Antibodies to SARS-CoV-2 protect against re-infection during outbreaks in care homes, September and October 2020.

Two London care homes experienced a second COVID-19 outbreak, with 29/209 (13.9%) SARS-CoV-2 RT-PCR-positive cases (16/103 residents, 13/106 staff). In those with prior SARS-CoV-2 exposure, 1/88 (1.1%) individuals (antibody positive: 87; RT-PCR-positive: 1) became PCR-positive compared with 22/73 (30.1%) with confirmed seronegative status. After four months protection offered by prior infection against re-infection was 96.2% (95% confidence interval (CI): 72.7-99.5%) using risk ratios from comparison of proportions and 96.1% (95% CI: 78.8-99.3%) using a penalised logistic regression model.

BURMESE ROOFED TURTLE (BATAGUR TRIVITTATA) DISEASE SCREENING IN MYANMAR.

The Burmese roofed turtle (Batagur trivittata), a critically endangered freshwater turtle, is endemic to Myanmar. Once thought to be extinct, remnant wild populations were discovered in 2001 and limited captive individuals identified in pagoda ponds or confiscated from fishers in Myanmar. These and their offspring are maintained in five facilities in Myanmar and form the basis of a conservation program (habitat protection, captive breeding, nest protection, egg collection, head-starting, and release). Prerelease health screenings were performed in 2014 and 2018 at Yadanabon Zoological Gardens, a head-starting facility in Limpha Village, and Lawkanandar Wildlife Park. One hundred forty-three turtles were assessed (37 male, 50 female, 56 juveniles [too young to determine sex]; two females were assessed in both years), age range of 1 to 12 y (one unknown age adult founder), and body mass range of 0.111 to 32.72 kg. Health evaluations both years included physical examination and combined choanal/cloacal swab samples for polymerase chain reaction testing of the potential chelonian pathogens intranuclear coccidia, Mycoplasma, Herpesvirus, Ranavirus, and Adenovirus (not all tests performed each year). In 2018, cloacal swabs from 30 and 20 turtles at the Yadanabon Zoological Gardens and Lawkanandar Wildlife Park, respectively, were cultured for Salmonella. All turtles were assessed as healthy based on normal physical examination findings, and all had negative test results. Prerelease health screening, such as performed in this study, is an important component of release, reintroduction, and translocation projects to prevent introduction of novel pathogens into naïve wild populations.

CoNTe: A Core Network Temporal Blockchain for 5G.

Virtual Network Functions allow the effective separation between hardware and network functionality, a strong paradigm shift from previously tightly integrated monolithic, vendor, and technology dependent deployments. In this virtualized paradigm, all aspects of network operations can be made to deploy on demand, dynamically scale, as well as be shared and interworked in ways that mirror behaviors of general cloud computing. To date, although seeing rising demand, distributed ledger technology remains largely incompatible in such elastic deployments, by its nature as functioning as an immutable record store. This work focuses on the structural incompatibility of current blockchain designs and proposes a novel, temporal blockchain design built atop federated byzantine agreement, which has the ability to dynamically scale and be packaged as a Virtual Network Function (VNF) for the 5G Core.

Conservation genomics of the endangered Burmese roofed turtle.

The Burmese roofed turtle (Batagur trivittata) is one of the world's most endangered turtles. Only one wild population remains in Myanmar. There are thought to be 12 breeding turtles in the wild. Conservation efforts for the species have raised >700 captive turtles since 2002, predominantly from eggs collected in the wild. We collected tissue samples from 445 individuals (approximately 40% of the turtles' remaining global population), applied double-digest restriction-site associated DNA sequencing (ddRAD-Seq), and obtained approximately 1500 unlinked genome-wide single nucleotide polymorphisms. Individuals fell into 5 distinct genetic clusters, 4 of which represented full-sib families. We inferred a low effective population size (≤10 individuals) but did not detect signs of severe inbreeding, possibly because the population bottleneck occurred recently. Two groups of 30 individuals from the captive pool that were the most genetically diverse were reintroduced to the wild, leading to an increase in the number of fertile eggs (n = 27) in the wild. Another 25 individuals, selected based on the same criteria, were transferred to the Singapore Zoo as an assurance colony. Our study demonstrates that the research-to-application gap in conservation can be bridged through application of cutting-edge genomic methods.

Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes.

Single-strain outbreaks of Streptococcus pyogenes infections are common and often go undetected. In 2013, two clusters of invasive group A Streptococcus (iGAS) infection were identified in independent but closely located care homes in Oxfordshire, United Kingdom. Investigation included visits to each home, chart review, staff survey, microbiologic sampling, and genome sequencing. S. pyogenes emm type 1.0, the most common circulating type nationally, was identified from all cases yielding GAS isolates. A tailored whole-genome reference population comprising epidemiologically relevant contemporaneous isolates and published isolates was assembled. Data were analyzed independently using whole-genome multilocus sequencing and single-nucleotide polymorphism analyses. Six isolates from staff and residents of the homes formed a single cluster that was separated from the reference population by both analytical approaches. No further cases occurred after mass chemoprophylaxis and enhanced infection control. Our findings demonstrate the ability of 2 independent analytical approaches to enable robust conclusions from nonstandardized whole-genome analysis to support public health practice.

Fauna Associated with American Alligator (Alligator mississippiensis) Nests in Coastal South Carolina, USA.

Crocodilians are considered to be "ecosystem engineers" because their modification of habitats provides opportunities for feeding, drinking, breeding, and other vital life activities to a wide variety of other animals. One such habitat modification is the construction of nest mounds during the breeding season by most crocodilian species, including American alligators (Alligator mississippiensis). While many reports exist describing wildlife associated with alligator nests, no studies have quantified faunal associates and their corresponding behaviors while visiting nests. To address this data gap, we used automated game cameras to monitor wildlife and their behaviors at alligator nests during the egg incubation period (June-September) in coastal South Carolina, USA (2016-2021). We documented a total of 81 species (79 vertebrates and 2 invertebrates) at 78 alligator nests representing six taxonomic groups, including 48 birds (59.2%), 9 mammals (11.1%), 19 reptiles (23.4%), 3 amphibians (3.7%), 1 malacostracan (1.2%), and 1 insect (1.2%). Collectively, faunal associates primarily used alligator nests for feeding/foraging (51.8%), traveling (29.3%), and loafing (19.9%) and to a much lesser extent basking, burrowing/shelter, breeding, and nesting. However, trends in alligator nest use varied among faunal associate groups (birds, mammals, reptiles, amphibians, etc.), subgroups (e.g., passerines, raptors, wading birds, and waterfowl), and species. Several novel behaviors by some nest associates were also noted during the study, including the first observations of Virginia oppossum (Didelphis virginiana) opening and predating nests, bobcat (Lynx rufus) consuming alligator hatchlings, and Carolina wren (Thryothorus ludovicianus) feeding on the contents of a recently predated alligator egg. The results of this study indicate that a diverse assemblage of vertebrates (and some invertebrates) use alligator nest sites in coastal South Carolina for a variety of life activities during the egg incubation period, and the proportion of the behaviors exhibited varies among animal groups and species. This study provides a first step for investigations regarding the net impacts of alligator nest-faunal associate interactions and ultimately the greater ecological role of alligators and other crocodilians.

Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis.

Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.

Biodiversity conservation in a changing climate: a review of threats and implications for conservation planning in Myanmar.

High levels of species richness and endemism make Myanmar a regional priority for conservation. However, decades of economic and political sanctions have resulted in low conservation investment to effectively tackle threats to biodiversity. Recent sweeping political reforms have placed Myanmar on the fast track to economic development-the expectation is increased economic investments focused on the exploitation of the country's rich, and relatively intact, natural resources. Within a context of weak regulatory capacity and inadequate environmental safeguards, rapid economic development is likely to have far-reaching negative implications for already threatened biodiversity and natural-resource-dependent human communities. Climate change will further exacerbate prevailing threats given Myanmar's high exposure and vulnerability. The aim of this review is to examine the implications of increased economic growth and a changing climate within the larger context of biodiversity conservation in Myanmar. We summarize conservation challenges, assess direct climatological impacts on biodiversity and conclude with recommendations for long-term adaptation approaches for biodiversity conservation.

Nesting phenology and clutch characteristics of captive Siamese crocodiles (Crocodylus siamensis) in Cambodia.

The Siamese crocodile (Crocodylus siamensis) is considered one of the least studied and most critically endangered crocodilians in the world. Although few wild populations remain, more than 700,000 C. siamensis are held on commercial crocodile farms in Southeast Asia. Despite conservation concerns, many aspects of C. siamensis life history remain poorly known, particularly with regards to its reproductive biology. We studied nesting phenology, clutch characteristics, and other aspects of C. siamensis reproductive biology on crocodile farms in Cambodia during 2000 and 2001. Oviposition among captive crocodiles began in February and continued into early June. The mean (±1 SD) oviposition date based on pooled data from 2000 and 2001 was 5 April ± 24 days. Mean oviposition date differed significantly between 2000 and 2001, possibly as a result of annual variability among nesting cues. The mean incubation period was 72 ± 3 days and eggs hatched from 5 May to 18 August. Mean clutch size (25.0 ± 8.8 eggs; n = 183) differed significantly between years, possibly resulting from the >2.5-fold increase in sample size during 2001. There was no correlation between clutch size and oviposition date during either 2000 or 2001. A single female produced two clutches during 2001, complimenting previous reports of double-clutching among C. siamensis. The mean length and width of 515 eggs were 78.2 ± 4.9 and 48.1 ± 2.5 mm, respectively; mean egg mass was 90.8 ± 16.5 g (n = 471). One unpipped egg contained a set of twins.

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission.

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16-20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement.

Risk of symptomatic COVID-19 due to aircraft transmission: a retrospective cohort study of contact-traced flights during England's containment phase.

BACKGROUND: Knowledge gaps remain regarding SARS-CoV-2 transmission on flights. We conducted a retrospective cohort study to estimate risk of acquiring symptomatic SARS-CoV-2 on aircraft, to inform contact tracing and infection control efforts. METHODS: We identified co-passengers of infectious passengers on 18 England-bound flights from European cities up to 12/03/2020, using manifests received for contact tracing. Infectious passengers were laboratory-confirmed cases with symptom onset from 7 days before to 2 days after the flight. Possible aircraft-acquired cases were laboratory-confirmed with onset 3-14 days post-flight with no known non-flight exposure. Manifests was merged with the national case management dataset (identifying cases, onset dates, contact tracing status) and the national COVID-19 linelist. Contact tracing notes were reviewed to identify non-flight exposures. We calculated attack rates (ARs) among all co-passengers and within subgroups, including by distance from infectious cases and number of infectious cases on-board. RESULTS: There were 55 infectious passengers and 2313 co-passengers, including 2221 flight-only contacts. Five possible aircraft-acquired cases were identified; ARs of 0.2% (95%CI 0.1-0.5) among all flight-only contacts and 3.8% (95%CI 1.3-10.6) among contact-traced flight-only contacts sat within a two-seat radius. The AR among 92 co-travellers with known non-flight exposure to infectious cases was 13.0% (95%CI 7.6%-21.4%). There were insufficient numbers to assess differences between subgroups. CONCLUSION: We conclude that risk of symptomatic COVID-19 due to transmission on short to medium-haul flights is low, and recommend prioritising contact-tracing of close contacts and co-travellers where resources are limited. Further research on risk on aircraft is encouraged.

First description of neonate Batagur trivittata (Testudines: Geoemydidae).

The Burmese Roofed Turtle (Batagur trivittata Duméril Bibron, 1835) is a large (straight-line carapace length [CL] to 620 mm; Platt et al., 2019), aquatic, herbivorous turtle endemic to the major river systems of Myanmar (Smith 1931; TTWG 2017). Although historically widespread and apparently abundant, long-term population declines resulted from chronic egg collecting, subsistence harvesting of adults, and loss of critical nesting habitat (Platt et al. 2017a). By the late 1990s B. trivittata was considered a candidate for Extinct status (Bhupathy et al. 2000) until a living specimen purchased in a Chinese wildlife market came into the possession of an American turtle collector in the early 2000s (Platt et al. 2005; W.P. McCord, pers. comm.). Shortly thereafter, field surveys "rediscovered" two remnant populations in the Dokhtawady and upper Chindwin Rivers (Platt et al. 2005; Kuchling et al. 2006). Intense ex- and in-situ recovery efforts were launched shortly thereafter and continue today (Kuchling Tint Lwin 2004; Çilingir et al. 2017).

The ecological importance of crocodylians: towards evidence-based justification for their conservation.

Large-bodied predators are well represented among the world's threatened and endangered species. A significant body of literature shows that in terrestrial and marine ecosystems large predators can play important roles in ecosystem structure and functioning. By contrast, the ecological roles and importance of large predators within freshwater ecosystems are poorly understood, constraining the design and implementation of optimal conservation strategies for freshwater ecosystems. Conservationists and environmentalists frequently promulgate ecological roles that crocodylians are assumed to fulfil, but often with limited evidence supporting those claims. Here, we review the available information on the ecological importance of crocodylians, a widely distributed group of predominantly freshwater-dwelling, large-bodied predators. We synthesise information regarding the role of crocodylians under five criteria within the context of modern ecological concepts: as indicators of ecological health, as ecosystem engineers, apex predators, keystone species, and as contributors to nutrient and energy translocation across ecosystems. Some crocodylians play a role as indicators of ecosystem health, but this is largely untested across the order Crocodylia. By contrast, the role of crocodylian activities in ecosystem engineering is largely anecdotal, and information supporting their assumed role as apex predators is currently limited to only a few species. Whether crocodylians contribute significantly to nutrient and energy translocation through cross-ecosystem movements is unknown. We conclude that most claims regarding the importance of crocodylians as apex predators, keystone species, ecosystem engineers, and as contributors to nutrient and energy translocation across ecosystems are mostly unsubstantiated speculation, drawn from anecdotal observations made during research carried out primarily for other purposes. There is a paucity of biological research targeted directly at: understanding population dynamics; trophic interactions within their ecological communities; and quantifying the short- and long-term ecological impacts of crocodylian population declines, extirpations, and recoveries. Conservation practices ideally need evidence-based planning, decision making and justification. Addressing the knowledge gaps identified here will be important for achieving effective conservation of crocodylians.

Turtles and Tortoises Are in Trouble.

Turtles and tortoises (chelonians) have been integral components of global ecosystems for about 220 million years and have played important roles in human culture for at least 400,000 years. The chelonian shell is a remarkable evolutionary adaptation, facilitating success in terrestrial, freshwater and marine ecosystems. Today, more than half of the 360 living species and 482 total taxa (species and subspecies combined) are threatened with extinction. This places chelonians among the groups with the highest extinction risk of any sizeable vertebrate group. Turtle populations are declining rapidly due to habitat loss, consumption by humans for food and traditional medicines and collection for the international pet trade. Many taxa could become extinct in this century. Here, we examine survival threats to turtles and tortoises and discuss the interventions that will be needed to prevent widespread extinction in this group in coming decades.

Assessment of organochlorine pesticides and metals in ring-tailed lemurs (Lemur catta) at Beza Mahafaly Special Reserve, Madagascar.

Like most of Madagascar's endemic primates, ring-tailed lemurs (Lemur catta) face a number of threats to their survival. Although habitat loss is of greatest concern, other anthropogenic factors including environmental contamination may also affect lemur health and survival. In this study, we examined ring-tailed lemurs from the Beza Mahafaly Special Reserve (BMSR), southern Madagascar for exposure to organochlorine (OC) pesticides and metals and examined differences in contaminant concentrations between sexes and among age groups, troops, and habitats. A total of 14 pesticides and 13 metals was detected in lemur blood (24 individuals) and hair (65 individuals) samples, respectively. p,p'-DDT, heptachlor, aldrin, heptachlor epoxide, endrin aldehyde, and endrin were among the most prevalent pesticides detected. Surprisingly, the persistent metabolite of p,p'-DDT, p,p'-DDE, was not detected. The most commonly detected metals were aluminum, zinc, boron, phosphorus, silicon, and copper, whereas metals considered more hazardous to wildlife (e.g. arsenic, cadmium, lead, selenium, vanadium) were not found above detection limits. Overall, concentrations of OC pesticides and metals were low and similar to those considered to be background concentrations in other studies examining the ecotoxicology of wild mammals. Few inter-sex, -age, -troop, and -habitat differences in contaminant concentrations were observed, suggesting a uniform distribution of contaminants within the reserve. Several statistically significant relationships between lemur body size and contaminant concentrations were observed, but owing to the lack of supportive data regarding contaminant exposure in wild primates, the biological significance of these findings remains uncertain. Results of this study document exposure of ring-tailed lemurs at BMSR to multiple OC pesticides and metals and provide essential baseline data for future health and toxicological evaluations of lemurs and other wild primates, especially those in regions with expanding agricultural and mining operations.

Correlation between increased postpubertal phallic growth and the initiation of cranial sexual dimorphisms in male Morelet's crocodile.

While puberty is an animal commonality, little is known of its timing or process in crocodylians. Males copulate with an intromittent phallus that has a distinct glans morphology which directly interacts with the female cloaca, putatively effecting effective semen transfer and ultimately increased fecundity. Here we present, during the Morelet's crocodile lifecycle, a well-defined body length (65 cm snout-vent length) inflection point that marks a subsequent increase of phallic glans growth rates. Putatively, this postpubescent growth produces a copulatory-effective phallus. While not as robust of a trend as snout-vent length, this growth inflection concomitantly begins with a body condition index (CI = BM/SVL3 ) between 2.0 and 2.5 and is most distinct above a CI of 2.5. Also, in males, this 65 cm size threshold also aligns with the initiation of more robust growth in caniniform alveoli associated with prominent maxillary and mandibular teeth. This inflection was not observed in females, thus marking a sexual dimorphism that begins to present with the onset of puberty. This bodily manifestation of puberty other than those changes observed in the reproductive tracts is a novel observation for crocodylians and lays a foundation for further study among species of how changing endocrine signaling within sexually maturing males may also influence a broader range of secondary sex characteristics.

Plasma vitellogenin in Morelet's crocodiles from contaminated habitats in northern Belize.

Vitellogenin induction has been widely used as a biomarker of endocrine disruption in wildlife, but few studies have investigated its use in wild reptiles living in contaminated habitats. This study examined vitellogenin induction in Morelet's crocodiles (Crocodylus moreletii) from wetlands in northern Belize contaminated with organochlorine (OC) pesticides. Vitellogenin was measured in 381 crocodile plasma samples using a vitellogenin ELISA previously developed for this species. Vitellogenin was detected in nine samples, all from adult females sampled during the breeding season. Males and juvenile females did not contain detectable levels of vitellogenin; however, many of these animals contained OC pesticides in their caudal scutes, confirming contaminant exposure. The lack of a vitellogenic response in these animals may be attributable to several factors related to the timing and magnitude of exposure to endocrine-disrupting chemicals and should not be interpreted as an absence of other contaminant-induced biological responses.

New Species of Falcaustra (Nematoda: Kathlaniidae) in Batagur trivittata (Testudines: Geoemydidae) from Myanmar.

Falcaustra tintlwini sp. nov. (Ascaridida, Kathlaniidae) from the large intestine of Batagur trivittata (Testudines, Geoemydidae) is described and illustrated. Falcaustra tintlwini represents the 20th Oriental species assigned to the genus and is distinguished from other Oriental species by the distribution pattern of the caudal papillae (6 precloacal, 12 postcloacal, and 1 median), length of spicules (0.43-0.50 mm) and absence of a pseudosucker.

Mercury bioaccumulation in bats reflects dietary connectivity to aquatic food webs.

Mercury (Hg) is a persistent and widespread heavy metal with neurotoxic effects in wildlife. While bioaccumulation of Hg has historically been studied in aquatic food webs, terrestrial consumers can become contaminated with Hg when they feed on aquatic organisms (e.g., emergent aquatic insects, fish, and amphibians). However, the extent to which dietary connectivity to aquatic ecosystems can explain patterns of Hg bioaccumulation in terrestrial consumers has not been well studied. Bats (Order: Chiroptera) can serve as a model system for illuminating the trophic transfer of Hg given their high dietary diversity and foraging links to both aquatic and terrestrial food webs. Here we quantitatively characterize the dietary correlates of long-term exposure to Hg across a diverse local assemblage of bats in Belize and more globally across bat species from around the world with a comparative analysis of hair samples. Our data demonstrate considerable interspecific variation in hair total Hg concentrations in bats that span three orders of magnitude across species, ranging from 0.04 mg/kg in frugivorous bats (Artibeus spp.) to 145.27 mg/kg in the piscivorous Noctilio leporinus. Hg concentrations showed strong phylogenetic signal and were best explained by dietary connectivity of bat species to aquatic food webs. Our results highlight that phylogeny can be predictive of Hg concentrations through similarity in diet and how interspecific variation in feeding strategies influences chronic exposure to Hg and enables movement of contaminants from aquatic to terrestrial ecosystems.

Metals and organochlorine pesticides in caudal scutes of crocodiles from Belize and Costa Rica.

Despite high animal diversity in the Neotropics and the largely unregulated use and disposal of pesticides and industrial chemicals in Central America, few data exist regarding accumulation of environmental contaminants in Central American wildlife. In this study we examined accumulation of metals and organochlorine (OC) pesticides in caudal scutes of crocodiles from Belize and Costa Rica. Scutes from Morelet's crocodiles (Crocodylus moreletii) from two sites in northern Belize were analyzed for metals, and scutes from American crocodiles (C. acutus) from one site in Costa Rica were analyzed for metals and OC pesticides. All scutes (n=25; one scute from each of 25 individuals) contained multiple contaminants. Mercury was the predominant metal detected, occurring in all scutes examined from both species. Other metals detected include cadmium, copper, lead, and zinc. American crocodile scutes from Costa Rica contained multiple OC pesticides, including endrin, methoxychlor, p,p'-DDE, and p,p'-DDT, all of which occurred in 100% of scutes analyzed (n=6). Mean metal and OC concentrations varied in relation to those previously reported in crocodilian scutes from other localities in North, Central, and South America. OC concentrations in American crocodile scutes were generally higher than those previously reported for other Costa Rican wildlife. Currently, caudal scutes may serve as general, non-lethal indicators of contaminant accumulation in crocodilians and their areas of occurrence. However, a better understanding of the relationships between pollutant concentrations in scutes, internal tissues, and environmental matrices at sample collection sites are needed to improve the utility of scutes in future ecotoxicological investigations.