several bat genera.

Screening for syphilis among men who have sex with men in various clinical settings

OBJECTIVES

To assess the prevalence of syphilis infections among men who have sex with men (MSM) accessing the Brisbane Sexual Health Clinic during the period 1997 up to May 2003, data were collated through three clinical programmes conducted by the service-a large inner city mainstream sexual health clinic and two small outreach sessional clinics conducted on the site of male sex on premises venues (SOPV). Data analysis also provided the opportunity to evaluate the effectiveness of the smaller outreach clinics to access populations of MSM less likely to attend or identify at the larger mainstream clinic, and therefore enhance the detection of previously undiagnosed sexually transmissible infections.

METHODS

Computerised records from 1997-2003 were collated for a statistical analysis of syphilis and other STI pathology results for all MSM accessing the mainstream clinic, and two outreach clinics.

RESULTS

A review of client charts showed that 16 new syphilis diagnoses were made over the previous 5 years, but only two of these infections (both through the mainstream clinic) were early syphilis and therefore transmissible. All other cases were latent infections. A higher proportion of bisexual men was identified with positive syphilis serology but this was just below significance (p=0.06). Significantly, almost a third of syphilis diagnoses (all latent) were made at SOPV outreach clinics, despite the much lower proportion of clients seen overall through the SOPV clinics. For other sexually transmissible infections, the mainstream clinic demonstrated greater efficiency at case detection.

CONCLUSION

Outreach clinics located in male saunas may serve an effective function in syphilis screening by facilitating access for a particular subpopulation of MSM (bisexual, married men). These outreach clinics may provide important outlets for education and opportunistic screening of asymptomatic MSM and foster a greater willingness for men to honestly self identify. However, larger, mainstream clinics serve a more anonymous venue for the testing of symptomatic men.

A cluster of tuberculosis associated with use of a marijuana water pipe

SETTING

New cases of pulmonary tuberculosis (TB) were noted in a cluster of young Caucasian males, an unusual ethnic group for this disease in Queensland, Australia. It was noted that marijuana water pipe ('bong') smoking was common amongst cases and contacts.

OBJECTIVE

To report this cluster of TB and to investigate whether shared use of a marijuana water pipe was associated with transmission of TB.

DESIGN

All contacts were identified and screened according to standard protocols. Cases were asked to list contacts with whom they had shared a marijuana water pipe.

RESULTS

Five cases of open pulmonary TB were identified clinically and on sputum culture, and all isolates of Mycobacterium tuberculosis were identical on typing. Of 149 contacts identified, 114 (77%) completed screening, and 57 (50%) had significant tuberculin skin test (TST) reactions on follow-up. Of 45 contacts who had shared a marijuana water pipe with a case, 29 (64%) had a significant TST reaction.

CONCLUSION

Sharing a marijuana water pipe with a case of pulmonary TB was associated with transmission of TB (OR 2.22, 95 % CI 0.96-5.17), although the most important risk factor for acquiring TB infection in this cluster was close household contact with a case (OR 4.91, 95% CI 1.13-20.70).

Detection of Chlamydia trachomatis in an Australian high school student population

OBJECTIVE

To assess the prevalence of Chlamydia trachomatis infections among an Australian high school adolescent population.

METHODS

Over a 4 year period, 14 high schools were selected in which an infertility prevention programme targeting C. trachomatis was delivered to senior student populations. Coded first catch urine specimens were analysed by Amplicor PCR and infected students treated. Data retrospectively obtained from chlamydia screening programmes conducted among disadvantaged young people detached from formal education were also collated for comparison.

RESULTS

Of a total student test population of 1174, 15 (1.3%; 95% CI 0.7% to 2.1%) were diagnosed with C. trachomatis. Of 516 females and 658 males, 12 (2.3%; 95% CI 1.1% to 4.1%) and 3 (0.5%; 95% CI 0.1% to 1.4%) were tested positive respectively. Data collated for three populations of disadvantaged youth returned at total of 89 C. trachomatis infections out of 560 people (15.9% 95%CI 13.0-19.2%).

CONCLUSION

The overall prevalence of C. trachomatis infection among this population of senior high school adolescents is low, and significantly differs from the higher chlamydia rates detected in disadvantaged adolescents detached from formal schooling (p<0.0001).