SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark.

Severe acute respiratory syndrome coronavirus 2 has caused a pandemic in humans. Farmed mink (Neovison vison) are also susceptible. In Denmark, this virus has spread rapidly among farmed mink, resulting in some respiratory disease. Full-length virus genome sequencing revealed novel virus variants in mink. These variants subsequently appeared within the local human community.

The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial.

The occasional westward transport of warm water of the Agulhas Current, "Agulhas leakage", around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic and Indian oceans, but the "Agulhas leakage" hypothesis does not explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The "warm-water corridor" hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported a model where Southwest Indian Ocean and Caribbean populations diverged from the East Atlantic population during the transition from the last interglacial period (130-115 thousand years ago; kya) to the last glacial period (115-90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials.

Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles.

BACKGROUND: Fibropapillomatosis (FP) is a neoplastic disease characterized by cutaneous tumours that has been documented to infect all sea turtle species. Chelonid fibropapilloma-associated herpesvirus (CFPHV) is believed to be the aetiological agent of FP, based principally on consistent PCR-based detection of herpesvirus DNA sequences from FP tumours. We used a recently described PCR-based assay that targets 3 conserved CFPHV genes, to survey 208 green turtles (Chelonia mydas). This included both FP tumour exhibiting and clinically healthy individuals. An additional 129 globally distributed clinically healthy individual sea turtles; representing four other species were also screened. RESULTS: CFPHV DNA sequences were obtained from 37/37 (100%) FP exhibiting green turtles, and 45/300 (15%) clinically healthy animals spanning all five species. Although the frequency of infected individuals per turtle population varied considerably, most global populations contained at least one CFPHV positive individual, with the exception of various turtle species from the Arabian Gulf, Northern Indian Ocean and Puerto Rico. Haplotype analysis of the different gene markers clustered the CFPHV DNA sequences for two of the markers (UL18 and UL22) in turtles from Turks and Caicos separate to all others, regardless of host species or geographic origin. CONCLUSION: Presence of CFPHV DNA within globally distributed samples for all five species of sea turtle was confirmed. While 100% of the FP exhibiting green turtles yielded CFPHV sequences, surprisingly, so did 15% of the clinically healthy turtles. We hypothesize that turtle populations with zero (0%) CFPHV frequency may be attributed to possible environmental differences, diet and/or genetic resistance in these individuals. Our results provide first data on the prevalence of CFPHV among seemingly healthy turtles; a factor that may not be directly correlated to the disease incidence, but may suggest of a long-term co-evolutionary latent infection interaction between CFPHV and its turtle-host across species. Finally, computational analysis of amino acid variants within the Turks and Caicos samples suggest potential functional importance in a substitution for marker UL18 that encodes the major capsid protein gene, which potentially could explain differences in pathogenicity. Nevertheless, such a theory remains to be validated by further research.

Epidemiology of marine turtle fibropapillomatosis and tumour-associated chelonid alphaherpesvirus 5 (ChHV5; Scutavirus chelonidalpha5) in North-Western Mexico: a scoping review implementing the one health approach.

Fibropapillomatosis (FP) - tumour-associated chelonid alphaherpesvirus 5 (ChHV5; Scutavirus chelonidalpha5) - is a disease that affect marine turtles around the world, and characterized by the formation of cutaneous tumours that can appear anywhere on the body. We carried out a thorough literature search (from 1990 to 2024) in the feeding sites of North-western Mexico, a region that hosts important habitats for feeding, development, and reproduction for five of the seven existing sea turtle species. We found 18 reports recording a total of 32 cases of FP and/or ChHV5/Scutavirus chelonidalpha5 in coastal and insular areas of North-western Mexico. Baja California Sur resulted with the highest number of cases (75%). While the first case of ChHV5/Scutavirus chelonidalpha5 infection was reported in 2004, the presence of FP tumours was reported in 2014 and became more frequent between 2019 and 2024. The affected species were black, Chelonia mydas (50%), olive ridley, Lepidochelys olivacea (46.8%) and loggerhead turtles, Caretta caretta (3.2%). Tumours occurred mainly in anterior flippers (46.1%) and neck (22.5%), and most had a nodular and verrucous appearance with a rough surface. In the study region, there is a potential sign of the emergence of the ChHV5/Scutavirus chelonidalpha5 infections and FP disease during the last 20 years, with a rapid increase during the last 10 years. As long as infections by ChHV5/Scutavirus chelonidalpha5 and the prevalence of the FP disease may be potentially influenced by anthropogenic activities, a One Health approach is needed to understand and improve sea turtles' health.

Macro and microplastic intake in seafood variates by the marine organism's feeding behaviour: Is it a concern to human health?

Seafood is considered one of the healthiest sources of food intake for humans, mainly because of its high protein content. However, oceans are among the most polluted environments, and microplastics have been widely reported to be ingested, absorbed or bioaccumulated by marine organisms. The different feeding behaviour may contribute to infer the amounts of microplastic particles accidently intake by marine organisms. We investigated the putative levels of microplastics in different edible species of fish, molluscs, and crustaceans. Plastic fragments larger than 200 µm were detected in the digestive tract of 277 out of 390 specimens (71.5 ± 22.2%) of the 26 different species analysed. There was no evidence of microplastic translocation or bioaccumulation in the muscle tissue of fish, molluscs, and crustaceans. Organisms with carnivorous feeding habits had the highest prevalence of plastic ingestion (79 ± 9.4%), followed by planktivorous species (74 ± 15.5%), and detritivorous species (38 ± 36.9%), suggesting a transfer through the food chain. Moreover, we found evidence that species with less selective feeding habits may be the most affected by the ingestion of large microplastic particles. Our results provide further evidence to the ubiquitous presence of microplastics in marine organisms representing a direct threat to marine wildlife, and to human health with potential consequences for future generations according to the One Health initiatives approach.

Feasibility of aquaculture cultivation of elkhorn sea moss (Kappaphycus alvarezii) in a horizontal long line in the Tropical Eastern Pacific.

Seaweed aquaculture has become a profitable and an attractive alternative of cultivation thanks to its quick biomass production for food, feed, and other non-food applications. In addition, the ecosystem services generated by seaweed cultivation towards carbon fixation represents a more sustainable solution to the ocean's acidification. The growth of elkhorn sea moss (Kappaphycus alvarezii) was evaluated in three plots with 200 propagules during a period of 70 days in a floating raft system covered by a fishing net underneath. Initial weight of propagules was 159.3 ± 12.74 g in wet biomass and 15.3 ± 1.43 g in dry biomass and were sampled up to 19 days (in the lag growth phase; period I), up to 33 days (in the exponential growth phase; period II) and up to 70 days (in the stationarity growth phase; period III). The variations of sea surface water temperature, salinity, turbidity (Secchi depth), total ammonium, nitrites, nitrates, and phosphate were determined. The growth increase was more evident in the exponential phase II when a dry biomass of 28.0 ± 2.48 (1153.3 ± 6.25 g in wet mass) was reached, more than 7 times the biomass of propagules with an average daily growth rate of 15.2% g.day-1. The carrying capacity of the zone was estimated at 86.2% in the area where 53 cultivation units would be projected. The economic analysis presented a financial feasibility with a net profit of 19% over the projected income and an IRR of 16.5%, recovering the investment in an estimated period of 4.3 years. We recommend to continue with larger-scale studies to optimize the cultivation of K. alvarezii in the study area.

Rapid and Flexible RT-qPCR Surveillance Platforms To Detect SARS-CoV-2 Mutations.

Multiple mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) increase transmission, disease severity, and immune evasion and facilitate zoonotic or anthropozoonotic infections. Four such mutations, ΔH69/V70, L452R, E484K, and N501Y, occurred in the SARS-CoV-2 spike glycoprotein in combinations that allow the simultaneous detection of VOCs. Here, we present two flexible reverse transcription-quantitative PCR (RT-qPCR) platforms for small- and large-scale screening (also known as variant PCR) to detect these mutations and schemes for adapting the platforms to future mutations. The large-scale RT-qPCR platform was validated by pairwise matching of RT-qPCR results with whole-genome sequencing (WGS) consensus genomes, showing high specificity and sensitivity. Both platforms are valuable examples of complementing WGS to support the rapid detection of VOCs. Our mutational signature approach served as an important intervention measure for the Danish public health system to detect and delay the emergence of new VOCs. IMPORTANCE Denmark weathered the SARS-CoV-2 crisis with relatively low rates of infection and death. Intensive testing strategies with the aim of detecting SARS-CoV-2 in symptomatic and nonsymptomatic individuals were available by establishing a national test system called TestCenter Denmark. This testing regime included the detection of SARS-CoV-2 signature mutations, with referral to the national health system, thereby delaying outbreaks of variants of concern. Our study describes the design of the large-scale RT-qPCR platform established at TestCenter Denmark in conjunction with whole-genome sequencing to report mutations of concern to the national health system. Validation of the large-scale RT-qPCR platform using paired WGS consensus genomes showed high sensitivity and specificity. For smaller laboratories with limited infrastructure, we developed a flexible small-scale RT-qPCR platform to detect three signature mutations in a single run. The RT-qPCR platforms are important tools to support the control of the SARS-CoV-2 endemic in Denmark.

Phylogenetic analysis reveals that the H5N1 avian influenza A outbreak in poultry in Ecuador in November 2022 is associated with the highly pathogenic clade 2.3.4.4b.

The ongoing H5N1 outbreak in the Americas caused by clade 2.3.4.4 is causing unprecedented impact in poultry and wild birds. In November 2022, a highly pathogenic avian influenza A outbreak was declared in poultry in Ecuador, affecting more than 1.1 million heads of poultry in two farms by February 2023. Phylogenetic analysis shows that the virus clade is 2.3.4.4b, and to the best of our knowledge, this is the first scientific publication reporting this clade in South America.

Marine turtle mitogenome phylogenetics and evolution.

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.

Deceiving scientific research, misconduct events are possibly a more common practice than foreseen.

Background: Today, scientists and academic researchers experience an enormous pressure to publish innovative and ground-breaking results in prestigious journals. This pressure may blight the general view concept of how scientific research needs to be done in terms of the general rules of transparency; duplication of data, and co-authorship rights might be compromised. As such, misconduct acts may occur more frequently than foreseen, as frequently these experiences are not openly shared or discussed among researchers. Main body: While there are some concerns about the health and the transparency implications of such normalised pressure practices imposed on researchers in scientific research, there is a general acceptance that researchers must take and accept it in order to survive in the competitive world of science. This is even more the case for junior and mid-senior researchers who have recently started their adventure into the universe of independent researchers. Only the slightest fraction manages to endure, after many years of furious and cruel rivalry, to obtain a long-term, and even less probable, permanent position. There is an evil circle; excellent records of good publications are needed in order to obtain research funding, but how to produce pioneering research during these first years without funding? Many may argue this is a necessary process to ensure good quality scientific investigation, possibly, but perseverance and resilience may not be the only values needed when rejection is received consecutively for years. Conclusion: There is a general culture that scientists rarely share previous bad experiences, in particular if they were associated to misconduct, as they may not be seen or considered as a relevant or hot topic to the scientific community readers. On next, a recent misconduct experience is shared, and a few additional reflections and suggestions on this topic were drafted in the hope other researchers might be spared unnecessary and unpleasant times.

Threats and Vulnerabilities for the Globally Distributed Olive Ridley (Lepidochelys olivacea) Sea Turtle: A Historical and Current Status Evaluation.

The olive ridley (Lepidochelys olivacea) is the most abundant of all seven sea turtles, found across the tropical regions of the Atlantic, Pacific, and Indian Oceans in over 80 different countries all around the globe. Despite being the most common and widely distributed sea turtle, olive ridley populations have been declining substantially for decades. Worldwide, olive ridleys have experienced a 30-50% decline, putting their populations at risk and being considered an Endangered Species by the IUCN. Natural habitat degradation, pollution, bycatch, climate change, predation by humans and animals, infectious diseases and illegal trade are the most notorious threats to explain olive ridley populations rapidly decline. The present review assesses the numerous dangers that the olive ridley turtle has historically faced and currently faces. To preserve olive ridleys, stronger conservation initiatives and strategies must continue to be undertaken. Policies and law enforcement for the protection of natural environments and reduction in the effects of climate change should be implemented worldwide to protect this turtle species.

A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern.

Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.

SARS-CoV-2 RNA stability in dry swabs for longer storage and transport at different temperatures.

During the current COVID-19 pandemic, different methods have been used to evaluate patients with suspected SARS-CoV-2 infection. In this study, we experimentally evaluate the ability of spiked saliva-moist swabs and spiked swabs without any transport medium to retain SARS-CoV-2 for storage and transport at different environmental settings during different incubation time periods. Our results show that at ambient temperature of 20°C, SARS-CoV-2 RNA remains stable for up to 9 days allowing a long-time span for transport and storage without compromising clinical results. Additionally, this study demonstrates that saliva-moist swabs can also be stored at -20°C and +4°C for up to 26 days without affecting RT-qPCR results. Our data are relevant for low-and middle-income countries, which have limited access to rapid refrigerated transport and storage of samples representing an economical alternative. Finally, our study demonstrates the practical and economic advantage of using swabs without transport medium.

The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae).

Cockatoos are the distinctive family Cacatuidae, a major lineage of the order of parrots (Psittaciformes) and distributed throughout the Australasian region of the world. However, the evolutionary history of cockatoos is not well understood. We investigated the phylogeny of cockatoos based on three mitochondrial and three nuclear DNA genes obtained from 16 of 21 species of Cacatuidae. In addition, five novel mitochondrial genomes were used to estimate time of divergence and our estimates indicate Cacatuidae diverged from Psittacidae approximately 40.7 million years ago (95% CI 51.6-30.3 Ma) during the Eocene. Our data shows Cacatuidae began to diversify approximately 27.9 Ma (95% CI 38.1-18.3 Ma) during the Oligocene. The early to middle Miocene (20-10 Ma) was a significant period in the evolution of modern Australian environments and vegetation, in which a transformation from mainly mesic to xeric habitats (e.g., fire-adapted sclerophyll vegetation and grasslands) occurred. We hypothesize that this environmental transformation was a driving force behind the diversification of cockatoos. A detailed multi-locus molecular phylogeny enabled us to resolve the phylogenetic placements of the Palm Cockatoo (Probosciger aterrimus), Galah (Eolophus roseicapillus), Gang-gang Cockatoo (Callocephalon fimbriatum) and Cockatiel (Nymphicus hollandicus), which have historically been difficult to place within Cacatuidae. When the molecular evidence is analysed in concert with morphology, it is clear that many of the cockatoo species' diagnostic phenotypic traits such as plumage colour, body size, wing shape and bill morphology have evolved in parallel or convergently across lineages.

Microplastic pollution in seawater and marine organisms across the Tropical Eastern Pacific and Galápagos.

Detection of plastic debris degrading into micro particles across all oceanic environments and inside of marine organisms is no longer surprising news. Microplastic contamination now appears as one of the world's environmental main concerns. To determine the levels of microplastic pollution at sea, water samples were collected across a 4000 km-trajectory in the Tropical Eastern Pacific and the Galápagos archipelago, covering an area of 453,000 square kilometres. Furthermore, 240 specimens of 16 different species of fish, squid, and shrimp, all of human consumption, were collected along the continental coast. Microplastic particles were found in 100% of the water samples and marine organisms. Microplastic particles ranging from 150 to 500 µm in size were the most predominant. This is one of the first reports simultaneously detecting and quantifying microplastic particles abundance and their impact on marine organisms of this region.

In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms.

In addition to humans, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit to animals that include hamsters, cats, dogs, mink, ferrets, tigers, lions, cynomolgus macaques, rhesus macaques, and treeshrew. Among these, mink are particularly susceptible. Indeed, 10 countries in Europe and North America reported SARS-CoV-2 infection among mink on fur farms. In Denmark, SARS-CoV-2 spread rapidly among mink farms and spilled-over back into humans, acquiring mutations/deletions with unknown consequences for virulence and antigenicity. Here we describe a mink-associated SARS-CoV-2 variant (Cluster 5) characterized by 11 amino acid substitutions and four amino acid deletions relative to Wuhan-Hu-1. Temporal virus titration, together with genomic and subgenomic viral RNA quantitation, demonstrated a modest in vitro fitness attenuation of the Cluster 5 virus in the Vero-E6 cell line. Potential alterations in antigenicity conferred by amino acid changes in the spike protein that include three substitutions (Y453F, I692V, and M1229I) and a loss of two amino acid residues 69 and 70 (ΔH69/V70), were evaluated in a virus microneutralization assay. Compared to a reference strain, the Cluster 5 variant showed reduced neutralization in a proportion of convalescent human COVID-19 samples. The findings underscore the need for active surveillance SARS-CoV-2 infection and virus evolution in susceptible animal hosts.

Genetic Analysis of Chelonid Herpesvirus 5 in Marine Turtles from Baja California Peninsula.

The Chelonid herpesvirus 5 (ChHV5) is the primary etiological agent associated with fibropapillomatosis (FP), a neoplastic disease in marine turtles. In this study, we report for the first time ChHV5 in marine turtles and a leech from Baja California Peninsula. Eighty-seven black, olive or loggerhead turtle species, one FP tumor and five leeches were analyzed. The tumor sample from an olive, a skin sample from a black and a leech resulted positive of ChHV5 for conventional PCR. Two viral variants were identified and grouped within the Eastern Pacific phylogenetic group, suggesting a possible flow of the virus in this region.

Fibropapillomatosis in a Green Sea Turtle ( Chelonia mydas) from the Southeastern Pacific.

Fibropapillomatosis is a neoplastic disease that afflicts sea turtles. Although it is disseminated worldwide, cases of the disease have not been reported in the southeastern Pacific region. We describe a case of fibropapillomatosis in a green sea turtle ( Chelonia mydas) during its rehabilitation at the Machalilla National Park Rehabilitation Center, Ecuador. Viral presence was confirmed by PCR, targeting fragments of the chelonid alphaherpesvirus 5 (ChHV5) unique long (UL) genes, UL27, UL28, and UL30. The amplicons were sequenced and included in a global phylogenetic analysis of the virus with other reported sequences from GenBank. Results showed that the available viral sequences segregated into five phylogeographic groups: western Atlantic and eastern Caribbean, central Pacific, western Pacific, Atlantic, and eastern Pacific groups. The concatenated ChHV5 sequences from Ecuador clustered with the eastern Pacific sequences.