FUBAR: a fast, unconstrained bayesian approximation for inferring selection

Evolutionary and functional analyses reveal a role for the RHIM in tuning RIPK3 activity across vertebrates

Receptor interacting protein kinases (RIPK) RIPK1 and RIPK3 play important roles in diverse innate immune pathways. Despite this, some RIPK1/3-associated proteins are absent in specific vertebrate lineages, suggesting that some RIPK1/3 functions are conserved, while others are more evolutionarily labile. Here, we perform comparative evolutionary analyses of RIPK1-5 and associated proteins in vertebrates to identify lineage-specific rapid evolution of RIPK3 and RIPK1 and recurrent loss of RIPK3-associated proteins. Despite this, diverse vertebrate RIPK3 proteins are able to activate NF-κB and cell death in human cells. Additional analyses revealed a striking conservation of the RIP homotypic interaction motif (RHIM) in RIPK3, as well as other human RHIM-containing proteins. Interestingly, diversity in the RIPK3 RHIM can tune activation of NF-κB while retaining the ability to activate cell death. Altogether, these data suggest that NF-κB activation is a core, conserved function of RIPK3, and the RHIM can tailor RIPK3 function to specific needs within and between species.

The complete chloroplast genomes of four Aspidopterys species and a comparison with other Malpighiaceae species

The genus Aspidopterys has multiple functions in medicine, food and ecological restoration. Due to the similar morphological characteristics of some species and the limited genomic information hinder the studies on germplasm identification and molecular phylogeny analysis. In this study, we compared and explored the six complete chloroplast (cp) genomes including four Aspidopterys species (A. glabriuscula, A. concava, A. cavaleriei, A. obcordata), Banisteriopsis caapi and Bunchosia argentea. Their cp genomes in length were 158,473 to 161,091 bp, displaying the high conserved degree in the structure, gene arrangement and GC content. Moreover, 57-80 long repeats and 61-92 SSRs were identified, most of which were forward or palindromic repeats and mononucleotides, respectively. Eleven non-coding regions and 12 coding regions, especially ndhH_ndhA, rpl32_ndhF and ycf1, had the higher nucleotide diversity values that could can be regarded as DNA barcodes of Malpighiaceae species. In addition, the 9 genes (like accD, atpE, atpF, clpP) were conducted positive selection (Ka/Ks > 1). As indicated by phylogenetic analysis, those four Aspidopterys were clustered into single clade with other Malpighiaceae species and were closely related to B. caapi and B. argentea. This study sheds more lights on further phylogenetic, evolutionary and genetic diversity studies on the genus Aspidopterys and even the Malpighiaceae species.

Characterization of an Emerging Recombinant Duck Circovirus in Northern Vietnam, 2023-2024

This study aimed to characterize the duck circovirus circulating in Northern Vietnam based on complete genome sequences. Between 2023 and 2025, 45 pooled tissue samples were collected from nine duck flocks in several provinces in Northern Vietnam. Of the 45 samples tested, 16 (35.56%) were positive for the DuCV genome, as determined using conventional polymerase chain reaction. Nine representative strains were selected for viral genome sequencing. The results indicated that the complete Vietnamese DuCV genomes were from 1992 to 1995 bp in length, and the degree of nucleotide identity shared among them ranged from 96.88% to 99.84%. Phylogenetic analysis of the complete genomes showed that the nine Vietnamese DuCV strains belonged to genotype I, subgenotypes Ia (two strains), Ib (four strains), and Ic (three strains). These viral strains were genetically related to viruses reported in China from 2019 to 2023. Recombination events occurred on the Cap gene sequences of three Vietnamese DuCV strains (Vietnam/VNUA-102/2023, Vietnam/VNUA-225/2023, and Vietnam/VNUA-318/2024). One positive selection was detected on the Rep protein sequence.

Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis

Caspases are evolutionarily conserved proteins essential for driving cell death in development and host defense. Caspase-8, a key member of the caspase family, is implicated in nonlytic apoptosis, as well as lytic forms of cell death. Recently, caspase-8 has been identified as an integral component of PANoptosomes, multiprotein complexes formed in response to innate immune sensor activation. Several innate immune sensors can nucleate caspase-8-containing PANoptosome complexes to drive inflammatory lytic cell death, PANoptosis. However, how the evolutionarily conserved and diverse functions of caspase-8 drive PANoptosis remains unclear. To address this, we performed evolutionary, sequence, structural, and functional analyses to decode caspase-8's complex-forming abilities and its interaction with the PANoptosome adaptor ASC. Our study distinguished distinct subgroups within the death domain superfamily based on their evolutionary and functional relationships, identified homotypic traits among subfamily members, and captured key events in caspase evolution. We also identified critical residues defining the heterotypic interaction between caspase-8's death effector domain and ASC's pyrin domain, validated through cross-species analyses, dynamic simulations, and in vitro experiments. Overall, our study elucidated recent evolutionary adaptations of caspase-8 that allowed it to interact with ASC, improving our understanding of critical molecular associations in PANoptosome complex formation and the underlying PANoptotic responses in host defense and inflammation. These findings have implications for understanding mammalian immune responses and developing new therapeutic strategies for inflammatory diseases.

Current Evolutionary Dynamics of Porcine Epidemic Diarrhea Virus (PEDV) in the U.S. a Decade After Introduction

Porcine Epidemic Diarrhea Virus (PEDV) was introduced in the United States (U.S.) in 2013, spreading rapidly and leading to economic losses. Two strains, S-INDEL and non-S-INDEL, are present in the U.S. We analyzed 313 genomes and 556 Spike protein sequences generated since its introduction. PEDV case numbers were highest during the first two years after its introduction (epidemic phase), then declined and stabilized in the following years (endemic phase). Sequence surveillance was higher during the initial epidemic phase. Our results suggest the non-S-INDEL strain is the predominant strain in U.S. The non-S-INDEL sequences exhibit pairwise nucleotide identity percentages above 97.6%. Most non-S-INDEL sequences sampled after 2017 clustered into two sub-clades. No descendants derived from other clades present in the epidemic period were detected in the contemporary data, suggesting that these clades are no longer circulating in the U.S. The two clades currently circulating are restricted to two respective geographic regions and our results suggest limited inter-regional spread. This insight helps determine the risk of re-introduction of PEDV if it were regionally eliminated. Ongoing molecular surveillance is essential to confirming that some older clades no longer circulate anymore in the U.S., mapping the distribution and spread of recent clades, and understanding PEDV's evolutionary diversification.

Complete mitogenomes reveal high diversity and recent population dynamics in Antarctic krill

BACKGROUND

The Antarctic krill (Euphausia superba) is a keystone species in the Southern Ocean ecosystem, influencing food web dynamics and ecosystem functionality. Despite its ecological importance, further exploration is essential to understand their population dynamics.

RESULTS

In this study, we present the complete mitogenome of the Antarctic krill. The assembly is 18,926 bp, including a notably large 3,952 bp control region (CR). The CR features a satellite repeat spanning 2,289 bp, showcasing the effectiveness of long-read sequencing in resolving complex genomic regions. Additionally, we identified 900 nuclear-mitochondrial segments (NUMTs) totaling 2.79 Mb, shedding light on the dynamic integration of mitochondrial DNA (mtDNA) into the nuclear genomes. By establishing a dataset comprising 80 krill mitogenomes, we unveil substantial mitochondrial diversity, particularly within the ND4 gene. While our analysis reveals no significant differentiation among four geographically distinct groups, we identify at least four maternal genetic clusters. Haplotype network analysis and demographic reconstructions suggest a recent population expansion, likely driven by favorable environmental conditions during the late Pleistocene. Furthermore, our investigation into selection pressures on mitochondrial genes reveals evidence of purifying selection across all 13 protein-coding genes, underscoring the pivotal role of mtDNA conservation in maintaining mitochondrial function under extreme environments.

CONCLUSIONS

This study provides a repository of Antarctic krill mitogenomes and insights into the population genetics and evolutionary history of this ecologically important species from a mitogenomic perspective, with implications for krill conservation and management in the Southern Ocean.

Genomic Alterations of the Infectious Bronchitis Virus (IBV) Strain of the GI-23 Lineage Induced by Passages in Chickens and Quails

Infectious bronchitis virus (IBV) of the GI-23 lineage, which first emerged in the Middle East in the late 1990s, has since spread worldwide. The factors driving its expansion, whether human involvement, wild bird migration, or the virus's biological traits, are still unclear. This study aimed to trace the genome evolution of GI-23 IBV in chickens and its adaptability to quails, which are susceptible to both gamma- and deltacoronaviruses. Thirty specific-pathogen-free (SPF) birds, aged between two and three weeks, were used. Initially, three birds were inoculated with the G052/2016 IBV via the oculo-nasal route. On the third day post-infection (dpi), oropharyngeal swabs were collected from the whole group, pooled, and subsequently used to infect three next birds. This process was repeated nine more times during consecutive IBV passages (P-I-P-X), and eventually, virus sequencing was performed using Next-Generation Sequencing (NGS). The obtained results showed that quails were not susceptible to the IBV GI-23 lineage, as the virus RNA was detected in low amounts only during the first passage (QP-I) with no further detections in later rounds of IBV passaging. In chickens, only mild diarrhea symptoms appeared in a few individuals. The NGS analysis identified sixty-two single nucleotide variants (SNVs), thirty of which caused amino acid changes, twenty-eight were synonymous, and one SNV introduced a stop codon. Three SNVs were found in untranslated regions. However, none of these SNVs lasted beyond seven passages, with forty-four being unique SNVs. The Shannon entropy values measured during passages varied for pol1a, pol1b, S, 5a, 5b, and N genes, with overall genome complexity peaking at CP-VI and CP-X. The highest complexity was observed in the pol1a (CP-X) and S genes (CP-IV, CP-VI, CP-VIII, and CP-X). Along with the S gene that was under positive selection, eight codons in pol1a were also positively selected. These findings suggest that even in an adapted host, IBV variability does not stabilize without immune pressure, indicating continuous molecular changes within its genome.

Molecular characterization, expression, evolutionary analysis and molecular docking of the Janus activated kinase family members of largemouth bass (Micropterus salmoides)

Janus kinases (JAKs) play crucial roles in the immune responses by binding the cytokine receptors. In the present study, five JAKs family members (JAK1, JAK2a, JAK2b, JAK3, and TYK2) were identified in largemouth bass (Micropterus salmoides). The five JAKs members of largemouth bass contained several conserved protein domains, including a FERM domain, an SH2 domain, a pseudokinase (STyrkc) domain, and a tyrosine kinase (Tyrkc) domain. Phylogenetic analysis revealed the JAK2/2a/2b and JAK3 formed a clade and the JAK1/TYK2 formed another separate clade. Realtime qPCR detection showed that all five JAKs genes were constitutively expressed in ten selected tissues, with highly expression in spleen and head kidney (HK). Following Edwardsiella piscicida infection, the five JAKs genes were significantly upregulated in the spleen and primary hepatocytes at different times post infection. Further selection pressure analysis revealed the five JAKs members underwent negative selection pressures during evolution. The FERM and Tyrkc domains of the five JAK members occurred purifying selection, and involved in interaction with STAT3, which confirmed by protein-protein interaction (PPI) network and molecular docking analysis. Also, molecular docking results indicated that the hydrogens bonds and salt bonds had crucial roles in the JAK/STAT3 complexes formation. Our results indicated that JAKs had important roles in the immune response against bacterial in largemouth bass, providing basis for elucidating the mechanism of JAK/STAT signaling pathway in fish.

Longitudinal population analysis of Plasmodium falciparum apical membrane antigen-1 in Indian field isolates

High genetic diversity is a major impediment to developing a universal malaria vaccine based on Plasmodium falciparum apical membrane antigen-1 (Pfama-1). Vaccine effectiveness against heterologous forms of the antigen requires information about existing genetic diversity of gene in circulation. Genotyping of Pfama-1 was performed on 147 archival samples from 14 different Indian states collected from 1993 to 2021. Genetic diversity and natural selection were assessed to explore the longitudinal variation in Pfama-1 in Indian P. falciparum field isolates. A total of 52 polymorphic sites were observed giving rise to 70 different haplotypes. Two novel amino acid substitutions S498C/G and F505Y, were observed in our samples. Highest genetic polymorphism was observed in Domain I (π = 0.025), while Domain II (π = 0.006) appeared to be most conserved across all states over the time. Non-significant positive Tajima D value (Taj D = 0.945, p > 0.10) was observed indicating that Indian Pfama-1 is under balancing natural selection. Although haplotype network was complex, structure analysis has shown no evidence of distinct genetic pattern state wise or change in Pfama-1 structure in time. Genetic structure of Pfama-1 in Indian field isolates is complex, exhibiting a high degree of genetic polymorphism. Since allele specific immunity is observed in the gene, Domain II which shows relative conservation across all states and between old and recent field isolates could have implications in vaccine design.

Evolution of antigenic diversity in the zoonotic multi-host parasite Schistosoma japonicum: implications for vaccine design

The multi-host zoonotic transmission of the blood fluke Schistosoma japonicum is complex, presenting challenges for China's schistosomiasis elimination strategy. How multi-host transmission impacts the genetic diversity of S. japonicum populations is poorly understood and the extent of Schistosoma japonicum antigen coding gene (SjACG) variability remains unknown despite the implications for parasite survival, vaccine development and disease control. To address this, we sequenced the host-interacting domains of three functionally significant SjACGs previously identified as promising vaccine targets (tetraspanin 23 (TSP-23), venom allergen-like protein 7 (VAL-7), and tegument allergen-like protein 1 (TAL-1)) from FTA-archived S. japonicum miracidia sampled from natural infections amongst different definitive host species in mainland China. This work represents the first known analysis of SjACG variation among different host species. SjACGs were genetically diverse across host species, with 10-20 SjACG haplotypes identified from 60 to 81 sequences. Host-derived immune selection pressures may be driving this variation, impacting antigen protein structure, function, and antigenic propensity. Antigen haplotypes were broadly shared across host species, supporting prior suggestions of gene flow and underscoring the importance of zoonotic transmission in disseminating diversity. Some host adaptation was inferred through identification of host species-specific variation. Parasites sampled from humans displayed the greatest overall diversity of SjACGs, and humans shared haplotypes with all other host species. SjACG diversification appears to have occurred rapidly, and before modern humans arrived in China (∼1.7-0.66 million years ago (MYA)), suggesting that animal hosts have been important in the evolutionary history of these antigens. Collectively, the results expand our understanding of the impact of zoonotic transmission on the co-evolutionary processes driving antigenic variability and provide possible evidence of adaptive molecular evolution of certain antigen haplotypes to specific host species. Our findings have implications for the development of anti-schistosome vaccines and, ultimately, for control of zoonotic schistosomiasis.

The Ongoing Epidemics of Seasonal Influenza A(H3N2) in Hangzhou, China, and Its Viral Genetic Diversity

This study examined the genetic and evolutionary features of influenza A/H3N2 viruses in Hangzhou (2010-2022) by analyzing 28,651 influenza-like illness samples from two sentinel hospitals. Influenza A/H3N2 coexisted with other subtypes, dominating seasonal peaks (notably summer). Whole-genome sequencing of 367 strains was performed on GridION platforms. Phylogenetic analysis showed they fell into 16 genetic groups, with multiple clades circulating simultaneously. Shannon entropy indicated HA, NA, and NS gene segments exhibited significantly higher variability than other genomic segments, with HA glycoprotein mutations concentrated in antigenic epitopes A-E. Antiviral resistance showed no inhibitor resistance mutations in PA, PB1, or PB2, but NA mutations were detected in some strains, and most strains harbored M2 mutations. A Bayesian molecular clock showed the HA segment exhibited the highest nucleotide substitution rate (3.96 × 10-3 substitutions/site/year), followed by NA (3.77 × 10-3) and NS (3.65 × 10-3). Selective pressure showed A/H3N2 strains were predominantly under purifying selection, with only sporadic positive selection at specific sites. The Pepitope model demonstrated that antigenic epitope mismatches between circulating H3N2 variants and vaccine strains led to a significant decline in influenza vaccine effectiveness (VE), particularly in 2022. Overall, the study underscores the complex circulation patterns of influenza in Hangzhou and the global importance of timely vaccine strain updates.

Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

Selection Pressure Regulates the Evolution-Structure-Function Paradigm of Monocyte Chemoattractant Protein Family

Monocyte chemoattractant proteins (MCPs) are involved in monocyte trafficking during severe inflammation by modulating the chemokine-glycosaminoglycan-receptor signaling axis. MCPs comprise a family of four chemokines (CCL2, CCL7, CCL8, and CCL13/12) that exhibit differential expression patterns in mammals, functional diversity, and receptor/glycosaminoglycan (GAG) binding promiscuity. In this context, the evolution-structure-function paradigm of MCP chemokines in mammals was established by assessing phylogeny, functional divergence, selection pressure, and coevolution in correlation with structural and surface characteristics. Comprehensive analyses were performed using an array of evolutionary and structural bioinformatic methods including molecular dynamics simulations. Our findings demonstrate that substitutions in receptor/GAG-interacting residues mediate episodic diversification and functional diversity in MCP chemokines. Additionally, a balanced interplay of selection pressures has driven the functional changes observed among MCP paralogs, with positive selection at various receptor/GAG-binding sites contributing to their promiscuous receptor/GAG interactions. Meanwhile, processes like purifying selection and coevolution maintain the classical chemokine structure and preserve the ancestral functions of MCP chemokines. Overall, this study suggests that selection pressure on sites within the N-terminal region [N-loop and 310-helix] and 40S loop of MCP chemokines alters surface properties to fine-tune the molecular interactions and functional characteristics without altering the overall chemokine structure.

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

Positive selection is an evolutionary process which increases the frequency of advantageous mutations because they confer a fitness benefit. Inferring the past action of positive selection on protein-coding sequences is fundamental for deciphering phenotypic diversity and the emergence of novel traits. With the advent of genome-wide comparative genomic datasets, researchers can analyze selection not only at the level of individual genes but also globally, delivering systems-level insights into evolutionary dynamics. However, genome-scale datasets are generated with automated pipelines and imperfect curation that does not eliminate all sequencing, annotation, and alignment errors. Positive selection inference methods are highly sensitive to such errors. We present BUSTED-E: a method designed to detect positive selection for amino acid diversification while concurrently identifying some alignment errors. This method builds on the flexible branch-site random effects model (BUSTED) for fitting distributions of dN/dS, with a critical modification: it incorporates an "error-sink" component to represent an abiological evolutionary regime. Using several genome-scale biological datasets that were extensively filtered using state-of-the art automated alignment tools, we show that BUSTED-E identifies pervasive residual alignment errors, produces more realistic estimates of positive selection, reduces bias, and improves biological interpretation. The BUSTED-E model promises to be a more stringent filter to identify positive selection in genome-wide contexts, thus enabling further characterization and validation of the most biologically relevant cases.

Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis

Since its first academic record in 1978, dengue epidemics have occurred in all provinces of China, except Xizang. The epidemiological and molecular features of the whole genome of dengue virus (DENV) have not yet been completely elucidated, interfering with prevention and control strategies for dengue fever in China. Here, we obtained 553 complete genomes of the four serotypes of DENV (DENV1-4) isolated in China from the GenBank database to analyze the phylogeny, recombination, genomic variants, and selection pressure and to estimate the substitution rates of DENV genomes. Phylogenetic analyses indicated that DENV sequences from China did not cluster together and were genetically closer to those from Southeast Asian countries in the maximum likelihood trees, indicating that DENV was not endemic in China. Thirty intra-serotype recombinant sequences were identified for DENV1-4, with the highest frequency in DENV4. Selection pressure analyses revealed that 13 codons under positive selection were located in the C, NS1, NS2A, NS3, and NS5 proteins. For DENV1 to DENV3, the substitution rates evaluated in this study were 9.23 × 10-4, 7.59 × 10-4, and 7.06 × 10-4 substitutions per site per year, respectively. These findings improve our understanding of the evolution of DENV in China.

Mitogenome of Neolissochilus pnar, the largest cavernicolous species of Mahseer

The study of the mitogenome of Neolissochilus pnar, the world's largest cave fish, uncovered its structural features, gene content and evolutionary dynamics within mahseer. Its mitogenome is of 16,440 base pairs, resembling those of the teleost species and exhibits a high degree of conservation in genes arrangement. It comprises 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs) and a control region. Notably, the distribution of genes on the L- and H-strands is consistent with that of the typical teleost. The study reveals the lengths and variations in PCGs in mahseer species, displaying a range from 164 to 11,404 bp. The tRNA and rRNA genes and the control region also demonstrate conservation among the species. A robust phylogenetic analysis, employing Bayesian and ASAP methods, supports the classification of N. pnar within the Neolissochilus genus and validates the taxonomic status of this species. Selection pressure analyses indicate positive selection in seven genes: COII , COIII, Cytb, ND1, ND2, ND5 and ND6. These findings suggest the dynamic nature of mitochondrial evolution in mahseer species. The purifying selection preserve essential mitochondrial functions, and additionally, the specific sites in ND5 and ND6 genes undergo episodic positive or diversifying selection, likely in response to environmental changes or selective pressures. In conclusion, this research enriches our understanding of N. pnar visa-vis other mahseers' mitogenomes, pointing to its possible mitogenome evolution to adaptation to cave environment.

The unexpected loss of the 'hunger hormone' ghrelin in true passerines: a game changer in migration physiology

Migratory birds must accumulate large amounts of fat prior to migration to sustain long flights. In passerines, the small body size limits the amount of energy stores that can be transported, and therefore birds undergo cycles of extreme fattening and rapid exhaustion of reserves. Research on these physiological adaptations was rattled by the discovery that birds have lost the main vertebrate regulator of fat deposition, leptin. Recent studies have thus focused on ghrelin, known as 'hunger hormone', a peptide secreted by the gastrointestinal tract to regulate, e.g. food intake and body mass in vertebrates. Studies on domestic species showed that, in birds, ghrelin has effects opposite to those described in mammals such as inhibiting instead of promoting food intake. Furthermore, recent studies have shown that ghrelin administration influences migratory behaviour in passerine birds. Using comparative genomics and immunoaffinity chromatography, we show that ghrelin has been lost in Eupasseres after the basic split from Acanthisitti about 50 Ma. We found that the ghrelin receptor is still conserved in passerines. The maintenance of a functional receptor system suggests that in Eupasserines, another ligand has replaced ghrelin, perhaps to bypass the feedback system that would hinder the large pre-migratory accumulation of subcutaneous fat.

Insect-specific Alphamesonivirus-1 (Mesoniviridae) in lymph node and lung tissues from two horses with acute respiratory syndrome

Members of the RNA virus order Nidovirales infect hosts ranging from marine invertebrates to terrestrial mammals. As such, understanding the determinants of host range in this group of viruses, as well as their patterns of emergence and disease potential, is of clear importance. The Mesoniviridae are a recently documented family within the Nidovirales. To date, mesoniviruses have only been associated with the infection of arthropod species, particularly mosquitoes, and hence are regarded as insect-specific viruses (ISVs). Herein, we report the first detection of a mesonivirus-Alphamesonivirus-1 -in mammals. Specifically, we utilized genomic and histological techniques to identify Alphamesonivirus-1 in lung and lymph node tissues of two horses (a mare and its foal) from Italy that succumbed to an acute respiratory syndrome. The genome sequences of Alphamesonivirus-1 obtained from the two horses were closely related to each other and to those from a local Culex mosquito pool and an Alphamesonivirus-1 previously identified in Italy, indicative of ongoing local transmission. The discovery of Alphamesonivirus-1 in horse tissues prompts further investigation into the host range of mesoniviruses, the possible role of insect-specific viruses in mammalian disease processes, the determinants of and barriers to cross-species virus transmission, and the potential epizootic threats posed by understudied viral families.

IMPORTANCE

Alphamesoniviruses, members of the family Mesoniviridaeare, are considered insect-specific RNA viruses with no known association with vertebrate hosts. Herein, we report the identification of Alphamesonivirus-1 in mammals. Using detailed molecular and histological analyses, we identified Alphamesonivirus-1 in lung and lymph node tissues of two horses that presented with an acute respiratory syndrome and that was phylogenetically related to virus sequences found in local Culex mosquitoes. Hence, Alphamesoniviruses may possess a broader host range than previously believed, prompting the investigation of their possible role in mammalian disease. This work highlights the need for increased surveillance of atypical viruses in association with unexplained respiratory illness, including those commonly assumed to be insect-specific, and may have implications for epizootic disease emergence.

Genomic and functional adaptations in guanylate-binding protein 5 (GBP5) highlight specificities of bat antiviral innate immunity

Bats are asymptomatic reservoirs of several zoonotic viruses. This may result from long-term coevolution between viruses and bats, that have led to host adaptations contributing to an effective balance between strong antiviral responses with innate immune tolerance. To better understand these virus-host interactions, we combined comparative transcriptomics, phylogenomics and functional assays to characterize the evolution of bat innate immune antiviral factors. First, we stimulated the type I interferon immune pathway in Myotis yumanensis primary cells and identified guanylate-binding protein 5 (GBP5) as the most differentially expressed interferon-stimulated gene (ISG). Phylogenomic analyses showed that bat GBP5 has been under strong episodic positive selection, with numerous rapidly evolving sites and species-specific gene duplications, suggesting past evolutionary arms races. Functional tests on GBP5 orthologs from ten bat species covering the >60 million years of Chiroptera evolution revealed species- and virus-specific restrictions against RNA viruses (retrovirus HIV, and rhabdoviruses European bat lyssavirus and VSV), which are typical signatures of adaptations to past viral epidemics. Interestingly, we also observed a lineage-specific loss of the GBP5 prenylation motif in the common ancestor of Pipistrellus and Eptesicus bats, associated with different GBP5 subcellular localization and loss of antiviral functions. Resurrection of the ancestral prenylation motif in Eptesicus fuscus GBP5 rescued its subcellular localization, but not the complete antiviral activities, suggesting that additional determinants are necessary for the antiviral restriction. Altogether, our results highlight adaptations that contribute to bat specific immunity and provide insights into the functional evolution of antiviral effector GBP5.

Decoding the blueprint of receptor binding by filoviruses through large-scale binding assays and machine learning

Evidence suggests that bats are important hosts of filoviruses, yet the specific species involved remain largely unidentified. Niemann-Pick C1 (NPC1) is an essential entry receptor, with amino acid variations influencing viral susceptibility and species-specific tropism. Herein, we conducted combinatorial binding studies with seven filovirus glycoproteins (GPs) and NPC1 orthologs from 81 bat species. We found that GP-NPC1 binding correlated poorly with phylogeny. By integrating binding assays with machine learning, we identified genetic factors influencing virus-receptor-binding and predicted GP-NPC1-binding avidity for additional filoviruses and bats. Moreover, combining receptor-binding avidities with bat geographic distribution and the locations of previous Ebola outbreaks allowed us to rank bats by their potential as Ebola virus hosts. This study represents a comprehensive investigation of filovirus-receptor binding in bats (1,484 GP-NPC1 pairs, 11 filoviruses, and 135 bats) and describes a multidisciplinary approach to predict susceptible species and guide filovirus host surveillance.

Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex

Recognition of "non-self" nucleic acids, including cytoplasmic dsDNA, dsRNA, or mRNAs lacking proper 5' cap structures, is critical for the innate immune response to viruses. Here, we demonstrate that short 5' untranslated regions (UTRs), a characteristic of many viral mRNAs, can also serve as a molecular pattern for innate immune recognition via the interferon-induced proteins IFIT2 and IFIT3. The IFIT2-IFIT3 heterodimer, formed through an intricate domain swap structure resolved by cryo-EM, mediates viral mRNA 5' end recognition, translation inhibition, and ultimately antiviral activity. Critically, 5' UTR lengths <50 nucleotides are necessary and sufficient to sensitize an mRNA to translation inhibition by the IFIT2-IFIT3 complex. Accordingly, diverse viruses whose mRNAs contain short 5' UTRs, such as vesicular stomatitis virus and parainfluenza virus 3, are sensitive to IFIT2-IFIT3-mediated antiviral activity. Our work thus reveals a pattern of antiviral nucleic acid immune recognition that takes advantage of the inherent constraints on viral genome size.

Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality

Visual systems are tuned to animals' ecologies, evolving in response to specific light environments and visual needs. Ecological transitions to fossorial lifestyles impose strong selective pressures favoring morphological adaptations for underground life, such as increased skull ossification and reduced eye protrusion. Fossoriality may simultaneously relax constraints on other aspects of vision leading to diminished visual capabilities. Caecilians (Gymnophiona)-specialized, fossorial amphibians-possess reduced eyes covered by skin or bone. For years, these traits, along with the presence of a single photoreceptor expressing one functional opsin gene, have been interpreted as evidence of limited visual capabilities, including an inability to focus or perceive color. Our results challenge these assumptions: we identified the long-wavelength-sensitive (LWS) opsin gene in 11 species of caecilians spanning 8 of 10 recognized families. Molecular evidence indicates that LWS is intact and transcribed in the eye of at least one species (Caecilia orientalis). Anatomical observations from five caecilian families indicate highly organized retinae even in families with vestigial eyes. While the presence of cone cells in our study species remains uncertain, a putatively functional LWS gene suggests that the visual capabilities of caecilians and the role of light perception in their ecology may be underestimated.

Phylogeography Analysis Reveals Rabies Epidemiology, Evolution, and Transmission in the Philippines

Rabies, caused by rabies virus, is a severe public health problem in the Philippines, where animal rabies epidemiology had been extensively investigated, but little is known about the national epidemiologic situations since 2010. Here, we report a 12-year nationwide animal rabies surveillance with systematic phylogenetic analysis, in which 353 whole genomes of rabies viruses collected from animal rabies cases between 2018 and 2022 were obtained. The phylogenetic and spatial-temporal evolutionary analyses showed that rabies viruses in the Philippines were exclusively classified into the SEA4 subclade within the Asian clade, but forming three major geographically specific lineages. Intra-island spread predominates the rabies transmission in three major island regions, while the inter-island transmission, between major island regions, is very limited, likely due to ocean barriers. Overall, our findings have provided the most comprehensive dataset on the infected animal species, geographic distribution, transmission dynamics, genetic diversity of rabies viruses, and transmission risk factors, thus established a basis to support WOAH-endorsed national control program for dog-mediated rabies in the Philippines.

A barley MLA immune receptor is activated by a fungal nonribosomal peptide effector for disease susceptibility

The barley Mla locus contains functionally diversified genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) and confer strain-specific immunity to biotrophic and hemibiotrophic fungal pathogens. In this study, we isolated a barley gene Scs6, which is an allelic variant of Mla genes but confers susceptibility to the isolate ND90Pr (BsND90Pr) of the necrotrophic fungus Bipolaris sorokiniana. We generated Scs6 transgenic barley lines and showed that Scs6 is sufficient to confer susceptibility to BsND90Pr in barley genotypes naturally lacking the receptor. The Scs6-encoded NLR (SCS6) is activated by a nonribosomal peptide (NRP) effector produced by BsND90Pr to induce cell death in barley and Nicotiana benthamiana. Domain swaps between MLAs and SCS6 reveal that the SCS6 leucine-rich repeat domain is a specificity determinant for receptor activation by the NRP effector. Scs6 is maintained in both wild and domesticated barley populations. Our phylogenetic analysis suggests that Scs6 is a Hordeum-specific innovation. We infer that SCS6 is a bona fide immune receptor that is likely directly activated by the nonribosomal peptide effector of BsND90Pr for disease susceptibility in barley. Our study provides a stepping stone for the future development of synthetic NLR receptors in crops that are less vulnerable to modification by necrotrophic pathogens.

Molecular Analysis of Human Respiratory Syncytial Virus Group B Strains Isolated in Kenya Before and During the Emergence of Pandemic Influenza A/H1N1

BACKGROUND

We conducted a retrospective study to explore molecular insights into human respiratory syncytial virus (HRSV) group B strains among patients attending outpatient clinics at government medical facilities both prior and during the onset of Influenza A/H1N1/2009 pandemic outbreak.

METHODS

We screened 2300 nasopharyngeal swabs using multiplex real time reverse transcriptase polymerase chain reaction. We amplified a segment of the first and second hypervariable regions, as well as the conserved portion of the third domain of the G-gene using HRSV-B specific primers, sequenced by Sanger di-deoxy chain termination method and thereafter analyzed the sequences.

RESULTS

We characterized the circulating strains into three known genotypes: SAB4 (1.4%), BA7 (1.4%), and multiple variants of BA9 (97.2%). The majority of BA9 viruses were uniquely Kenyan with only 4% aligning with BA9 lineages found elsewhere. The mean evolutionary rate of the HRSV-B was estimated to be 3.08 × 10-3 substitutions per site per year.

CONCLUSION

Our findings indicate that the circulating HRSV-B viruses in Kenya underwent a slower evolution during the period of 2007-2010. Additionally, our findings reveal the existence of a unique lineage as well as new variants that have not been reported elsewhere to date.

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2

Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using bioinformatics tools such as the Bayesian phylogenetics software BEAST 2 package (v.2.7.6), we constructed time-scale evolutionary trees based on the gene sequences. Most of the recent common ancestors (MRCAs) of the RdRp region and VP1 gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 RdRp region and VP1 gene were divided into two clusters. Further, the MRCAs of the RdRp region and VP1 gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for VP1 gene in HuSaV GI.1 than that in HuSaV GI.2, furthermore, were higher in GI.1 Cluster B than GI.1 Cluster A. In addition, a steep increase was observed in the time-scaled genome population size of the HuSaV GI.1 Cluster B. These results indicate that the HuSaV GI.1 Cluster B may be evolving more actively than other genotypes. The conformational B-cell epitopes were predicted with a higher probability in RdRp for GI.1 and in VP1 for GI.2, respectively. These results suggest that the RdRp region and VP1 gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the RdRp region and VP1 gene of HuSaV GI.1 and GI.2, emphasizing the need for a 'One Health' approach to better understand and combat this pathogen.

Evolutionary and functional analyses reveal a role for the RHIM in tuning RIPK3 activity across vertebrates

Receptor interacting protein kinases (RIPK) RIPK1 and RIPK3 play important roles in diverse innate immune pathways. Despite this, some RIPK1/3-associated proteins are absent in specific vertebrate lineages, suggesting that some RIPK1/3 functions are conserved while others are more evolutionarily labile. Here, we perform comparative evolutionary analyses of RIPK1-5 and associated proteins in vertebrates to identify lineage-specific rapid evolution of RIPK3 and RIPK1 and recurrent loss of RIPK3-associated proteins. Despite this, diverse vertebrate RIPK3 proteins are able to activate NF-κB and cell death in human cells. Additional analyses revealed a striking conservation of the RIP homotypic interaction motif (RHIM) in RIPK3, as well as other human RHIM-containing proteins. Interestingly, diversity in the RIPK3 RHIM can tune activation of NF-κB while retaining the ability to activate cell death. Altogether, these data suggest that NF-κB activation is a core, conserved function of RIPK3, and the RHIM can tailor RIPK3 function to specific needs within and between species.

Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus

The effectiveness of poultry vaccination in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been debated, and its impact on wild birds remains uncertain. Here, we reconstruct the movements of H5 subtype AIV lineages among vaccinated poultry, unvaccinated poultry, and wild birds, worldwide, from 1996 to 2023. We find that there is a time lag in viral transmission among different host populations and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry. Furthermore, our findings suggest that the HA (hemagglutinin) gene of the AIV lineage that circulated predominately in Chinese poultry experienced greater nonsynonymous divergence and adaptive fixation than other lineages. Our results indicate that the epidemiological, ecological, and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways and that much work is needed to better understand how such interventions may affect AIV transmission to, within, and from wild birds.

zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters

Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements, such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to handle thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) performing population genetic investigations of BGCs for a fungal species, and (iii) uncovering evolutionary trends for a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.

The Potassium Utilization Gene Network in Brassica napus and Functional Validation of BnaZSHAK5.2 Gene in Response to Potassium Deficiency

Potassium, an essential inorganic cation, is crucial for the growth of oil crops like Brassica napus L. Given the scarcity of potassium in soil, enhancing rapeseed's potassium utilization efficiency is of significant importance. This study identified 376 potassium utilization genes in the genome of B. napus ZS11 through homologous retrieval, encompassing 7 functional and 12 regulatory gene families. These genes are unevenly distributed across 19 chromosomes, and the proteins encoded by these genes are mainly localized in the cell membrane, vacuoles, and nucleus. Microsynteny analysis highlighted the role of small-scale replication events and allopolyploidization in the expansion of potassium utilization genes, identifying 77 distinct types of cis-acting elements within their promoter regions. The regulatory mechanisms of potassium utilization genes were provided by analyses of transcription factors, miRNA, and protein interaction networks. Under low potassium stress, the potassium utilization genes, particularly those belonging to the KUP and CBL families, demonstrate pronounced co-expression. RNA-seq and RT-qPCR analysis identified the BnaZSHAK5.2 gene, which is a high-affinity potassium ion transporter, playing a crucial role in the stress response to potassium deficiency in B. napus, as its expression is strongly induced by low potassium stress. A functional complementation study demonstrates that the BnaZSHAK5.2 gene could rescue the primary root growth of the Athak5 mutant under low potassium conditions, confirming its role in response to low potassium stress by sustaining root development.

Phylodynamic reconstruction of major chicken infectious anemia virus clades epidemiology, dispersal, and evolution

Introduction

Immunosuppressive diseases, such as chicken infectious anemia virus (CIAV), pose a major threat to livestock farming due to reduced disease resistance, poor vaccine response, and overall poor productivity. CIAV, recognized globally for decades, shows a significant genetic diversity, but its implications remain underexplored.

Methods

This study analyzed over 1,000 VP1 sequences and examined CIAV's epidemiology, evolution, and spread with various phylodynamic and phylogeographic approaches.

Results

Findings suggest that CIAV likely originated in Japan in the early 20th century, followed by worldwide diversification in two main clades. Both clades exhibited no significant competition and similar global patterns, characterized by a progressive increase until about 2000, when a transient decline was observed for some years, potentially reflecting the increasing use of vaccines. Accordingly, although significant selective pressures were shaping viral evolution, comparable strengths were estimated in the two viral populations. The phylogeographic analysis identified several connections involving also distantly related regions, and more generally, multiple introduction events occurred in several countries and were followed by local evolution, indicative of unconstrained viral circulation.

Discussion

Overall, the study highlights the ongoing circulation and evolution of different CIAV variants worldwide, where biosecurity measures and vaccination appear insufficient to prevent viral presence and dispersal.

AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides

Characterising functional diversity is a vital element to understanding a species' immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials. Here, we utilised data from 418 koala whole genomes to undertake the first comprehensive analysis of AMP diversity across a mammalian wildlife species' range. Overall, allelic diversity was lower than other immune gene families such as MHC, suggesting that AMPs are more conserved, although balancing selection was observed in PhciDEFB12. Some non-synonymous SNPs in the active peptide are predicted to change AMP function through stop gains, change in structure, and increase in peptide charge. Copy number variants (CNVs) were observed in two defensins and one cathelicidin. Interestingly, the most common CNV was the duplication of PhciCATH5, a cathelicidin with activity against chlamydia, which was more common in the southern part of the species range than the north. AMP copy number is correlated with expression levels, so we hypothesise that there is a selective pressure from chlamydia for duplications in PhciCATH5. Future studies should use phenotypic metadata to assess the functional impacts of this gene duplication.

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure

RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites in the viral genome. Understanding this variation can shed light on the mutational processes at play, and is crucial for quantitative modeling of viral evolution. Using the millions of available SARS-CoV-2 full-genome sequences, we estimate rates of synonymous mutations for all 12 possible nucleotide mutation types and examine how much these rates vary between sites. We find a surprisingly high level of variability and several striking patterns: the rates of four mutation types suddenly increase at one of two gene boundaries; the rates of most mutation types strongly depend on a site's local sequence context, with up to 56-fold differences between contexts; consistent with a previous study, the rates of some mutation types are lower at sites engaged in RNA secondary structure. A simple log-linear model of these features explains ~15-60% of the fold-variation of mutation rates between sites, depending on mutation type; more complex models only modestly improve predictive power out of sample. We estimate the fitness effect of each mutation based on the number of times it actually occurs versus the number of times it is expected to occur based on the model. We identify several small regions of the genome where synonymous or noncoding mutations occur much less often than expected, indicative of strong purifying selection on the RNA sequence that is independent of protein sequence. Overall, this work expands our basic understanding of SARS-CoV-2's evolution by characterizing the virus's mutation process at the level of individual sites and uncovering several striking mutational patterns that arise from unknown mechanisms.

Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease

The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.

Evolution and spread of Xanthomonas citri subsp. citri in the São Paulo, Brazil, citrus belt inferred from 758 novel genomes

The São Paulo state citrus belt in Brazil is a major citrus production region. Since at least 1957, citrus plantations in this region have been affected by citrus canker, an economically damaging disease caused by Xanthomonas citri subsp. citri (Xcc). For about 50 years, until 2017, a citrus canker eradication programme was carried out in this region. In this work, our aim was to investigate the effects of the eradication programme on genetic variability and evolution of Xcc. To this end, we sequenced and analysed 758 Xcc genomes sampled in the São Paulo citrus belt, together with 730 publicly available Xcc genomes from around the world. Our phylogenomic analyses show that these genomes can be grouped into seven major lineages and that in São Paulo, lineage L7 is dominant. Our time estimate for its appearance closely matches the date when citrus production expanded. L7 can be subdivided into lineages L7.1 and L7.2. In our samples, L7.2, which we estimate to have emerged around 1964, is by far the most abundant, showing that the eradication programme had little impact on strain diversification. On the other hand, oscillations in the estimated effective population size of L7.2 strains over time closely match the shifts in the eradication programme. In sum, we present a detailed view of the genomic diversity of Xcc in the world and in São Paulo, the largest such effort in terms of a number of genomes for a crop pathogen undertaken so far. The methods employed here can form the basis for active genomic surveillance of Xcc in major citrus production areas.

Detection and Molecular Characterization of Gyrovirus Galga 1 in Chickens in Northern Vietnam Reveals Evidence of Recombination

In total, 126 tissue-pooled samples were collected from suspected sick chickens showing signs of stunted growth, weakness, and diarrhea in five provinces/cities in Northern Vietnam. The Gyrovirus gala 1 (GyVg1) genome was detected in 26 (20.63%) of the 126 chicken samples based on a polymerase chain reaction assay. The five Vietnamese GyVg1 genomes obtained were all 2.375 nucleotides in length. Among them, the nucleotide identical rates ranged from 94.01% to 100%. Phylogenetic analysis of the complete genomes revealed that the current five GyVg1 strains belonged to different branches at two levels: GyVg1 II (two of five strains) and GyVg1 III (three of five strains). The Vietnamese GyVg1 strains were generically clustered with the Japanese and Chinese strains. Some amino acid substitutions were found in VPs 1, 2, and 3 of the Vietnamese GyVg1 strains. In addition, three and two positive selection sites of VPs 1 and 3 were detected, respectively. A recombination event occurred and generated a recombination Chicken/Vietnam/AGV/VNUA-TN12/2023 strain. These findings indicate the first evidence of GyVg1 viruses circulating in commercial chicken flocks in Vietnam.

Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection

The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection. Our data supported an extensive gene flow in European sardine. However, phylogenetic analyses of mitogenomes revealed diversification patterns related to climate shifts in the late Miocene and Pliocene that may indicate past divergence related to rapid demographic expansion. Tests of selection showed a significant signature of purifying selection, but positive selection was also detected in different sites and specific mitochondrial lineages. Our results showed that European sardine diversification has been strongly driven by climate shifts, and rapid changes in marine environmental conditions are likely to strongly affect the distribution and stock size of this species.

Widespread adaptive evolution in angiosperm photosystems provides insight into the evolution of photosystem II repair

Oxygenic photosynthesis generates the initial energy source that fuels nearly all life on Earth. At the heart of the process are the photosystems, which are pigment binding multiprotein complexes that catalyze the first step of photochemical conversion of light energy into chemical energy. Here, we investigate the molecular evolution of the plastid-encoded photosystem subunits at single-residue resolution across 773 angiosperm species. We show that despite an extremely high level of conservation, 7% of residues in the photosystems, spanning all photosystem subunits, exhibit hallmarks of adaptive evolution. Through in silico modeling of these adaptive substitutions, we uncover the impact of these changes on the predicted properties of the photosystems, focusing on their effects on cofactor binding and intersubunit interface formation. By analyzing these cohorts of changes, we reveal that evolution has repeatedly altered the interaction between Photosystem II and its D1 subunit in a manner that is predicted to reduce the energetic barrier for D1 turnover and photosystem repair. Together, these results provide insight into the trajectory of photosystem adaptation during angiosperm evolution.

Unveiling MHC-DAB Polymorphism Within the Western Balkan Salmonid Hotspot: Preliminary Outcomes from Native Trouts of Ohrid Lake and the Drin-Skadar Drainage (Albania)

Due to their involvement in pathogen-mediated immune responses, the hypervariable genes of the Major Histocompatibility Complex (MHC) have become a paradigm for investigating the evolution and maintenance of genetic (adaptive) diversity, contextually providing insight into the viability of wild populations, which is meaningful for conservation. Here, we provide the first preliminary characterization of MHC polymorphism and evolution in trouts from Albania, a known hotspot of Salmonid diversity harboring ecologically and phylogenetically distinct native (threatened) taxa. Overall, 36 trout-including Lake Ohrid-endemic Salmo ohridanus and S. letnica, and both riverine and lacustrine native brown trout (the S. trutta complex) from the Drin-Skadar drainage-were genotyped at the MHC-DAB locus through next-generation amplicon sequencing. We identified 34 alleles (including 30 novel alleles), unveiling remarkable population/taxon MHC-DAB distinctiveness. Despite apparent functional (supertype) similarity, S. letnica and the S. trutta complex showed MHC-typical high sequence/allele diversity and evidence of global/codon-specific positive selection, particularly at antigen-binding sites. Conversely, deep-water-adapted S. ohridanus revealed unexpectedly reduced allelic/supertype diversity and relaxed selection. Evolution by reticulation and signals of trans-species polymorphism emerged from sequence genealogies. Further investigations and increased sampling will provide a deeper understanding of the evolutionary mechanisms yielding the observed pattern of MHC diversity across Albanian trout taxa and populations.

HIV-1 Vif global diversity and possible APOBEC-mediated response since 1980

HIV-1 Vif's principal function is to counter the antiretroviral activities of DNA-editing APOBEC3 cytidine deaminases. Unconstrained APOBEC3 activity introduces premature stop codons in HIV-1 genes and can lead to viral inactivation. To investigate the evolution and diversification of Vif over the HIV-1 pandemic and document evidence of APOBEC3-mediated pressure, we analyzed 4612 publicly available sequences derived from 10 dominant subtypes and circulating recombinant forms (CRFs) using the Hervé platform. We found widespread evidence of diversifying selection that was convergent across subtypes and CRFs, but remarkable stability in consensus sequences over time. Divergence and selection did not favor APOBEC3-interacting sites. We furthermore found that APOBEC3-induced substitutions in env and gag-pol genes increased over time and were positively associated with vif diversity. These results suggest that APOBEC3-driven adaptation in Vif is relatively rare and that permissiveness to human APOBEC3-induced substitution as a mechanism for generating diversity may be advantageous to HIV-1 evolution.

A conserved fertilization complex bridges sperm and egg in vertebrates

Fertilization, the basis for sexual reproduction, culminates in the binding and fusion of sperm and egg. Although several proteins are known to be crucial for this process in vertebrates, the molecular mechanisms remain poorly understood. Using an AlphaFold-Multimer screen, we identified the protein Tmem81 as part of a conserved trimeric sperm complex with the essential fertilization factors Izumo1 and Spaca6. We demonstrate that Tmem81 is essential for male fertility in zebrafish and mice. In line with trimer formation, we show that Izumo1, Spaca6, and Tmem81 interact in zebrafish sperm and that the human orthologs interact in vitro. Notably, complex formation creates the binding site for the egg fertilization factor Bouncer in zebrafish. Together, our work presents a comprehensive model for fertilization across vertebrates, where a conserved sperm complex binds to divergent egg proteins-Bouncer in fish and JUNO in mammals-to mediate sperm-egg interaction.

Evolution and comparative transcriptome analysis of glucosinolate pathway genes in Brassica napus L

Glucosinolates (GSLs) are important secondary metabolites abundantly distributed in Brassicaceae plants, whose degradation products benefit plant resistance but are regarded as disadvantageous factors for human health. Thus, reducing GSL content is an important goal in the breeding program in crops, such as Brassica napus. In this study, 1280 genes in the GSL pathway were identified from 14 land plant genomes, which are specifically distributed in Brassicaceae and are extensively expanded in B. napus. Most GSL pathway genes had many positive selection sites, especially the encoding genes of transcription factors (TFs) and structural genes involved in the GSL breakdown process. There are 344 genes in the GSL pathway in the B. napus genome, which are unequally distributed on the 19 chromosomes. Whole-genome duplication mainly contributed to the gene expansion of the GSL pathway in B. napus. The genes in GSL biosynthesis were regulated by various TFs and cis-elements in B. napus and mainly response to abiotic stress and hormone induction. A comparative transcriptome atlas of the roots, stems, leaves, flowers, siliques, and seeds of a high- (ZY821), and a low-GSL-content (ZS11) cultivar was constructed. The features of the two cultivars may be attributed to diverse expression differences in each organ at different stages, especially in seeds. In all, 65 differential expressed genes (DEGs) concentrated on the core structure pathway were inferred to mainly influence the GSL contents between ZY821 and ZS11. This study provides an important RNA-seq dataset and diverse gene resources for future manipulating GSLs biosynthesis and distribution in B. napus using molecular breeding methods.

Levin T. Evolutionary Dynamics of Proinflammatory Caspases in Primates and Rodents

Caspase-1 and related proteases are key players in inflammation and innate immunity. Here, we characterize the evolutionary history of caspase-1 and its close relatives across 19 primates and 21 rodents, focusing on differences that may cause discrepancies between humans and animal studies. While caspase-1 has been retained in all these taxa, other members of the caspase-1 subfamily (caspase-4, caspase-5, caspase-11, and caspase-12 and CARD16, 17, and 18) each have unique evolutionary trajectories. Caspase-4 is found across simian primates, whereas we identified multiple pseudogenization and gene loss events in caspase-5, caspase-11, and the CARDs. Because caspase-4 and caspase-11 are both key players in the noncanonical inflammasome pathway, we expected that these proteins would be likely to evolve rapidly. Instead, we found that these two proteins are largely conserved, whereas caspase-4's close paralog, caspase-5, showed significant indications of positive selection, as did primate caspase-1. Caspase-12 is a nonfunctional pseudogene in humans. We find this extends across most primates, although many rodents and some primates retain an intact, and likely functional, caspase-12. In mouse laboratory lines, we found that 50% of common strains carry nonsynonymous variants that may impact the functions of caspase-11 and caspase-12 and therefore recommend specific strains to be used (and avoided). Finally, unlike rodents, primate caspases have undergone repeated rounds of gene conversion, duplication, and loss leading to a highly dynamic proinflammatory caspase repertoire. Thus, we uncovered many differences in the evolution of primate and rodent proinflammatory caspases and discuss the potential implications of this history for caspase gene functions.

Novel imported clades accelerated the RSV surge in Beijing, China, 2023-2024

OBJECTIVES

Despite the optimization of the zero-COVID policy in late 2022, there was a subsequent increase noted in the number of respiratory syncytial virus (RSV) cases in Northern China. In this study, we investigated and characterized the dynamics of this surge at the genomic level in Beijing, China.

METHODS

Patients with acute respiratory tract infections (ARTIs) were enrolled from 35 sentinel hospitals in Beijing, China. Epidemiological investigations, G gene amplification, and whole-genome sequencing were performed, followed by epidemiological analysis, imported clade detection, and mutation identification. We also combined global data to illustrate the biological and epidemiological characteristics of the emerging clades.

RESULTS

A total of 60,423 patients with ARTIs were recruited between January 2015 and January 2024. The RSV peak observed in the winter of 2023 was the highest in the past 9 years. Two novel imported clades, A.D.5.2 and B.D.E.1, were detected for the first time in China. This surge was mainly driven by B.D.E.1, which exhibited a significantly higher proportion of older individuals both in Beijing and globally. Seven non-synonymous mutations in B.D.E.1 were found in Beijing. B.D.E.1 had more sites suffering from positive selection than its parent.

CONCLUSIONS

The novel imported clade B.D.E.1 accelerated an unprecedented RSV surge in Beijing, presenting noteworthy epidemiological and biological characteristics. Continuous RSV genome monitoring has important implications for RSV outbreak identification, genetic diversity tracking, vaccine development, and strategy implementation.

Untangling Zebrafish Genetic Annotation: Addressing Complexities and Nomenclature Issues in Orthologous Evaluation of TCOF1 and NOLC1

Treacher Collins syndrome (TCS) is a genetic disorder affecting facial development, primarily caused by mutations in the TCOF1 gene. TCOF1, along with NOLC1, play important roles in ribosomal RNA transcription and processing. Previously, a zebrafish model of TCS successfully recapitulated the main characteristics of the syndrome by knocking down the expression of a gene on chromosome 13 (coding for Uniprot ID B8JIY2), which was identified as the TCOF1 orthologue. However, database updates renamed this gene as nolc1 and the zebrafish database (ZFIN) identified a different gene on chromosome 14 as the TCOF1 orthologue (coding for Uniprot ID E7F9D9). NOLC1 and TCOF1 are large proteins with unstructured regions and repetitive sequences that complicate alignments and comparisons. Also, the additional whole genome duplication of teleosts sets further difficulty. In this study, we present evidence that endorses that NOLC1 and TCOF1 are paralogs, and that the zebrafish gene on chromosome 14 is a low-complexity LisH domain-containing factor that displays homology to NOLC1 but lacks essential sequence features to accomplish TCOF1 nucleolar functions. Our analysis also supports the idea that zebrafish, as has been suggested for other non-tetrapod vertebrates, lack the TCOF1 gene that is associated with tripartite nucleolus. Using BLAST searches in a group of teleost genomes, we identified fish-specific sequences similar to E7F9D9 zebrafish protein. We propose naming them "LisH-containing Low Complexity Proteins" (LLCP). Interestingly, the gene on chromosome 13 (nolc1) displays the sequence features, developmental expression patterns, and phenotypic impact of depletion that are characteristic of TCOF1 functions. These findings suggest that in teleost fish, the nucleolar functions described for both NOLC1 and TCOF1 mediated by their repeated motifs, are carried out by a single gene, nolc1. Our study, which is mainly based on computational tools available as free web-based algorithms, could help to solve similar conflicts regarding gene orthology in zebrafish.

Evolutionary analysis of ZAP and its cofactors identifies intrinsically disordered regions as central elements in host-pathogen interactions

The zinc-finger antiviral protein (ZAP) is an innate immunity sensor of non-self nucleic acids. Its antiviral activity is exerted through the physical interaction with different cofactors, including TRIM25, Riplet and KHNYN. Cellular proteins that interact with infectious agents are expected to be engaged in genetic conflicts that often result in their rapid evolution. To test this possibility and to identify the regions most strongly targeted by natural selection, we applied in silico molecular evolution tools to analyze the evolutionary history of ZAP and cofactors in four mammalian groups. We report evidence of positive selection in all genes and in most mammalian groups. On average, the intrinsically disordered regions (IDRs) embedded in the four proteins evolve significantly faster than folded domains and most positively selected sites fall within IDRs. In ZAP, the PARP domain also shows abundant signals of selection, and independent evolution in different mammalian groups suggests modulation of its ADP-ribose binding ability. Detailed analyses of the biophysical properties of IDRs revealed that chain compaction and conformational entropy are conserved across mammals. The IDRs in ZAP and KHNYN are particularly compact, indicating that they may promote phase separation (PS). In line with this hypothesis, we predicted several PS-promoting regions in ZAP and KHNYN, as well as in TRIM25. Positively selected sites are abundant in these regions, suggesting that PS may be important for the antiviral functions of these proteins and the evolutionary arms race with viruses. Our data shed light into the evolution of ZAP and cofactors and indicate that IDRs represent central elements in host-pathogen interactions.

Molecular evolution and genetic diversity of defective chorion 1 in Anastrepha fraterculus and Anastrepha obliqua (Diptera, Tephritidae)

The family Tephritidae comprises numerous fruit fly species, some of which are economically significant, such as several in the genus Anastrepha. Most pest species in this genus belong to the fraterculus group, characterized by closely related species that are difficult to differentiate due to recent divergence and gene flow. Identifying genetic markers for their study is paramount for understanding the group's evolution and eventual phytosanitary control. Because there is variation in eggshell morphology among species in the genus, the study of the rapidly evolving defective chorion 1 (dec-1) gene, which is crucial for chorion formation and reproduction, could provide relevant information for Anastrepha differentiation. We compared transcriptome sequences of dec-1 from two of the most important pest species in the genus, Anastrepha fraterculus and Anastrepha obliqua to dec-1 sequences from Anastrepha ludens, which was used for structure prediction. Furthermore, we amplified a conserved exon across populations of these species. These data revealed three alternative transcripts in A. fraterculus and A. obliqua, consistent with patterns found in other Tephritidae; we obtained orthologous sequences for these other tephritids from NCBI to investigate patterns of selection affecting this gene at different hierarchical levels using different methods. These analyses show a general pattern of purifying selection across the whole gene and throughout its history at different hierarchical levels, from populations to more distantly related species. That notwithstanding, we still found evidence of positive and episodic diversifying selection at different levels. Different parts of the gene have shown distinct evolutionary rates, which were associated with the diverse proproteins produced by posttranslational changes of DEC-1, with proproteins that are incorporated in the chorion earlier in egg formation being in general more conserved than others that are incorporated later. This correlation appears more evident in certain lineages, including the branch that separates Anastrepha, as well as other internal branches that differentiate species within the genus. Our data showed that this gene shows remarkable variation across its different exons, which has proven to be informative at different evolutionary levels. These changes hold promise not only for studying differentiation in Anastrepha but also for the eventual management of selected pest species.

Complete coding region sequence analyses and antigenic characterization of emerging lineage G-IX of foot- and-mouth disease virus serotype Asia1

Foot-and-mouth disease Virus (FMDV) serotype Asia1 is prevalent in the Indian subcontinent, with only G-III and G-VIII reported in India until 2020. However, in 2019, a novel genetic group within serotype Asia1, designated as G-IX, emerged in Bangladesh, followed by its detection in India in 2020. This report presents analyses of the complete coding region sequences of the G-IX lineage isolates. The length of the open reading frame (ORF) of the two G-IX isolates was 6990 nucleotides without any deletion or insertion. The G-IX isolates showed the highest sequence similarity with an isolate of G-III at the ORF, L, P2, and P3 regions, and with an isolate of G-VIII at the P1 region. Phylogenetic analysis based on the capsid region (P1) supports the hypothesis that G-VIII and G-IX originated from a common ancestor, as speculated earlier. Further, VP1 region-based phylogenetic analyses revealed the re-emergence of G-VIII after a gap of 3 years. One isolate of G-VIII collected during 2023 revealed a codon insertion in the G-H loop of VP1. The vaccine matching studies support the suitability of the currently used Indian vaccine strain IND63/1972 to contain outbreaks due to viruses belonging to G-IX.

Phylogenetic and phylodynamic analysis of respiratory syncytial virus strains circulating in children less than five years of age in Karachi-Pakistan

BACKGROUND

Respiratory syncytial virus (RSV) is one of the leading causes of infant morbidity and mortality worldwide, especially in Pakistan. To date, few studies have explored RSV epidemiology in different areas of Pakistan. However, none have performed comprehensive phylogenetic and phylodynamic analyses of RSV strains. This study presents a comprehensive genetic and phylodynamic analysis of RSV strains in children less than five years old in Karachi, Pakistan.

METHODS

This study used retrospectively collected nasopharyngeal (swab) samples from 155 children with qPCR-confirmed RSV infection. The samples were used to perform RSV genotyping using PCR employing RSV glycoprotein gene-specific primers. The RSVA and RSVB genotyping was performed using BLAST and Maximum-likelihood (ML) phylogenetic methods. Similarly, the relationship with other RSV strains was analyzed using ML phylogenetic cluster analysis. The RSVA and RSVB mean genetic diversity and coefficient of differentiation were calculated using MEGA7 software. Furthermore, the time to the most common recent ancestor (tMRCA) and effective population size of RSV genotypes A and B were estimated using a Bayesian MCMC analysis. Finally, site selection pressure and glycosylation analyses were performed using FUBAR and NetNGlyc/NetOGlyc tools.

RESULTS

Out of 155, 98 and 57 sequences were RSVA and RSVB, respectively. The tMRCA was estimated to be around 2002 and 2005 for RSVA and RSVB, respectively. RSVA sequences formed two NA1 genotype clusters, comprising 95 and three sequences, respectively. RSVB formed three clusters, where 24 and two sequences clustered with BA9 and BA12 genotypes, respectively, while 31 sequences formed a unique cluster. The RSVA and RSVB glycoprotein gene sequences exhibited N- and O- glycosylation and selection pressure at several sites. RSV B exhibited slightly higher (0.042) nucleotide diversity per site (π) as compared to RSVA (0.019).

CONCLUSIONS

Our results suggest that RSVA and RSVB strains in Pakistan exhibit distinct genotypic clusters and differ in their estimated tMRCA. Additionally, both genotypes showed glycosylation and selection pressure at specific sites, with RSVB exhibiting higher nucleotide divergence per site (π), indicating its potential to undergo further evolutionary changes and adaptation. Overall, this study provides unique insights into RSV molecular epidemiology. The study may also help improve our understanding of RSV evolutionary changes and the emergence of new genotypes in different regions worldwide and within Pakistan.