Priority research needs to inform amphibian conservation in the Anthropocene

The problem of global amphibian declines has prompted extensive research over the last three decades. Initially, the focus was on identifying and characterizing the extent of the problem, but more recently efforts have shifted to evidence‐based research designed to identify best solutions and to improve conservation outcomes. Despite extensive accumulation of knowledge on amphibian declines, there remain knowledge gaps and disconnects between science and action that hamper our ability to advance conservation efforts. Using input from participants at the ninth World Congress of Herpetology, a U.S. Geological Survey Powell Center symposium, amphibian on‐line forums for discussion, the International Union for Conservation of Nature Assisted Reproductive Technologies and Gamete Biobanking group, and respondents to a survey, we developed a list of 25 priority research questions for amphibian conservation at this stage of the Anthropocene. We identified amphibian conservation research priorities while accounting for expected tradeoffs in geographic scope, costs, and the taxonomic breadth of research needs. We aimed to solicit views from individuals rather than organizations while acknowledging inequities in participation. Emerging research priorities (i.e., those under‐represented in recently published amphibian conservation literature) were identified, and included the effects of climate change, community‐level (rather than single species‐level) drivers of declines, methodological improvements for research and monitoring, genomics, and effects of land‐use change. Improved inclusion of under‐represented members of the amphibian conservation community was also identified as a priority. These research needs represent critical knowledge gaps for amphibian conservation although filling these gaps may not be necessary for many conservation actions

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK

Background A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. Methods This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. Findings Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0–75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4–97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8–80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3–4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. Interpretation ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK.

BACKGROUND: A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. METHODS: This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. FINDINGS: Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0-75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4-97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8-80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3-4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. INTERPRETATION: ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials. FUNDING: UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, Bill & Melinda Gates Foundation, Lemann Foundation, Rede D'Or, Brava and Telles Foundation, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, and AstraZeneca

Conservation assessment of threatened frogs in KwaZulu–Natal and a national assessment of chytrid infection in threatened South African species

Thesis (PhD (Zoology))--North-West University, Potchefstroom Campus, 2012Amphibians are the most threatened Class of vertebrate on Earth, with 30% of all species IUCN Red Listed. This proportion is reflected in South Africa, where 29% of all species assessed in 2011 (SA-FRoG 2010; IUCN 2011; Measey 2011) fall into the threatened categories of Critically Endangered (7%), Endangered (12%) or Vulnerable (10%). This study is focussed on these species, with a particular emphasis on those that occur in the KwaZulu-Natal Province. The thesis is structured as follows: CHAPTER 1 gives a broad introduction to the global situation with regard to amphibian declines and the threats causing them as based on the literature. Additional information pertinent to successive chapters is given, including descriptions of KwaZulu-Natal's threatened frogs, detail on the disease chytridiomycosis and its causal agent, Batrachochytrium dendrobatidis (Bd), and the importance of the application of systematics for conservation. CHAPTER 2 provides baseline information on a national scale regarding the occurrence and prevalence of infection with Bd in South Africa's threatened frogs. This pathogen causes the disease chytridiomycosis and is responsible for amphibian declines globally. Samples were collected by means of skin swabs and analysed using quantitative PCR. Prevalence varied widely between threatened species (Avg. = 14.8%), with infection intensity being predominantly influenced by life history characteristics. The study also provides, for the first time, a distribution model for B. dendrobatidis occurrence in South Africa, indicating regions that are likely to harbour the pathogen. Such information is useful for application in disease prevention and control plans. CHAPTER 3 provides threat assessments for certain of the threatened species in KwaZulu-Natal, focussing on two sites per species, and makes recommendations on additional research requirements and appropriate conservation actions for these species. Particular emphasis is placed on Hyperolius pickersgilli, the province's only Critically Endangered species. CHAPTER 4 is focussed on the distribution of Hyperolius pickersgilli. Ecological niche modelling using Maxent was employed to predict the distribution of this species, and high probability areas were surveyed over two breeding seasons. Known historical sites were also re-visited and assessed for species presence. As a result of surveying, 5 new localities for the species were revealed, but half of the historical sites have been transformed to such an extent that the species no longer occurs there. In total, the species currently occurs at 17 localities, the majority of which are highly fragmented and threatened by human activity. The results of the survey were used to recalculate the area of occupancy (AOO) and extent of occurrence (EOO) for H. pickersgilli. Based on these findings, and the level of threat at the majority of sites and degree of fragmentation between them, the Critically Endangered status of this species remains warranted. CHAPTER 5 reviews the systematics of the Afrixalus spinifrons complex using morphological, call and molecular analysis. Although the first two methods have been used historically to delimit boundaries for taxa within this complex, genetic analysis has not been previously conducted. This study makes use of DNA sequencing from mitochondrial and nuclear gene markers to elucidate phylogenetic relationships within the complex. The results confirm that A. knysnae is part of the A. spinifrons clade, but is a separate species. Afrixalus spinifrons spinifrons and A. s. intermedius form distinct clusters, but are closely related confirming that the subspecies diagnosis as a representation of evolutionary divergence is accurate. The study does however differ from previous conclusions in that populations from the Eastern Cape group with A. s. intermedius from the KwaZulu-Natal midlands as opposed to A. s. spinifrons from the coast. Although these findings do not warrant designation of the subspecies to full species, they should be treated as evolutionary significant units for the purposes of conservation.Doctora

Using predictive modelling to guide the conservation of a critically endangered coastal wetland amphibian

Amphibians are the most threatened Class of vertebrate, with wetland-associated anurans in particularsuffering high levels of habitat loss. We used predictive modelling to better understand the distribution ofa critically endangered South African endemic (Hyperolius pickersgilli) and to guide conservation action.MaxEnt distribution models were produced based on limited occurrence data. Predicted localities withprobability of occurrence ≥60% were surveyed. Ten new sub-populations were discovered. The meanprobability of occurrence for the species at wetlands where it was detected was greater than that atwetlands where it was not detected or absent. In addition, 17 known historical localities were re-visitedand the species deemed absent at 8 of these. The total number of localities at which the species is nowknown to occur is 18, which is an increase in the known extant sub-populations of six. We recalculate thearea of occupancy and extent of occurrence for the species as 108 km2and 2081.5 km2, respectively; bothincreases on previous estimates. Implications of these changes on the IUCN Red List status of H. pickersgilliare discussed. A friction map was created to identify possible linkages between sub-populations, whichcan be used to guide habitat restoration and population repatriation. Given the degree of isolation ofsubpopulations and the potentially severe threats to most of these, urgent conservation action for H.pickersgilli remains crucial. This study provides a method for use in conservation planning for wetland-breeding amphibians in eastern coastal regions of Africa and elsewhere.http://www.journals.elsevier.com/journal-for-nature-conservation

Do public attitudes affect conservation effort? Using a questionnaire-based survey to assess perceptions, beliefs and superstitions associated with frogs in South Africa

Globally, amphibians are among the least appreciated vertebrates and are often negatively perceived by the general public. Such attitudes are particularly prevalent in South Africa, where fear, superstitions and myths associated with frogs are pervasive in some cultures. These attitudes could have harmful consequences both for the animals concerned and conservation efforts. This study aimed to investigate attitudes to frogs throughout South Africa across multiple age and ethnic groups. We used a multi-language survey in both hard-copy and online versions. Respondents (n = 2 295) comprised both genders across six age groups and five ethnic groups. A functionalist approach using structural equation modelling was used to assess how liking of frogs and cultural beliefs varied with socio-demographic factors. Attitudes varied significantly between groups, with males more likely to like frogs than females and age and level of education also significantly linked to liking. The influence of cultural beliefs and lack of knowledge also directly influenced negative attitudes towards frogs. More than 60% of respondents expressed an interest in learning more about frogs, indicating an opportunity for improving attitudes through educational outreach. The findings of this study can be used to inform current efforts to protect amphibians in South Africa through social interventions.Keywords: attitudes, conservation, cultural beliefs, frogs, South Afric

Spatial assessment of amphibian chytrid fungus (Batrachochytrium dendrobatidis) in South Africa confirms endemic and widespread infection

Chytridiomycosis has been identified as a major cause of global amphibian declines. Despite widespread evidence of Batrachochytrium dendrobatidis infection in South African frogs, sampling for this disease has not focused on threatened species, or whether this pathogen poses a disease risk to these species. This study assessed the occurrence of Bd-infection in South African Red List species. In addition, all known records of infection from South Africa were used to model the ecological niche of Bd to provide a better understanding of spatial patterns and associated disease risk. Presence and prevalence of Bd was determined through quantitative real-time PCR of 360 skin swab samples from 17 threatened species from 38 sites across the country. Average prevalence was 14.8% for threatened species, with pathogen load varying considerably between species. MaxEnt was used to model the predicted distribution of Bd based on 683 positive records for South Africa. The resultant probability threshold map indicated that Bd is largely restricted to the wet eastern and coastal regions of South Africa. A lack of observed adverse impacts on wild threatened populations supports the endemic pathogen hypothesis for southern Africa. However, all threatened species occur within the limits of the predicted distribution for Bd, exposing them to potential Bd-associated risk factors. Predicting pathogen distribution patterns and potential impact is increasingly important for prioritising research and guiding management decisionsThe Green Trust - Project number GT 1489. National Research Foundation, South Africahttp://www.plosone.org/http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069591DOI: 10.1371/journal.pone.006959

Spatial assessment of amphibian chytrid fungus (Batrachochytrium dendrobatidis) in South Africa confirms endemic and widespread infection.

Chytridiomycosis has been identified as a major cause of global amphibian declines. Despite widespread evidence of Batrachochytrium dendrobatidis infection in South African frogs, sampling for this disease has not focused on threatened species, or whether this pathogen poses a disease risk to these species. This study assessed the occurrence of Bd-infection in South African Red List species. In addition, all known records of infection from South Africa were used to model the ecological niche of Bd to provide a better understanding of spatial patterns and associated disease risk. Presence and prevalence of Bd was determined through quantitative real-time PCR of 360 skin swab samples from 17 threatened species from 38 sites across the country. Average prevalence was 14.8% for threatened species, with pathogen load varying considerably between species. MaxEnt was used to model the predicted distribution of Bd based on 683 positive records for South Africa. The resultant probability threshold map indicated that Bd is largely restricted to the wet eastern and coastal regions of South Africa. A lack of observed adverse impacts on wild threatened populations supports the endemic pathogen hypothesis for southern Africa. However, all threatened species occur within the limits of the predicted distribution for Bd, exposing them to potential Bd-associated risk factors. Predicting pathogen distribution patterns and potential impact is increasingly important for prioritising research and guiding management decisions