Article
Marine & Freshwater Biology
Iraj Hashemzadeh Segherloo, Seyedeh Narjes Tabatabaei, Asghar Abdoli, Joerg Freyhof, Eric Normandeau, Boris Levin, Matthias F. Geiger, Martin Laporte, Eric Hallerman, Louis Bernatchez
Summary: This study investigated the eastern-most members of the Salmo trutta species complex in the Aralo-Caspian Sea region. The genetic analysis revealed differences between the trout populations in the southern Caspian Sea and those in the western and northern Caspian Sea. Six conservation/management units for the trouts were proposed based on the findings.
Article
Environmental Sciences
Tammy Iwasa-Arai, Silvana G. L. Siqueira, Juliana L. Segadilha, Fosca P. P. Leite
Summary: This study conducted the first survey on the biodiversity of Peracarida from Trindade Island in Brazil, revealing new species and suggesting an Indo-Pacific origin for the genus based on phylogenetic and biogeographical analyses. A comparison with the closest Abrolhos Archipelago showed a high percentage of endemic species on Trindade Island.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Parasitology
Caitlin A. O'Brien, Bixing Huang, David Warrilow, Jessamine E. Hazlewood, Helle Bielefeldt-Ohmann, Sonja Hall-Mendelin, Cassandra L. Pegg, Jessica J. Harrison, Devina Paramitha, Natalee D. Newton, Benjamin L. Schulz, Andreas Suhrbier, Jody Hobson-Peters, Roy A. Hall
Summary: A subset of Australians bitten by ticks experience chronic and debilitating symptoms that cannot be explained by known pathogenic bacteria. In an effort to understand these symptoms, researchers in Australia are identifying and characterising viruses in ticks. This study successfully characterises five tick-borne viruses and provides insights into their replication and antigenic profiles.
PARASITES & VECTORS
(2022)
Article
Multidisciplinary Sciences
Yu-Zu Guo, Yi Zhang, Qing Wang, Jun Yu, Qiu-Hong Wan, Jun Huang, Sheng-Guo Fang
Summary: Alligators are suitable for studying anti-aging molecular mechanisms because they have low adult mortality rates and no significant telomere shortening. Selection analyses have shown that certain genes in alligators have undergone positive selection, and ALT-related genes are expressed at higher levels, which may contribute to anti-aging strategies.
Article
Entomology
Beniamin Waclawik, Francesco Nugnes, Umberto Bernardo, Marco Gebiola, Maja Przybycien, Dorota Lachowska-Cierlik
Summary: The study confirmed the taxonomic status and validity of Liophloeodes species, revealing low morphological variation among the species and the presence of bacterial endosymbionts. The phylogenetic analysis based on molecular and morphometric techniques suggested that Liophloeodes consists of young lineages possibly influenced by cyclic climate change events.
ARTHROPOD SYSTEMATICS & PHYLOGENY
(2021)
Article
Plant Sciences
Yu Feng, Hans Peter Comes, Jun Chen, Shanshan Zhu, Ruisen Lu, Xinyi Zhang, Pan Li, Jie Qiu, Kenneth M. Olsen, Yingxiong Qiu
Summary: This study investigates the genomic analysis of two East Asian Tertiary relict trees. It reveals large-scale genome reorganizations and species-specific genes under positive selection. The findings suggest that demographic history plays a significant role in the long-term survival and extinction risk of these Tertiary relict trees.
Article
Zoology
Ko Tomikawa, Yuichiro Nishimoto, Naoyuki Nakahama, Takafumi Nakano
Summary: This study describes a new species of Pseudocrangonyx, Pseudocrangonyx dunan sp. nov., from Yonaguni Island, Ryukyu Islands, Japan. Phylogenetic analyses revealed its sister relationship with Pseudocrangonyx sp. 4 from Honshu Island, Japan. The study also identified three monophyletic groups within the genus Pseudocrangonyx, with the phylogenetic positions of several species still unknown. Divergence dating showed that the differentiation of major lineages of Pseudocrangonyx concentrated around 20 million years ago, and the formation of the Sea of Japan is suggested to have played a major role in promoting the speciation of Pseudocrangonyx endemic to the archipelago.
ZOOLOGICAL SCIENCE
(2022)
Article
Plant Sciences
Satoshi Kikuchi, Makiko Mimura, Naohiro Naruhashi, Suzuki Setsuko, Wajiro Suzuki
Summary: This study used molecular phylogenetic analysis to reveal the evolutionary timescale and processes of diversity in Rubus in the Japanese Archipelago. The results showed that most northern species in Japan belong to early diverged lineages, with R. ikenoensis forming a unique lineage. Other species were divided into two evolutionary groups, one of which was well-supported and the other had unresolved phylogenetic structures.
PLANT SYSTEMATICS AND EVOLUTION
(2022)
Article
Geosciences, Multidisciplinary
M. Botero-Garcia, C. J. Vinasco, S. A. Restrepo-Moreno, D. A. Foster, G. D. Kamenov
Summary: The Northern Andes in Colombia developed along an active, convergent margin with a complex subduction-accretion/collision history since Triassic times. Two sedimentary sequences, the Late Cretaceous-Paleocene siliciclastic member of the Penderisco Formation and the Miocene Beibaviejo Formation, were analyzed in this study. The results provide insights into the evolution of volcaniclastic sequences at the northwestern margin of South America and constrain the timing of collision between the Panama-Choc 'o Block and the Andean margin during the middle Miocene.
JOURNAL OF SOUTH AMERICAN EARTH SCIENCES
(2023)
Article
Statistics & Probability
Gabriel Hassler, Max R. Tolkoff, William L. Allen, Lam Si Tung Ho, Philippe Lemey, Marc A. Suchard
Summary: Comparative biologists are interested in inferring covariation between multiple biological traits in related taxa. To avoid spurious inference, controlling for shared evolutionary history is necessary. A proposed inference technique integrates missing measurements analytically and scales linearly with the number of taxa, improving computational efficiency by orders-of-magnitude.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2022)
Article
Virology
Tim Blokker, Guy Baele, Philippe Lemey, Simon Dellicour
Summary: In this study, we present PhyCovA, a web-based application that allows users to quickly explore the association between candidate covariates and the number of phylogenetically informed transition events among locations. The application enables univariate and multivariate linear regression analyses as well as exploratory variable selection analysis. Additionally, it provides various visualizations related to regression analysis or the annotated phylogenetic tree.
Article
Infectious Diseases
Maria Ortuno, Clara Munoz, Tatiana Spitzova, Petra Sumova, Maria Asuncion Iborra, Pedro Perez-Cutillas, Nazli Ayhan, Remi N. Charrel, Petr Volf, Eduardo Berriatua
Summary: In a study conducted in Murcia Region, southeast Spain, the prevalence of antibodies against Phlebotomus perniciosus sandfly salivary gland homogenate (SGH) and recombinant protein rSP03B was found to be 69% and 88%, respectively. The prevalence of Toscana virus (TOSV), Sandfly Fever Sicilian virus (SFSV), and Leishmania infections were 26%, 0%, and 1%, respectively. The study also questioned the diagnostic value of rSP03B as a marker for these infections in humans.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Virology
Nazli Ayhan, Aissam Hachid, Laurence Thirion, Kamel Eddine Benallal, Laura Pezzi, Fayez Ahmed Khardine, Chahrazed Benbetka, Sihem Benbetka, Zoubir Harrat, Remi Charrel
Summary: Sindbis virus (SINV), a zoonotic alphavirus, has been identified as a cause of human diseases in Africa, Europe, Asia, and Australia. In this study, SINV was detected and isolated from mosquitoes in Algeria, and genetic analysis revealed its similarity to a strain found in Kenya.
Article
Virology
Dorine Decarreaux, Marie Pouquet, Cecile Souty, Ana-Maria Vilcu, Pol Prevot-Monsacre, Toscane Fourie, Paola Mariela Saba Villarroel, Stephane Priet, Helene Blanche, Jean-Marc Sebaoun, Jean-Francois Deleuze, Clement Turbelin, Andreas Werner, Fabienne Kochert, Brigitte Grosgogeat, Pascaline Rabiega, Julien Laupie, Nathalie Abraham, Caroline Guerrisi, Harold Noel, Sylvie van der Werf, Fabrice Carrat, Thomas Hanslik, Remi Charrel, Xavier de Lamballerie, Thierry Blanchon, Alessandra Falchi
Summary: This study aimed to investigate the immune response and neutralizing activity against SARS-CoV-2 among primary health care workers (PHCW) in France and assess the association between neutralizing activity and various factors, including the COVID-19 vaccination scheme. The study found that individuals with previous SARS-CoV-2 infection were more likely to have neutralizing antibodies, regardless of vaccination status. Among those vaccinated with two doses, the time since vaccination was associated with the detection of neutralizing antibodies.
Article
Virology
Khalil Dachraoui, Ifhem Chelbi, Mourad Ben Said, Raja Ben Osman, Saifedine Cherni, Remi Charrel, Elyes Zhioua
Summary: The study investigated the transmission dynamics of Punique virus (PUNV) in Tunisia and found that Phlebotomus perniciosus is the main vector of PUNV. The research provided evidence of intensive circulation of PUNV in sandflies and hosts, reaching a peak during the autumn season.
Article
Environmental Sciences
Dorine Decarreaux, Julie Sevila, Shirley Masse, Lisandru Capai, Toscane Fourie, Paola Mariela Saba Villarroel, Abdennour Amroun, Elif Nurtop, Matthieu Vareille, Marie Pouquet, Thierry Blanchon, Xavier de Lamballerie, Remi Charrel, Alessandra Falchi
Summary: This study estimated the seroprevalence of SARS-CoV-2 infection among the staff and students of the University of Corsica during the second wave of the epidemic. The overall seroprevalence was found to be 12.8%, and factors such as residence, public transportation usage, and contact with infected individuals were associated with seropositivity. The main symptoms associated with seropositivity were acute respiratory infection and loss of smell.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Review
Virology
Simon Dellicour, Philippe Lemey, Marc A. Suchard, Marius Gilbert, Guy Baele
Summary: This paper reviews different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates are described and compared.
Article
Environmental Sciences
Dorine Decarreaux, Julie Sevila, Shirley Masse, Lisandru Capai, Toscane Fourie, Paola Mariela Saba Villarroel, Abdennour Amroun, Elif Nurtop, Matthieu Vareille, Thierry Blanchon, Xavier de Lamballerie, Remi Charrel, Alessandra Falchi
Summary: This study investigated the humoral immune response to SARS-CoV-2 in a French adult population. The results showed that single infection does not provide effective protection, and vaccination significantly affects antibody levels and neutralizing activity.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Virology
Khalil Dachraoui, Ifhem Chelbi, Imen Labidi, Raja Ben Osman, Aida Sayadi, Mourad Ben Said, Saifedine Cherni, Mohammed Abdo Saghir Abbas, Remi Charrel, Elyes Zhioua
Summary: This study investigated the role of dogs as reservoir hosts for Toscana virus (TOSV) and Leishmania infantum infections. Dogs exposed to sandfly bites were examined for TOSV and L. infantum infections, and the sandflies were screened for the presence of these pathogens. The results showed that dogs with zoonotic visceral leishmaniasis (ZVL) can serve as reservoirs for both TOSV and L. infantum, and can transmit TOSV to sandfly vectors in natural settings.
News Item
Virology
Thomas S. Postler, Martin Beer, Bradley J. Blitvich, Jens Bukh, Xavier de Lamballerie, J. Felix Drexler, Allison Imrie, Amit Kapoor, Galina G. Karganova, Philippe Lemey, Volker Lohmann, Peter Simmonds, Donald B. Smith, Jack T. Stapleton, Jens H. Kuhn
Summary: This review provides an overview of the recent changes in genus and species nomenclature within the virus family Flaviviridae. The changes were made to address potential ambiguity and to adhere to binomial format conventions. The genus name Flavivirus was changed to Orthoflavivirus, and all species names were modified accordingly. The revised taxonomy of the Flaviviridae family approved by the ICTV in April 2023 is outlined.
ARCHIVES OF VIROLOGY
(2023)
Article
Virology
Wan-Ting He, Dongyan Li, Guy Baele, Jin Zhao, Zhiwen Jiang, Xiang Ji, Michael Veit, Marc A. Suchard, Edward C. Holmes, Philippe Lemey, Maciej F. Boni, Shuo Su
Summary: Through retrospective epidemiological study, new lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) were discovered in swine populations in China. These novel lineages cause respiratory symptoms without neurological symptoms typically associated with classical PHEV infection. The novel lineages have been circulating in at least eight provinces in southeastern China.
Article
Biochemistry & Molecular Biology
Alexander A. Fisher, Xiang Ji, Akihiko Nishimura, Guy Baele, Philippe Lemey, Marc A. Suchard
Summary: This study proposes a shrinkage clock model with autocorrelation to overcome the weaknesses of current local clock inference methods. The model achieves scalability and recovers known local clocks, and the efficient sampler allows the model to be applied to large trees.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Virology
Kanika D. Nahata, Filip Bielejec, Juan Monetta, Simon Dellicour, Andrew Rambaut, Marc A. Suchard, Guy Baele, Philippe Lemey
Summary: SPREAD 4 is a feature-rich web-based application that visualizes estimates of pathogen dispersal resulting from Bayesian phylogeographic inference. It allows customized visualization based on input phylogenies and generates publication-ready figures. SPREAD 4 also features account-based storage and easy sharing of visualizations using unique web addresses.
Article
Virology
Nidia Sequeira Trovao, Marijn Thijssen, Bram Vrancken, Andrea-Clemencia Pineda-Pena, Thomas Mina, Samad Amini-Bavil-Olyaee, Philippe Lemey, Guy Baele, Mahmoud Reza Pourkarim
Summary: This study uses Bayesian phylodynamic inference to investigate the evolutionary history and spatio-temporal dynamics of hepatitis B virus subgenotype D1 (HBV-D1). By calibrating the molecular clock using ancient sequences and reconstructing spatial dynamics based on publicly available HBV-D1 genomes, the researchers pinpoint the origin of HBV-D1 and reveal its global transmission patterns.
