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Social media platforms, such as Twitter, are an increasingly important source of information and are forums for discourse within and between interest groups. Research highlights how social media communities have amplified movements such as the Arab Spring, #MeToo, and Black Lives Matter. But environmental digital discourse remains underexplored. In the present article, we apply automated text analysis to 200,000 Twitter users in several countries following leading environmental nongovernmental organizations. Some issues such as public action to decarbonize society or species conservation were discussed more intensely than agriculture or marine conservation. Our results illustrate where environmental discourse diverges and converges on Twitter across countries, states, and characteristics, such as political ideology. Using the coterminous United States as a case study, we observed that the prominence of issues varies across states and, in some cases, covaries with political ideology across counties. Our findings show paths forward to characterizing environmental priorities across many issues at unprecedented scale and extent.

BackgroundEarly evidence suggested that the impact of the COVID-19 pandemic was less severe in Africa compared to other parts of the world. However, more recent studies indicate higher SARS-CoV-2 infection and COVID-19 mortality rates on the continent than previously documented. Research is needed to better understand SARS-CoV-2 seroprevalence and immunity in Africa.MethodsOur collaboration with the Lagos State COVID-19 Taskforce, enabled secondary analyses of immune responses in healthcare workers (HCWs) and Oxford/AstraZeneca COVID-19 vaccine recipients from the general population across 5 local government areas (LGAs) in Lagos State, Nigeria. Western blots were used to simultaneously detect SARS-CoV-2 spike and nucleocapsid (N) antibodies and stimulation of peripheral blood mononuclear cells with N followed by an IFN-γ ELISA was used to examine T cell responses.FindingsAntibody data demonstrated high SARS-CoV-2 seroprevalence of 71.6% (96/134) in HCWs and 54.8% (63/115) in the general population. Antibodies directed to only SARS-CoV-2 N, suggesting pre-existing coronavirus immunity, were seen in 10.4% (14/134) of HCWs and 20.0% (23/115) of the general population. T cell data showed that IFN-γ responses against SARS-CoV-2 N were robust in detecting exposure to the virus, demonstrating 87.5% sensitivity and 92.3% specificity.InterpretationThese results have important implications for understanding the paradoxical high SARS-CoV-2 infection with low mortality rate in Africa as compared to other parts of the world, as well as for the development of T cell-based diagnostics and vaccines.FundingHarvard University, Motsepe Presidential Research Accelerator Fund for Africa

Although antiretroviral therapy (ART) effectively suppresses HIV replication, the latent reservoir remains the barrier to HIV eradication. It remains unknown whether long-term ART impacts levels of inducible replication-competent provirus. To address this knowledge gap, we assessed the proviral reservoir in HIV-1 perinatally infected adolescents having received ART for >13 years. We recruited 15 vertically infected adolescents living with HIV in Botswana. Historical viral load, CD4(+) T cell count, and treatment data were retrieved from their outpatient medical records. Inducible replication-competent proviruses from cryopreserved peripheral blood mononuclear cells were quantified using a TZM-bl based assay (TZA). Total proviral DNA copies were quantified using droplet digital PCR. The mean age of study participants was 16 years (standard deviation = 0.7) and median CD4(+) T cell count at enrollment was 784 [interquartile range (IQR) = 728.8–1,288] cells/mm(3). Median age at ART initiation was 8 (IQR = 6–12) months. Fourteen (93%) participants had HIV-1 RNA 12 months, p = .85). The median total HIV DNA count was 129.1 copies per million cells (IQR = 18.9–212.3). Our data suggest that long-term ART initiated within the 1st year in perinatally infected infants did not eliminate proviral DNA or inducible replication-competent proviruses.

Indigenous knowledge is a multilayered knowledge system that can effectively manage global ecosystem and biodiversity conservation. Conservation is an applied discipline with the goal of preserving the world’s biodiversity and ecosystems. However, settler–coloniser conservation practices often fail to fully examine how settler–coloniser epistemologies are centred at the expense of Indigenous conservation praxis. Evaluating how conservation practices outside of an Indigenous lens can become more inclusive and just is a critical area for research and reflection. We draw on our own experiences as early-career researchers working towards anticolonial, just and inclusive approaches to conservation science and practice by discussing what it means to be for a Place. We believe that a non-Indigenous conservationist who is for a Place advocates for inclusive stewardship with Indigenous Peoples and other marginalised communities to conserve species and ecosystems and the connections that bind communities to their landscapes. As an example of how settler–coloniser conservation practitioners can be for a Place, we discuss writing a policy statement in 2019 on behalf of the Society for Conservation Biology opposing the construction of the Thirty Meter Telescope on the summit of Mauna Kea, Hawai‘i. We describe the thought process behind our policy statement and provide examples of other actions for conservation researchers and practitioners working to be for a Place. We aim to provide our colleagues, particularly those trained in settler–coloniser conservation practices, an opportunity to identify more just practices for the Places we aspire to conserve.

To define the relationship of SARS-CoV-2 antigen, viral load determined by RT-qPCR, and viral culture detection. Presumptively, viral culture can provide a surrogate measure for infectivity of sampled individuals and thereby inform how and where to most appropriately deploy antigen and nucleic acid amplification-based diagnostic testing modalities.We compared the antigen testing results from three lateral flow and one microfluidics assay to viral culture detection and viral load determination performed in parallel in up to 189 nasopharyngeal swab samples positive for SARS-CoV-2. Sample viral loads, determined by RT-qPCR, were distributed across the range of viral load values observed in our testing population.Antigen tests were predictive of viral culture positivity, with the LumiraDx microfluidics method showing enhanced sensitivity (90%; 95% CI 83-94%) compared with the BD Veritor (74%, 95% CI 65-81%), CareStart (74%, 95% CI 65-81%) and Oscar Corona (74%, 95% CI 65-82%) lateral flow antigen tests. Antigen and viral culture positivity were also highly correlated with sample viral load, with areas under the receiver operator characteristic curves of 0.94 to 0.97 and 0.92, respectively. A viral load threshold of 100 000 copies/mL was 95% sensitive (95% CI, 90-98%) and 72% specific (95% CI, 60-81%) for predicting viral culture positivity. Adjusting for sample dilution inherent in our study design, sensitivities of antigen tests were ≥95% for detection of viral culture positive samples with viral loads10Antigen testing results and viral culture were correlated. For culture positive samples, the sensitivity of antigen tests was high at high viral loads that are likely associated with significant infectivity. Therefore, our data provides support for use of antigen testing in ruling out infectivity at the time of sampling.

Globally, the overexploitation of wildlife presents one of the greatest challenges for biodiversity conservation and sustainable rural livelihoods. Research on the human dimensions of hunting is critical for identifying potential levers for behavioral change interventions. This is especially true in China where hunting threatens to extirpate avian species such as the green peafowl (Pavo muticus) and great hornbill (Buceros bicornis). Nevertheless, regulations restricting gun ownership and hunting have made interviews on this topic highly sensitive. Direct questions about conservation non-compliance are often affected by response bias such as refusals to answer or self-protective denials. We used the randomized response technique (RRT) to estimate the prevalence and drivers of illegal hunting targeting four focal bird taxa (barbets, bulbuls, partridges, and pheasants). Furthermore, we used statistical models that have recently been introduced to the conservation science literature to perform multivariate analyses for RRT data. We measured economic, demographic, and attitudinal covariates that could be associated with hunting. We found high awareness of laws banning hunting in Southwest China, but we also observed that 29.2% of the adult male population may have hunted birds in the past year. Contrary to previous findings highlighting subsistence and finance as major factors driving hunting, the most important predictors of hunting activity in this landscape were related to attitudes regarding the enjoyment of hunting. Extra-economic motivations, such as the entertainment value of hunting, may be underappreciated drivers of hunting behavior. Behavioral change interventions such as pride campaigns may be a promising approach to regulate bird hunting in Xishuangbanna in collaboration with local communities.

Indigenous knowledge is a multilayered knowledge system that can effectively manage global ecosystem and biodiversity conservation. Conservation is an applied discipline with the goal of preserving the world's biodiversity and ecosystems. However, settler–coloniser conservation practices often fail to fully examine how settler–coloniser epistemologies are centred at the expense of Indigenous conservation praxis. Evaluating how conservation practices outside of an Indigenous lens can become more inclusive and just is a critical area for research and reflection. We draw on our own experiences as early-career researchers working towards anticolonial, just and inclusive approaches to conservation science and practice by discussing what it means to be for a Place. We believe that a non-Indigenous conservationist who is for a Place advocates for inclusive stewardship with Indigenous Peoples and other marginalised communities to conserve species and ecosystems and the connections that bind communities to their landscapes. As an example of how settler–coloniser conservation practitioners can be for a Place, we discuss writing a policy statement in 2019 on behalf of the Society for Conservation Biology opposing the construction of the Thirty Meter Telescope on the summit of Mauna Kea, Hawai‘i. We describe the thought process behind our policy statement and provide examples of other actions for conservation researchers and practitioners working to be for a Place. We aim to provide our colleagues, particularly those trained in settler–coloniser conservation practices, an opportunity to identify more just practices for the Places we aspire to conserve.

Across the tropics, unregulated hunting targeting many different species presents a major conservation challenge. Prioritizing resources for monitoring and enforcement is difficult when multiple prey species are exploited. However, identifying which prey species are subject to hunting pressure can be achieved with diet choice models. We evaluate hunter diet sets using data from Southwest China and compare two diet choice models: optimal foraging theory and a relatively new diet model originating from economic optimal stopping problems. The optimal stopping diet choice model required fewer field parameters than optimal foraging models and more accurately reflected hunter catch in Southwest China. The optimal stopping model also indicated that hunters should be less selective when they experience a larger opportunity cost for their time. Finally, we illustrate a new method to evaluate harvest impact from single sites with limited data using dietary thresholds. This technique could be used to evaluate whether or not the community of exploited wildlife has shifted in its trait distribution, providing a means to anticipate trait-biased defaunation from minimal data.

Indigenous knowledge is a multilayered knowledge system that can effectively manage global ecosystem and biodiversity conservation. Conservation is an applied discipline with the goal of preserving the world's biodiversity and ecosystems. However, settler–coloniser conservation practices often fail to fully examine how settler–coloniser epistemologies are centred at the expense of Indigenous conservation praxis. Evaluating how conservation practices outside of an Indigenous lens can become more inclusive and just is a critical area for research and reflection. We draw on our own experiences as early-career researchers working towards anticolonial, just and inclusive approaches to conservation science and practice by discussing what it means to be for a Place. We believe that a non-Indigenous conservationist who is for a Place advocates for inclusive stewardship with Indigenous Peoples and other marginalised communities to conserve species and ecosystems and the connections that bind communities to their landscapes. As an example of how settler–coloniser conservation practitioners can be for a Place, we discuss writing a policy statement in 2019 on behalf of the Society for Conservation Biology opposing the construction of the Thirty Meter Telescope on the summit of Mauna Kea, Hawai‘i. We describe the thought process behind our policy statement and provide examples of other actions for conservation researchers and practitioners working to be for a Place. We aim to provide our colleagues, particularly those trained in settler–coloniser conservation practices, an opportunity to identify more just practices for the Places we aspire to conserve.

Rubber is one of the most rapidly expanding monocultures in the tropics, and has precipitated biodiversity and ecosystem function loss. Identifying measures to improve biodiversity outcomes in rubber-forest mosaics is critical for tropical fauna. We evaluated how avian diversity responded to plantation- and landscape-level environmental variables. The most parsimonious model at the plot scale contained inter-tree planting distance for rubber, plantation age, and inverse distance weight of forest as predictors. The most supported model at the landscape scale contained both distance to forest patches larger than 100 ha and natural forest area as predictors. Model predictions indicated that natural forest area had the largest contribution to bird richness at landscape levels; avian diversity was projected to more than double when natural forest area increased from 25% to 75%. Frugivores and insectivores exhibited the strongest response to gains in natural forest area. Our results indicated that plantation smallholders could achieve biodiversity gains by retaining older trees and planting rubber trees with larger gaps, but that the most critical intervention is retaining large natural forest patches.

First identified in 1947 in Uganda, Zika virus (ZIKV) has remained largely unstudied until the recent outbreak in Latin America. This study aimed to measure the prevalence of ZIKV in febrile patients in Senegal and Nigeria in samples collected from 1992 to 2016. The seroprevalence of ZIKV was 6.2% based on ZIKV immunoglobulin M and negative for dengue reactivity. ZIKV envelope was amplified from 4 samples. Phylogenetic analysis showed that the ZIKVs belonged to the African lineage, grouping with either the Nigerian or MR766 sublineages. This study provides evidence that ZIKV has been silently circulating in West Africa for 2 decades.

IntroductionAdherence to antiretroviral therapy (ART) and retention in treatment programs are required for successful virologic suppression and treatment outcomes. As the number of adolescents living with HIV continues to increase globally, more information about adherence and retention patterns during and through transition from child- to adult-centered care is needed to ensure provision of a high level of care and inform development of targeted interventions to improve patient outcomes in this vulnerable population. In this analysis, we sought to describe long-term trends in adherence, retention, and virologic suppression in adolescents receiving ART at a pediatric HIV clinic in Nigeria through transition to the adult clinic.SettingThe Jos University Teaching Hospital, United States President's Emergency Plan for AIDS Relief (PEPFAR)-funded HIV clinic in Jos, Plateau State, Nigeria.MethodsWe conducted a retrospective observational longitudinal evaluation of data that had been collected during the course of care in a large pediatric ART program in Nigeria. We used descriptive statistics to define our patient population and quantify retention from ART initiation through adolescence and transition to adult-centered care. Logistic regression was used to evaluate predictors of loss to follow-up. We used medication possession ratio (MPR) to quantify adherence for each year a patient was on ART. To evaluate adherence and virologic suppression, we measured the proportion of patients with ≥95% MPR and the proportion with virologic suppression (viral load ≤400 copies/mL) within each age cohort, and used bivariate analyses to examine any association between MPR and VL suppression for all person-years observed.ResultsA total of 476 patients received at least one dose of ART as an adolescent (ages 10-19 years). The proportions of patients lost to follow-up were: 11.9% (71/597) prior to adolescence, 19.1% (31/162) during adolescence, and 13.7% (10/73) during transition to adult-centered care. While over 80% of patients had ≥95% medication adherence in all age groups, their viral load suppression rates through adolescence and post-transition were only 55.6%-64.0%. For patients that successfully transitioned to adult-centered care, we observed 87.7% (50/57) retention at month 12 post-transition, but only 34.6% (9/26) viral load suppression.ConclusionsOur evaluation found considerable proportions of adolescents lost to follow-up throughout the ART program cascade. We also found discrepancies between the proportions of patients with ≥95% MPR and the proportions with VL suppression, suggesting that true medication adherence in this population may be poor. Significant attention and targeted interventions to improve retention and adherence focused on adolescents are needed in order for global programs to achieve 90-90-90 goals.

Across the tropics, millions of rural families rely on non-timber forest products for protein, subsistence, and other financial or cultural uses. Often, communities exploit biotically dispersed trees and their mammalian or avian seed disperser. Empirical findings have indicated that many plant and animal resources are overexploited, presenting challenges for biodiversity conservation and sustainable rural livelihoods. However, there has been limited research investigating the impacts of harvest that targets both seed dispersers and zoochoric trees. We formulated a discrete-time model for interacting seed dispersers and plants under harvest. We found that the more dependent species will dictate the sustainable threshold level of harvest, and that higher levels of dependence could drive the species pair to local extinction. We illustrated the application of sensitivity analysis to our modeling framework in order to facilitate future analyses and applications using this approach.

Background TB is the leading cause of death among HIV-infected children, yet treatment options for those who require PI-based ART are suboptimal. Rifabutin is the preferred rifamycin for adults on PI-based ART; only one study has evaluated its use among children on PIs and two of six children developed treatment-limiting neutropenia. Methods Since 2009, rifabutin has been available for HIV/TB-coinfected children requiring PI-based ART in the Harvard/APIN programme in Nigeria. We retrospectively analysed laboratory and clinical toxicities at baseline and during rifabutin therapy, and examined HIV/TB outcomes. Results Between 2009 and 2015, 48 children received rifabutin-containing TB therapy with PI (lopinavir/ritonavir)-based ART: 50% were female with a median (IQR) baseline age of 1.7 (0.9–5.0) years and a median (IQR) CD4+ cell percentage of 15% (9%–25%); 52% were ART experienced. Eighty-five percent completed the 6 month rifabutin course with resolution of TB symptoms and 79% were retained in care at 12 months. Adverse events (grade 1–4) were more common at baseline (27%) than during rifabutin treatment (15%) (P = 0.006). Absolute neutrophil count was lower during rifabutin compared with baseline (median = 1762 versus 2976 cells/mm3, respectively), but only one instance (2%) of grade 3 neutropenia occurred during rifabutin treatment. Conclusions With clinical and laboratory monitoring, our data suggest that rifabutin is a safe option for TB therapy among children on PI-based ART. By contrast with the only other study of this combination in children, severe neutropenia was rare. Furthermore, outcomes from this cohort suggest that rifabutin is effective, and a novel option for children who require PI-based ART. Additional study of rifabutin plus PIs in children is urgently needed.

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Recent studies on the role of T cells in Zika virus (ZIKV) infection have shown that T cell responses to Asian ZIKV infection are important for protection, and that previous dengue virus (DENV) exposure amplifies the protective T cell response to Asian ZIKV. Human T cell responses to African ZIKV infection, however, remain unexplored. Here, we utilized the modified anthrax toxin delivery system to develop a flavivirus enzyme-linked immunosorbent spot (ELISPOT) assay. Using human ZIKV and DENV samples from Senegal, West Africa, our results demonstrate specific and cross-reactive T cell responses to nonstructural protein 3 (NS3). Specifically, we found that T cell responses to NS3 protease are ZIKV and DENV specific, but responses to NS3 helicase are cross-reactive. Sequential sample analyses revealed immune responses sustained many years after infection. These results have important implications for African ZIKV/DENV vaccine development, as well as for potential flavivirus diagnostics based on T cell responses. IMPORTANCE The recent Zika virus (ZIKV) epidemic in Latin America and the associated congenital microcephaly and Guillain-Barré syndrome have raised questions as to why we have not recognized these distinct clinical diseases in Africa. The human immunologic response to ZIKV and related flaviviruses in Africa represents a research gap that may shed light on the mechanisms contributing to protection. The goal of our study was to develop an inexpensive assay to detect and characterize the T cell response to African ZIKV and DENV. Our data show long-term specific and cross-reactive human immune responses against African ZIKV and DENV, suggesting the usefulness of a diagnostic based on the T cell response. Additionally, we show that prior flavivirus exposure influences the magnitude of the T cell response. The identification of immune responses to African ZIKV and DENV is of relevance to vaccine development.

Introduction : High levels of adherence to antiretroviral therapy (ART) and retention in treatment programs are required for successful virologic suppression and treatment outcomes. While there have been numerous studies focusing on adherence and loss to follow-up (LTFU) in adults, studies in children and young adolescents are limited. For this study, we examined patterns of adherence and LTFU in HIV-infected pediatric patients receiving ART in PEPFAR-funded sites in Nigeria. Methods : We conducted a retrospective observational study utilizing data that had been collected during the course of care in a large pediatric ART program in Nigeria. Results : A total of 3,513 children ages 0-14.9 years enrolled at 31 different sites between June 2005 and March 2011 were included in the study. Of the enrolled patients, 1,987 (56%) were LTFU by the end of the study period. LTFU was highest in those ages versus aged 2-12.9 years). Year of ART initiation was a strong predictor of LTFU across all age groups. For those patients retained to 12 months, less than half showed optimal adherence (≥95%). While there were no differences in adherence rates at month 12 by age group, those aged 10 years and older did have declining adherence starting at 18 months. Discussion : Adherence is critical for optimal ART patient outcomes. We found both low adherence and high LTFU rates in our study cohort. Additional studies focused on barriers to adherence and development of age-specific intervention programs are critical to improving overall pediatric outcomes.

Coffee is a major tropical commodity crop that can provide supplementary habitat for native wildlife. In Asia, coffee production is an increasingly important driver of landscape transformation and shifts between different coffee species is a major dimension of agroforestry trends. Yet few studies have compared the ecological impacts of conversion between different coffee species. We evaluated whether or not the two species of coffee grown globally—Coffea arabica and C. canephora (denoted “robusta”)—had equivalent avian conservation value in the Western Ghats, India, where robusta production has become increasingly dominant. We found that habitat specialist and functional guild diversity was higher in arabica, and that arabica was more profitable. However, robusta farms generally supported the same or slightly higher abundances of habitat specialists and functional guilds, largely due to dense canopy and landscape-level forest cover. Farming practices, chiefly pesticide use, may affect the suitability of coffee agroforests as habitat for avian specialists, and at present, robusta farmers tended to use less pesticide. Given future projections for arabica to robusta conversion in tropical Asia, our study indicates that certification efforts should prioritize maintaining native canopy shade trees and forest cover to ensure that coffee landscapes can continue providing biodiversity benefits.

Understanding violations of laws or social norms designed to protect natural resources from overexploitation is a priority for conservation research and management. Because direct questioning about stigmatized behaviors can produce biased responses, researchers have adopted more complex, indirect questioning techniques. The randomized response technique (RRT) is one of the most powerful indirect survey methods, yet analyses of these data require sophisticated statistical models. To date, there has been limited user-friendly software to analyze RRT data, particularly for models that combine information from multiple RRT questions. We developed an R package, zapstRR (ZoologicAl Package for RRT) that provides functions for 3 RRT models that can be applied to single or multiple RRT questions. With these functions, researchers can estimate the prevalence of conservation noncompliance, determine the number of violations by individuals, perform regressions for univariate and multivariate RRT data, and correct prevalence estimates for evasive-response bias. We illustrate the use of these estimators for RRT data through an examination of 2 case studies: illegal bird hunting where the interview consisted of a standard RRT question design and a novel implementation designed to offer further anonymity to respondents and reveal the impact of educational interventions on illegal bushmeat consumption. The case studies demonstrate how the models can work in tandem to uncover distinct patterns within RRT data sets. The case studies also show how several assumptions are central to the application of the multivariate models.

Hunting is one of the greatest threats to tropical vertebrates. Examining why people hunt is crucial to identifying policy levers to prevent excessive hunting. Overhunting is particularly relevant in Southeast Asia, where a high proportion of mammals and birds are globally threatened. We interviewed hunters in Southwest China to examine their social behavior, motivations, and responses to changes in wildlife abundance. Respondents viewed hunting as a form of recreation, not as an economic livelihood, and reported that they would not stop hunting in response to marked declines in expected catch. Even in scenarios where the expected catch was limited to minimal quantities of small, low-price songbirds, up to 36.7% of respondents said they would still continue to hunt. Recreational hunting may be a prominent driver for continued hunting in increasingly defaunated landscapes; this motivation for hunting and its implications for the ecological consequences of hunting have been understudied relative to subsistence and profit hunting. The combination of a preference for larger over smaller game, reluctance to quit hunting, and weak enforcement of laws may lead to hunting-down-the-web outcomes in Southwest China.

Background While there has been a rapid global scale-up of antiretroviral therapy programs over the past decade, there are limited data on long-term outcomes from large cohorts in resource-constrained settings. Our objective in this evaluation was to measure multiple outcomes during first-line antiretroviral therapy in a large treatment program in Nigeria. Methods We conducted a retrospective multi-site program evaluation of adult patients (age ≥15 years) initiating antiretroviral therapy between June 2004 and February 2012 in Nigeria. The baseline characteristics of patients were described and longitudinal analyses using primary endpoints of immunologic recovery, virologic rebound, treatment failure and long-term adherence patterns were conducted. Results Of 70,002 patients, 65.2% were female and median age was 35 (IQR: 29-41) years; 54.7% were started on a zidovudine-containing and 40% on a tenofovir-containing first-line regimen. Median CD4+ cell counts for the cohort started at 149 cells/mm3 (IQR: 78-220) and increased over duration of ART. Of the 70,002 patients, 1.8% were reported as having died, 30.1% were lost to follow-up, and 0.1% withdrew from treatment. Overall, of those patients retained and with viral load data, 85.4% achieved viral suppression, with 69.3% achieving suppression by month 6. Of 30,792 patients evaluated for virologic failure, 24.4% met criteria for failure and of 45,130 evaluated for immunologic failure, 34.0% met criteria for immunologic failure, with immunologic criteria poorly predicting virologic failure. In adjusted analyses, older age, ART regimen, lower CD4+ cell count, higher viral load, and inadequate adherence were all predictors of virologic failure. Predictors of immunologic failure differed slightly, with age no longer predictive, but female sex as protective; additionally, higher baseline CD4+ cell count was also predictive of failure. Evaluation of long-term adherence patterns revealed that the majority of patients retained through 84 months maintained ≥95% adherence. Conclusion While improved access to HIV care and treatment remains a challenge in Nigeria, our study shows that a high quality of care was achieved as evidenced by strong long-term clinical, immunologic and virologic outcomes.

We review the conservation issues facing migratory shorebird populations that breed in temperate regions and use wetlands in the non-breeding season. Shorebirds are excellent model organisms for understanding ecological, behavioural and evolutionary processes and are often used as indicators of wetland health. A global team of experienced shorebird researchers identified 45 issues facing these shorebird populations, and divided them into three categories (natural, current anthropogenic and future issues). The natural issues included megatsunamis, volcanoes and regional climate changes, while current anthropogenic threats encompassed agricultural intensification, conversion of tidal flats and coastal wetlands by human infrastructure developments and eutrophication of coastal systems. Possible future threats to shorebirds include microplastics, new means of recreation and infectious diseases. We suggest that this review process be broadened to other taxa to aid the identification and ranking of current and future conservation actions.

Road salt is a common, anthropogenic source of NaCl in many temperate ecosystems. Sodium is also an essential and potentially limiting element for inland animal populations. This suggests that Na limitation in inland ecosystems, and hence attraction to Na sources, should increase with distance from salted roads. 2. In a North Temperate forest, we tested the prediction that Na recruitment would increase, as soil (Na) decreased, with distance from a salted two-lane highway. We presented ants with three concentrations of NaCl and sucrose solution along four pairs of transects ca 1, 10, 100, and 1000 m from the road. 3. Consistent with the Na-limitation hypothesis, the ratio of NaCl to sucrose use increased with distance from the road from 1:13 vials at 1 m to 1:5 vials at 1 km. Genera characterised by high Na use did not accumulate farther from the road. For the common and widespread Tapinoma sessile (Say), a 10-fold increase in distance from the road resulted in ants doubling their use of NaCl relative to sucrose. 4. Road salt is a well-known pollutant, especially of freshwater ecosystems. However, by suppressing plants and potentially promoting consumers, road salt may have more complex effects on terrestrial ecosystems, especially those far inland from oceanic aerosols.

Background Ebola virus (EBOV) caused more than 11,000 deaths during the 2013–2016 epidemic in West Africa without approved vaccines or immunotherapeutics. Despite its high lethality in some individuals, EBOV infection can produce little to no symptoms in others. A better understanding of the immune responses in individuals who experienced minimally symptomatic and asymptomatic infection could aid the development of more effective vaccines and antivirals against EBOV and related filoviruses. Methodology/Principle findings Between August and November 2017, blood samples were collected from 19 study participants in Lagos, Nigeria, including 3 Ebola virus disease (EVD) survivors, 10 individuals with documented close contact with symptomatic EVD patients, and 6 control healthcare workers for a cross-sectional serosurvey and T cell analysis. The Lagos samples, as well as archived serum collected from healthy individuals living in surrounding areas of the 1976 Democratic Republic of Congo (DRC) epidemic, were tested for EBOV IgG using commercial enzyme-linked immunosorbent assays (ELISAs) and Western blots. We detected antibodies in 3 out of 3 Lagos survivors and identified 2 seropositive individuals not known to have ever been infected. Of the DRC samples tested, we detected antibodies in 9 out of 71 (12.7%). To characterize the T cell responses in the Lagos samples, we developed an anthrax toxin-based enzyme-linked immunospot (ELISPOT) assay. The seropositive asymptomatic individuals had T cell responses against EBOV nucleoprotein, matrix protein, and glycoprotein 1 that were stronger in magnitude compared to the survivors. Conclusion/Significance Our data provide further evidence of EBOV exposure in individuals without EVD-like illness and, for the first time, demonstrate that these individuals have T cell responses that are stronger in magnitude compared to severe cases. These findings suggest that T cell immunity may protect against severe EVD, which has important implications for vaccine development., Author summary The 2013–2016 West African Ebola virus (EBOV) outbreak is the largest on record with over 28,000 reported symptomatic cases and more than 11,000 deaths. We developed a simple and inexpensive modified anthrax toxin-based ELISPOT assay to detect and characterize the T cell responses elicited by prior exposure to EBOV. Our data show robust T cell responses to several EBOV proteins in individuals who experienced both severe and asymptomatic EBOV infections. These results provide further evidence that EBOV transmission events can go undetected. We also show that the seropositive asymptomatic individuals have stronger T cell responses compared to survivors, which has important implications for vaccine development.

Background. Despite the benefits of antiretroviral therapy (ART), tuberculosis (TB) is the leading cause of mortality among human immunodeficiency virus (HIV)-infected persons in Africa. Nigeria bears the highest TB burden in Africa and second highest HIV burden globally. This long-term multicenter study aimed to determine the incidence rate and predictors of TB in adults in the Harvard/AIDS Prevention Initiative in Nigeria (APIN) and President's Emergency Plan for AIDS Relief (PEPFAR) Nigeria ART program. Methods. This retrospective evaluation used data collected from 2004 to 2012 through the Harvard/APIN PEPFAR program. Risk factors for incident TB were determined using multivariate Cox proportional hazards regression with time-dependent covariates. Results. Of 50 320 adults enrolled from 2005 to 2010, 11 092 (22%) had laboratory-confirmed active TB disease at ART initiation, and 2021 (4%) developed active TB after commencing ART. During 78 228 total person-years (PY) of follow-up, the TB incidence rate was 25.8 cases per 1000 PY (95% confidence interval [CI], 24.7–27.0) overall, and it decreased significantly both with duration on ART and calendar year. Risk factors at ART initiation for incident TB included the following: earlier ART enrollment year, tenofovir-containing initial ART regimen, and World Health Organization clinical stage above 1. Time-updated risk factors included the following: low body mass index, low CD4+ cell count, unsuppressed viral load, anemia, and ART adherence below 80%. Conclusions. The rate of incident TB decreased with longer duration on ART and over the program years. The strongest TB risk factors were time-updated clinical markers, reinforcing the importance of consistent clinical and laboratory monitoring of ART patients in prompt diagnosis and treatment of TB and other coinfections.

Background : The 2013 WHO guidelines incorporated simplified and more effective antiretroviral regimens for the purposes of preventing mother-to-child transmission of HIV. With ideal implementation of these recommendations, perinatal HIV transmission could be reduced to less than 2%. However, loss to follow-up (LTFU) has the potential to erode the success of programs and a number of studies report high rates of LTFU within the prevention of mother-to-child transmission (PMTCT) care cascade. We evaluated the timing and magnitude of LTFU in a large programmatic PMTCT cohort in Nigeria in order to focus future efforts to reduce loss in this high burden setting. Methods : From 2004-2014, the APIN/Harvard PEPFAR program supported antenatal HIV screening for nearly one million pregnant women and provided PMTCT care to over 30,000 women. The care cascade for women enrolling in the PMTCT program includes antenatal, delivery, and infant follow-up services through 12-18 months of life. In this retrospective cohort analysis, we examined data collected between 2004-2014 from 31 clinical sites in Nigeria and assessed the numbers of mothers and infants enrolled and LTFU at various points along the care cascade. Results : Among 31,504 women (median age 30, IQR: 27-34) entering PMTCT care during the antenatal period, 20,679 (66%) completed the entire cascade of services including antenatal, delivery, and at least one infant follow-up visit. The median gestational age at presentation for antenatal care services was 23 weeks (IQR: 17-29). The median infant age at last follow-up visit was 12 months (IQR: 5-18). The greatest loss in the PMTCT care cascade occurred prior to delivery care (21%), with a further 16% lost prior to first infant visit. Of the 38,223 women who entered at any point along the PMTCT cascade, an HIV DNA PCR was available for 20,202 (53%) of their infants. Among infants for whom DNA PCR results were available, the rate of HIV transmission for infants whose mothers received any antenatal and/or delivery care was 2.8% versus 20.0% if their mother received none. Conclusion : In this large cohort analysis, the proportion of women LTFU in the PMTCT care cascade was lower than that reported in previous cohort analyses. Nevertheless, this proportion remains unacceptably high and inhibits the program from maximally achieving the goals of PMTCT care. We also provide the largest analysis to date on rates of perinatal HIV transmission, with low rates among women receiving NNRTI- or PI-based regimens, approaching that reported in clinical trials. However, among mothers who received any antenatal care, infant outcomes were unknown for 48%, and women presented later in pregnancy than that recommended by current guidelines. Implementation research to evaluate ways to improve integration of services, particularly transitions from antenatal to delivery and pediatric care, are critically needed to reduce LTFU within PMTCT programs and achieve the ultimate goal of eliminating pediatric HIV infection.

Evaluation of time-dependent predictors of loss to follow-up in a large HIV treatment program revealed that early adherence patterns, in addition to CD4 count and viral load, predicted loss to follow-up and should be used as measures in devising targeted interventions to increase program retention., Background Most evaluations of loss to follow-up (LTFU) in human immunodeficiency virus (HIV) treatment programs focus on baseline predictors, prior to antiretroviral therapy (ART) initiation. As risk of LTFU is a continuous issue, the aim of this evaluation was to augment existing information with further examination of time-dependent predictors of loss. Methods This was a retrospective evaluation of data collected between 2004 and 2012 by the Harvard School of Public Health and the AIDS Prevention Initiative in Nigeria as part of PEPFAR-funded program in Nigeria. We used multivariate modeling methods to examine associations between CD4+ cell counts, viral load, and early adherence patterns with LTFU, defined as no refills collected for at least 2 months since the last scheduled appointment. Results Of 51 953 patients initiated on ART between 2004 and 2011, 14 626 (28%) were LTFU by 2012. Factors associated with increased risk for LTFU were young age, having nonincome-generating occupations or no education, being unmarried, World Health Organization (WHO) stage, having a detectable viral load, and lower CD4+ cell counts. In a subset analysis, adherence patterns during the first 3 months of ART were associated with risk of LTFU by month 12. Conclusions In settings with limited resources, early adherence patterns, as well as CD4+ cell counts and unsuppressed viral load, at any time point in treatment are predictive of loss and serve as effective markers for developing targeted interventions to reduce rates of attrition.

Objectives The implementation of PEPFAR programs in resource-limited settings was accompanied by the need to document patient care on a scale unprecedented in environments where paper-based records were the norm. We describe the development of an electronic medical records system (EMRS) put in place at the beginning of a large HIV/AIDS care and treatment program in Nigeria. Methods Databases were created to record laboratory results, medications prescribed and dispensed, and clinical assessments, using a relational database program. A collection of stand-alone files recorded different elements of patient care, linked together by utilities that aggregated data on national standard indicators and assessed patient care for quality improvement, tracked patients requiring follow-up, generated counts of ART regimens dispensed, and provided ‘snapshots’ of a patient's response to treatment. A secure server was used to store patient files for backup and transfer. Results By February 2012, when the program transitioned to local in-country management by APIN, the EMRS was used in 33 hospitals across the country, with 4,947,433 adult, pediatric and PMTCT records that had been created and continued to be available for use in patient care. Ongoing trainings for data managers, along with an iterative process of implementing changes to the databases and forms based on user feedback, were needed. As the program scaled up and the volume of laboratory tests increased, results were produced in a digital format, wherever possible, that could be automatically transferred to the EMRS. Many larger clinics began to link some or all of the databases to local area networks, making them available to a larger group of staff members, or providing the ability to enter information simultaneously where needed. Conclusions The EMRS improved patient care, enabled efficient reporting to the Government of Nigeria and to U.S. funding agencies, and allowed program managers and staff to conduct quality control audits.

The Amazon basin is one of the most biologically diverse places on earth. However, agricultural expansion and infrastructure development have led to widespread deforestation that threatens the survival of many taxa. Conservation strategies to contest these threats include protected areas and environmental legislation. Nevertheless, the basic biology of many taxa is largely unknown, which poses an immense challenge when devising effective strategies to safeguard such species in the long-term. This is particularly true for primates. Monkeys from the genus Mico are poorly studied with half of the currently known species being described after 1976, and their distribution and threats remain poorly understood. Using the model Maxent, we re-evaluated the distribution range for Rondon’s marmoset, one of the most threatened species in this genus. Our results estimated a distribution that is 15,500 km2 smaller than previously described for this species (68,649 km2). Furthermore, much of its modeled distribution (71%) lies outside of protected areas. Agriculture expansion and infrastructure development have converted/destroyed 20,532 km2 of forest within its range (38%) mainly in areas without protection. Another 10,316 km2 of forest is projected to be cleared by 2040 under current deforestation patterns. The expected cumulative loss of over 50% of its range size in the coming 15 years raise awareness about the threaten category of this species. In the absence of new protected areas, it remains to be seen whether Rondon’s marmoset can be effectively conserved in remaining fragments of forest in farmlands.

Background In this paper, we address the evidence for the Ambush Hypothesis. Proposed by Seligmann and Pollock, this hypothesis posits that there exists a selection for off-frame stop codons (OSCs) to counteract the possible deleterious effects of translational frameshifts, including the waste of resources and potential cytotoxicity. Two main types of study have been used to support the hypothesis. Some studies analyzed codon usage and showed that codons with more potential to create OSCs seem to be favored over codons with lower potential; they used this finding to support the Ambush Hypothesis. Another study used 342 bacterial genomes to evaluate the hypothesis directly, finding significant excesses of OSCs in these genomes. Results We repeated both analyses with newer datasets and searched for other factors that could explain the observed trends. In the first case, the relative frequency of codons with the potential to create OSCs is directly correlated with the GC content of organisms, as stop codons are GC-poor. When evaluating the frequency of OSCs directly in 1,976 bacterial genomes we also detected a significant excess. However, when comparing the excess of OSCs with similarly obtained results for the frequency of out-of-frame sense codons, some sense codons have a more significant excess than stop codons. Conclusions Two avenues of study have been used to support the Ambush Hypothesis. Using the same methods as these previous studies, we demonstrate that the evidence in support of the Ambush Hypothesis does not hold up against more rigorous testing.