SARS-CoV-2 Remained Airborne for a Prolonged Time in a Lockdown Confined Space by Xinyue Li, Xiao Qi, Jianxin Ma, Yang Pan, Tian Tian, Yue Zhang, Zhen Li, Wenjing Li, Lingli Sun, Lu Zhang, Zheng Zhang, Quanyi Wang, Maosheng Yao

“…The traveler did not have any contacts with the two employees; however, genome sequencing showed that SARS-CoV-2 variants from three patients and two environmental surface samples belonged to 20B viral clade, sharing a nucleic acid identity of more than 99.9%. …”
Get full text

Transmitted Drug Resistance among People Living with HIV/Aids at Major Cities of Sao Paulo State, Brazil by Joao Leandro Paula Ferreira, Rosangela Rodrigues, Andre Minhoto Lança, Valeria Correia de Almeida, Simone Queiroz Rocha, Taisa Grotta Ragazzo, Denise Lotufo Estevam, Luis Fernando de Macedo Brigido

“…The HIV Reference Center of Campinas presented more cases with TDR, with a significant association of TDR with clade B infection (P<0.05).…”
Get full text

Modeling compositional heterogeneity resolves deep phylogeny of flowering plants by Yongli Wang, Yan-Da Li, Shuo Wang, Erik Tihelka, Michael S. Engel, Chenyang Cai

“…Under site-heterogeneous models, the approximately unbiased test favored our preferred tree recovered from various datasets: Ceratophyllales (coontails) are robustly recovered as sister to monocots, and they together are sister to the clade comprising magnoliids, Chloranthales, and eudicots. …”
Get full text

Six new species of zombie-ant fungi from Yunnan in China by Dexiang Tang, Ou Huang, Weiqiu Zou, Yuanbing Wang, Yao Wang, Quanying Dong, Tao Sun, Gang Yang, Hong Yu

“…Six novel species of Ophiocordyceps from China were identified as the Ophiocordyceps unilateralis core clade, forming a separate lineage with other species. …”
Get full text

Detection and Phylogenetic Characterization of Influenza D in Swedish Cattle by Ignacio Alvarez, Fereshteh Banihashem, Annie Persson, Emma Hurri, Hyeyoung Kim, Mariette Ducatez, Erika Geijer, Jean-Francois Valarcher, Sara Hägglund, Siamak Zohari

“…The IDV strains collected in 2021 (n = 7) belonged to the D/OK clade, whereas samples from 2023 (n = 4) and 2024 (n = 5) consisted of reassortants between the D/OK and D/660 clades, for the PB2 gene. …”
Get full text

Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem by Paige E. Payne, Loren N. Knobbe, Patricia Chanton, Julian Zaugg, Behzad Mortazavi, Olivia U. Mason

“…Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an ‘omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. …”
Get full text

The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution by Eleftheriadi, Klara, Guiglielmoni, Nadège, Salces-Ortiz, Judit, Vargas-Chavez, Carlos, Martínez-Redondo, Gemma I., Gut, Marta, Flot, Jean-François, Schmidt-Rhaesa, Andreas, Fernández, Rosa

“…Nematomorpha, also known as Gordiacea or Gordian worms, are a phylum of parasitic organisms that belong to the Ecdysozoa, a clade of invertebrate animals characterized by molting. …”
Get full text

Nasal microbial diversity is associated with survival in piglets infected by a highly virulent PRRSV-1 strain by Pau Obregon-Gutierrez, Martí Cortey, Gerard E. Martín-Valls, Hepzibar Clilverd, Florencia Correa-Fiz, Virginia Aragón, Enric Mateu

“…On the other hand, a dysbiotic community dominated by Escherichia and a different clade of Moraxella was found in piglets with bad outcome. …”
Get full text

The MSDIN family in amanitin-producing mushrooms and evolution of the prolyl oligopeptidase genes by Hong Luo, Qing Cai, Yunjiao Lüli, Xuan Li, Rohita Sinha, Heather E. Hallen-Adams, Zhu L. Yang

“…Phylogenies of POPB and POPA based on both coding and amino acid sequences showed very different results: while POPA genes clearly reflected the phylogeny of the host species, POPB did not; strikingly, it formed a wellsupported monophyletic clade, despite that the species belong to different genera in disjunct families. …”
Get full text

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation by Jing Li, Li-Hong Han, Xiao-Bin Liu, Zhi-Wei Zhao, Zhu L. Yang

“…The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. …”
Get full text

Genome evolution following an ecological shift in nectar-dwelling Acinetobacter by Vivianna A. Sanchez, Tanya Renner, Lydia J. Baker, Tory A. Hendry

“…Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. …”
Get full text

Révision de l’espèce Homo erectus (Dubois, 1893) by Valéry Zeitoun

“…The first step is to seek criteria allowing to define this species as a clade or as a grade; id est as a monophyletic unit or as an archaic evolutionary step of the species Homo sapiens. …”
Get full text

Spatial and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula by Swan L. S. Sow, Willem H. van de Poll, Rachel Eveleth, Jeremy J. Rich, Hugh W. Ducklow, Patrick D. Rozema, Catherine M. Luria, Henk Bolhuis, Michael P. Meredith, Linda A. Amaral-Zettler, Julia C. Engelmann

“…Up to 62.3% of the negative causal effects were driven by Syndiniales at Rothera compared to only 13.5% at Palmer, suggesting that parasitism drives community dynamics at Rothera more strongly than at Palmer. Conversely, SAR11 Clade II, which was less abundant but persistent year-round at both sites, was the dominant driver at Palmer, evidenced by many (28.2% and 37.4% of positive and negative effects respectively) strong causal effects. …”
Get full text

Salivary peptidomic profiling of chronic gingivostomatitis in cats by matrix‐assisted laser desorption/ionization‐time‐of‐flight mass spectrometry and nanoscale liquid chromatograp... by Sekkarin Ploypetch, Apisit Pornthummawat, Sittiruk Roytrakul, Janthima Jaresitthikunchai, Narumon Phaonakrop, Sabrina Wahyu Wardhani, Sitthichok Lacharoje, Somporn Techangamsuwan

“…In FCGS, 26 salivary peptides were altered, including apolipoprotein A1, nuclear receptor subfamily 1 group I member 3, fibrinogen alpha chain, interleukin 2 receptor gamma, interleukin 23 receptor, hemoglobin subunit alpha, and serpin peptidase inhibitor clade A (alpha‐1 antiproteinase, antitrypsin) member 12, protein‐tyrosine‐phosphatase, and cholinergic receptor nicotinic alpha 10 subunit. …”
Get full text

Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus by Pingxuan Xie, Tinglu Wang, Jiawei Tan, Linyuan Fan, Changkun Liu, Hanjing Yan

“…Phylogenetic analyses yielded a robust phylogeny for Asparagus taxa, which were split into Clades I, II, and III. Notably, medicinal Asparagus species were mainly found in Clade III. …”
Get full text

Genome-wide identification of the bHLH gene family in Scutellaria baicalensis and their relationship with baicalin biosynthesis under drought stress by Yingxin Sun, Beier Wang, Lichao Zhang, Xiaohan Zheng, Peng Xu, Meng Zhang, Meiguang Han, Peng Di, Mei Han, Lin Cheng, Limin Yang

“…Phylogenetic and conserved motif analyses revealed that the gene structures within each SbbHLH clade are relatively conserved. Gene duplication analysis identified 29 duplication events in the SbbHLH gene family, most of which involved gene pairs under purifying selection. …”
Get full text

Novel H16N3 avian influenza viruses isolated from migratory gulls in China in 2023 by Peng Peng, Peng Peng, Peng Peng, Jinyan Shen, Wenjun Shi, Jing Guo, Mengjing Wang, Wenxi Li, Zhiqin Yue, Xiaohong Sun, Mengdi Guan, Lili Liu, Hongke Xu, Yujiao Xie, Anran Ren, Mingfeng Liu, Wenqiang Liu, Zhibin Zhang, Zhibin Zhang, Zhishu Xiao, Zhishu Xiao, Xuyong Li

“…Furthermore, the gull origin H13 and H16 viruses collectively served as gene donors for the newly emerged highly pathogenic clade 2.3.4.4b H5N1 viruses because the H13/H16-like PA, NP, and NS genes have been introduced into circulating H5N1 viruses since May 2022 in Europe. …”
Get full text

A Model H5N2 Vaccine Strain for Dual Protection Against H5N1 and H9N2 Avian Influenza Viruses by Jin-Ha Song, Seung-Eun Son, Ho-Won Kim, Se-Hee An, Chung-Young Lee, Hyuk-Joon Kwon, Kang-Seuk Choi

“…<b>Methods:</b> In this study, we generated a model PR8-derived recombinant H5N2 vaccine strain with hemagglutinin (HA) and neuraminidase (NA) genes from clade 2.3.2.1c H5N1 and Y439-like H9N2 viruses, respectively. …”
Get full text

Genomic characteristics of ST6115 carbapenem-resistant Klebsiella pneumoniae coharboring blaNDM-1 and blaIMP-4 by Xiaofang Xie, Xiaofang Xie, Yaxuan Zhai, Zhichen Zhu, Feinan Qian, Feinan Qian, Jie Zhu, Qizhao Gao, Hong Du, Hong Du

“…Finally, the conjugation transfer experiment was conducted to assess the transferability of the plasmid pHD8428-NDM-IMP.ResultsA comparable phylogenetic analysis revealed that ST6115 HD8428 and the majority of ST17 strains (9/12) were clustered on the same clade, which suggests a close relationship between two ST types. …”
Get full text

Energetic and genomic potential for hydrogenotrophic, formatotrophic, and acetoclastic methanogenesis in surface-expressed serpentinized fluids of the Samail Ophiolite by Alta E. G. Howells, Alta E. G. Howells, Lilja M. Quinn, Lilja M. Quinn, Miguel G. Silva, Miguel G. Silva, Kylie Akiyama, Kylie Akiyama, Lucas M. Fifer, Lucas M. Fifer, Grayson Boyer, Srishti Kashyap, Kirt Robinson, Kirt Robinson, Jared Broddrick, Everett L. Shock, Tori M. Hoehler

“…Acetoclastic methanogenesis is also shown to be energetically favorable in these fluids, and we report the first detection of a potential acetoclastic methanogen of the family Methanosarcinaceae, which forms a distinct clade with a genome from the serpentinizing seafloor hydrothermal vent field, Lost City. …”
Get full text