Evolutionary Sequence Analysis Research Articles

Evolutionary Dynamics of RuBisCO: Emergence of the Small Subunit and its Impact Through Time.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an ancient protein critical for CO2-fixation and global biogeochemistry. Form-I RuBisCO complexes uniquely harbor small subunits that form a hexadecameric complex together with their large subunits. The small subunit protein is thought to have significantly contributed to RuBisCO's response to the atmospheric rise of O2 ∼2.5 billion years ago, marking a pivotal point in the enzyme's evolutionary history. Here, we performed a comprehensive evolutionary analysis of extant and ancestral RuBisCO sequences and structures to explore the impact of the small subunit's earliest integration on the molecular dynamics of the overall complex. Our simulations suggest that the small subunit restricted the conformational flexibility of the large subunit early in its history, impacting the evolutionary trajectory of the Form-I RuBisCO complex. Molecular dynamics investigations of CO2 and O2 gas distribution around predicted ancient RuBisCO complexes suggest that a proposed "CO2-reservoir" role for the small subunit is not conserved throughout the enzyme's evolutionary history. The evolutionary and biophysical response of RuBisCO to changing atmospheric conditions on ancient Earth showcase multi-level and trackable responses of enzymes to environmental shifts over long timescales.

Genomic Characterization and Comparative Genomic Analysis of the Foodborne Burkholderia gladioli pv. cocovenenans.

The Burkholderia gladioli pv. cocovenenans (B. cocovenenans) has been linked to fatal food poisoning cases, which could produce the deadly toxin of bongkrekic acid (BA). However, genomic characterization and toxin production pathways of B. cocovenenans strains remain elusive. This study aimed to explore the BA-producing ability associated with the evolution of the bon gene cluster and to analyze the intraspecies genomic diversity and phylogenetic relationships of B. gladioli based on the 17 genomes of B. cocovenenans strains isolated from Shenzhen City, China. Genome sequencing results suggested that the genome sizes of these B. cocovenenans strains were mostly approximately 8 Mb, with a GC content of approximately 68%. The evolutionary tree analysis of the whole-genome sequences showed that significant divergences and distinct cluster were exhibited among these B. cocovenenans strains. Comparative genomic analysis indicated that the genomes of strains 2020051, 2021031, and 2021067 contained the complete and entire bon gene cluster, supporting that these strains displayed obviously BA-producing ability. The genomes of strains 2021028 and 2020041 lacked the entire bon gene cluster. However, the genomes of strains 2021037, 2021024, 2021035, and 2021031 exhibited disruptions in their bon gene clusters. This finding indicated the loss of specific genes within the cluster, suggesting a reduced capability for BA production in these strains. The present results indicated that the bon gene cluster in the genome played a key role in the toxin BA biosynthesis of different B. cocovenenans strains. This study provided a comprehensive understanding of the relationship between genomic diversity and BA production of this lethal foodborne pathovar, which will potentially contribute to the risk identification and food poisoning outbreak prevention of B. cocovenenans.

Microscopic and Transcriptome Analysis Reveals that the Self-incompatibility in Rabbiteye Blueberry Belongs to the S-RNase-based Gametophytic Type

Berry fruits produced by Vaccinium (Ericaceae) plants are small but have a signature flavor and have become increasingly popular in the 21st century. However, self-incompatibility (SI) results in a relatively low fruit-set ratio and reduced fruit quality in Vaccinium. In this study, using Vaccinium ashei (V. ashei) styles after cross-pollination (CP) and self-pollination (SP) as material, transcriptomics and gene expression analyses were performed using high-throughput RNA sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). Subsequently, evolutionary analysis and conserved sequences analysis of candidate genes were conducted. Among the 135,324 unigenes, 30,863 were shown to be differentially expressed, and eight randomly selected differentially expressed genes were expressed in the styles at 96 hours after SP and CP. The transcriptomics and qRT-PCR results were significantly correlated, which confirmed the reliability of the differentially expressed genes obtained in our study. Compared with SP96, six differentially expressed ribonuclease T2 family genes were obtained in CP96, which were considered candidates for S-RNase. Additionally, the spatiotemporal and organizational expression trends of six candidates for S-RNase were confirmed by qRT-PCR, and the evolutionary and conservative sequence analysis indicated six candidate S-RNases with the typical S-RNase structure. The spatiotemporal and organizational expression results and evolutionary and conservative sequence analyses of the six candidate S-RNases suggest that SI in V. ashei is likely an S-RNase-mediated gametophytic one. This finding suggests the involvement of novel, previously undiscovered components involved in the V. ashei SI system. These findings help elucidate the molecular mechanisms of SI in rabbiteye blueberry and may also benefit breeding, production, and genomics research in V. ashei and other Vaccinium species.

Nutrient Signaling-Dependent Quaternary Structure Remodeling Drives the Catalytic Activation of metazoan PASK.

The Per-Arnt-Sim (PAS) domains are characterized by diverse sequences and feature tandemly arranged PAS and PAS-associated C-terminal (PAC) motifs that fold seamlessly to generate the metabolite-sensing PAS domain. Here, using evolutionary scale sequence, domain mapping, and deep learning-based protein structure analysis, we deconstructed the sequence-structure relationship to unearth a novel example of signal-regulated assembly of PAS and PAC subdomains in metazoan PAS domain-regulated kinase (PASK). By comparing protein sequence, domain architecture, and computational protein models between fish, bird, and mammalian PASK orthologs, we propose the existence of previously unrecognized third PAS domain of PASK (PAS-C) formed through long-range intramolecular interactions between the N-terminal PAS fold and the C-terminal PAC fold. We experimentally validated this novel structural design using residue-level cross-linking assays and showed that the PAS-C domain assembly is nutrient-responsive. Furthermore, by combining structural phylogeny approaches with residue-level cross-linking, we revealed that the PAS-C domain assembly links nutrient sensing with quaternary structure reorganization in PASK, stabilizing the kinase catalytic core of PASK. Thus, PAS-C domain assembly likely integrates environmental signals, thereby relaying sensory information for catalytic control of the PASK kinase domain. In conclusion, we theorize that during their horizontal transfer from bacteria to multicellular organisms, PAS domains gained the capacity to integrate environmental signals through dynamic modulation of PAS and PAC motif interaction, adding a new regulatory layer suited for multicellular systems. We propose that metazoan PAS domains are likely to be more dynamic in integrating sensory information than previously considered, and their structural assembly could be targeted by regulatory signals and exploited to develop therapeutic strategies.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles

BackgroundVenoms have evolved independently over a hundred times in the animal kingdom to deter predators and/or subdue prey. Venoms are cocktails of various secreted toxins, whose origin and diversification provide an appealing system for evolutionary researchers. Previous studies of the ant venom of Tetramorium bicarinatum revealed several Myrmicitoxin (MYRTX) peptides that gathered into seven precursor families suggesting different evolutionary origins. Analysis of the T. bicarinatum genome enabling further genomic approaches was necessary to understand the processes underlying the evolution of these myrmicitoxins.ResultsHere, we sequenced the genome of Tetramorium bicarinatum and reported the organisation of 44 venom peptide genes (vpg). Of the eleven chromosomes that make up the genome of T. bicarinatum, four carry the vpg which are organized in tandem repeats. This organisation together with the ML evolutionary analysis of vpg sequences, is consistent with evolution by local duplication of ancestral genes for each precursor family. The structure of the vpg into two or three exons is conserved after duplication events while the promoter regions are the least conserved parts of the vpg even for genes with highly identical sequences. This suggests that enhancer sequences were not involved in duplication events, but were recruited from surrounding regions. Expression level analysis revealed that most vpg are highly expressed in venom glands, although one gene or group of genes is much more highly expressed in each family. Finally, the examination of the genomic data revealed that several genes encoding transcription factors (TFs) are highly expressed in the venom glands. The search for binding sites (BS) of these TFs in the vpg promoters revealed hot spots of GATA sites in several vpg families.ConclusionIn this pioneering investigation on ant venom genes, we provide a high-quality assembly genome and the annotation of venom peptide genes that we think can fosters further genomic research to understand the evolutionary history of ant venom biochemistry.

Evolution shapes interaction patterns for epistasis and specific protein binding in a two-component signaling system

The elegant design of protein sequence/structure/function relationships arises from the interaction patterns between amino acid positions. A central question is how evolutionary forces shape the interaction patterns that encode long-range epistasis and binding specificity. Here, we combined family-wide evolutionary analysis of natural homologous sequences and structure-oriented evolution simulation for two-component signaling (TCS) system. The magnitude-frequency relationship of coupling conservation between positions manifests a power-law-like distribution and the positions with highly coupling conservation are sparse but distributed intensely on the binding surfaces and hydrophobic core. The structure-specific interaction pattern involves further optimization of local frustrations at or near the binding surface to adapt the binding partner. The construction of family-wide conserved interaction patterns and structure-specific ones demonstrates that binding specificity is modulated by both direct intermolecular interactions and long-range epistasis across the binding complex. Evolution sculpts the interaction patterns via sequence variations at both family-wide and structure-specific levels for TCS system.

Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution.

Understanding gene evolution across genomes and organisms, including ctenophores, can provide unexpected biological insights. It enables powerful integrative approaches that leverage sequence diversity to advance biomedicine. Sequencing and bioinformatic tools can be inexpensive and user-friendly, but numerous options and coding can intimidate new users. Distinct challenges exist in working with data from diverse species but may go unrecognized by researchers accustomed to gold-standard genomes. Here, we provide a high-level workflow and detailed pipeline to enable animal collection, single-molecule sequencing, and phylogenomic analysis of gene and species evolution. As a demonstration, we focus on (1) PacBio RNA-seq of the genome-sequenced ctenophore Mnemiopsis leidyi, (2) diversity and evolution of the mechanosensitive ion channel Piezo in genetic models and basal-branching animals, and (3) associated challenges and solutions to working with diverse species and genomes, including gene model updating and repair using single-molecule RNA-seq. We provide a Python Jupyter Notebook version of our pipeline (GitHub Repository: Ctenophore-Ocean-To-Tree-2023 https://github.com/000generic/Ctenophore-Ocean-To-Tree-2023 ) that can be run for free in the Google Colab cloud to replicate our findings or modified for specific or greater use. Our protocol enables users to design new sequencing projects in ctenophores, marine invertebrates, or other novel organisms. It provides a simple, comprehensive platform that can ease new user entry into running their evolutionary sequence analyses.

Streptomyces fuscus sp. nov., a brown-black pigment producing actinomycete isolated from dry mudflat sand.

A novel Gram-stain-positive, aerobic actinobacterial strain, designated GXMU-J15T, was isolated from dry mudflat sand. A polyphasic approach was employed for its taxonomic characterization. The strain developed extensively branched yellowish white to light yellow substrate mycelia and white aerial mycelia, and produced smooth cylindrical spores in a loose straight spore chain on International Streptomyces Project 2-7 agar media. Strain GXMU-J15T grew at 20-50 °C (optimum, 35 °C), at pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-8 % (w/v) NaCl. Analysis of 16S rRNA gene sequences indicated that strain GXMU-J15T represents a member of the genus Streptomyces. Strain GXMU-J15T showed the highest 16S rRNA gene sequence similarity to Streptomyces lusitanus CGMCC 4.1745T (99.1 %) and Streptomyces thermocarboxydus CGMCC 4.1883T (98.8 %). Phylogenetic tree analysis based on multilocus sequence analysis (MLSA) and whole genome sequence construction revealed that strain GXMU-J15T was most closely related to Streptomyces cupreus PSKA01T, Streptomyces cinnabarinus DSM 40467T and Streptomyces davaonensis JCM 4913T. The MLSA and genome-to-genome distances between strain GXMU-J15T and its relatives were 0.0418, 0.0443 and 0.0485 and 0.1237, 0.1188 and 0.1179, respectively. The results of orthologous average nucleotide identity and digital DNA-DNA hybridization analysis corroborated the results of the MLSA and whole genome sequence evolution analysis, indicating that the novel isolate represents a distinct species of the genus Streptomyces. The whole-cell sugars of strain GXMU-J15T were xylose, glucose and galactose. The characteristic diamino acid in the cell-wall hydrolysate was ll-diaminopimelic acid. The lipids contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylglycerides, phosphatidylcholine, two phospholipids of an unknown structure containing glucosamine, one unknown phospholipid and two unknown lipids. The major cellular fatty acid components were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The main respiratory quinone types were MK-9(H6) and MK-9(H8). The whole genome size of strain GXMU-J15T was 8.68 Mbp, with 71.23 mol% G+C content. Genomic analysis indicated that strain GXMU-J15T has the potential to synthesize polyketides, terpenes and a series of important antibiotics besides the gene cluster for melanin synthesis. Based on these genotypic and phenotypic data, strain GXMU-J15T is proposed to represent a new species of the genus Streptomyces named Streptomyces fuscus sp. nov. The type strain is GXMU-J15T (=MCCC 1K08211T=JCM 35917T).

New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group

Phylogenetics is the study of ancestral relationships among biological species. Such sequence analyses are often represented as phylogenetic trees. The branching pattern of each tree and its topology reflect the evolutionary relatedness between analyzed sequences. We present a Klein four-group algorithm (K4A) for the evolutionary analysis of nucleotide and amino acid sequences. Klein four-group set of operators consists of: identity e (U), and three elements—a = transition (C), b = transversion (G) and c = transition-transversion or complementarity (A). We generated Klein four-group based distance matrices of: 1. Cayley table (CK4), 2. Table rows (K4R), 3. Table columns (K4C), and 4. Euclidean 2D distance (K4E). The performance of the matrices was tested on a dataset of RecA proteins in bacteria, eukaryotes (Rad51 homolog) and archaea (RadA homolog). RecA and its functional homologs are found in all species, and are essential for the repair and maintenance of DNA. Consequently, they represent a good model for the study of evolutionary relationship of protein and nucleotide sequences. The ancestral relationship between the sequences was correctly classified by all K4A matrices concerning general topology. All distance matrices exhibited small variations among species, and overall results of tree classification were in agreement with the general patterns obtained by standard BLOSUM and PAM substitution matrices. During the evolution of a code there is a phase of optimization of system rules, the ambiguity of a code is eliminated, and the system starts producing specific components. Klein four-group algorithm is consistent with the concept of ambiguity reduction. It also enables the use of different genetic code table variants optimized for particular transitions in evolution based on biological specificity.

Evolutionary analysis and quality assessment of ζ-carbonic anhydrase sequences from environmental microbiome.

Carbonic anhydrase (CA) is one of the most vital enzymes in living cells. This study has been performed due to the significance of this metalloenzyme for life and the novelty of some CA families like ζ-CA to evaluate evolutionary processes and quality check their sequences. In this study, bioinformatics methods revealed the presence of ζ-CA in some eukaryotic and prokaryotic microorganisms. Notably, it has not been previously reported in prokaryotes. The coexistence of β- and ζ-CAs in some microorganisms is also a novel finding as well. Also, our analysis identified several CA proteins with 6-14 amino acid intervals between histidine and cysteine in the second highly conserved motif, which can be classified as the novel ζ-CA subfamily members that emerged under the Zn deficiency of aquatic ecosystems and selection pressure in these environments. There is also a possibility that the achieved results are rooted in the contamination of samples from the environmental microbiome genome with genomes of diatom species and the occurrence of errors was observed in the DNA sequencing outcomes. Combining of all results from evolutionary analysis to quality control of ζ-CA DNA sequences is the incentive motivation to explore more the hidden aspects of ζ-CAs.

Serological relationships among strains of grapevine leafroll-associated virus 4 reflect the evolutive behavior of its coat protein gene

This research studied serological relationships and genetic diversity of Argentinean isolates of grapevine leafroll-associated virus-4 (GLRaV-4). Phylogenetic analysis of coat protein (CP) sequences from 19 local isolates revealed clustering with the previously described GLRaV-4 strain 5, strain 6, and strain 9 groups. Evolutionary sequence analysis of the obtained and database-available sequences showed evidence of recombination events. Additionally, both CP N- and C-terminal regions appeared to be under purifying selection, but the N-terminal region presented seven sites under positive selection, with a dN/dS ratio 5-fold greater than that of the C-terminal region. Serological reactivity against monoclonal antibodies supports a higher occurrence probability for linear epitopes in the N-terminal region, as inferred by the sequence analysis. The obtained results reflect an unusual evolutionary behavior of the CP that, together with protein serological reactivity, suggests biological significance of the observed variability. Highlights: The occurrence of GLRaV-4 strains -5, -6 and -9 was recorded in Argentina. The coat protein sequence showed a highly variable N-terminal region among the strains. An evolutionary analysis inferred the occurrence of sites under positive diversifying selection pressure. The most variable region of the coat protein presented the highest probability of occurrence of linear epitopes.

Evolutionary analysis of JC polyomavirus in Misiones’ population yields insight into the population dynamics of the early human dispersal in the Americas

BackgroundJC polyomavirus (JCV) has an ethno-geographical distribution across human populations. ObjectiveStudy the origins of the population of Misiones (Argentina) by using JCV as genetic marker. MethodsViral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. Results22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383–30,177), followed by a sustained demographic expansion around 5000 years ago. ConclusionsJCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.

Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis

We describe an approach to identify enzyme mutants with increased turnover using the enzyme DszC as a case study. Our approach is based on recalculating the barriers of alanine mutants through single-point energy calculations at the hybrid QM/MM level in the wild-type reactant and transition state geometries. We analyze the difference in the electron density between the reactant and transition state to identify sites/residues where electrostatic interactions stabilize the transition state over the reactants. We also assess the insertion of a unit probe charge to identify positions in which the introduction of charged residues lowers the barrier.

Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency

The support of pluripotent cells over time is an essential feature of development. In eutherian embryos, pluripotency is maintained from naïve states in peri-implantation to primed pluripotency at gastrulation. To understand how these states emerged, we reconstruct the evolutionary trajectory of the Pou5 gene family, which contains the central pluripotency factor OCT4. By coupling evolutionary sequence analysis with functional studies in mouse embryonic stem cells, we find that the ability of POU5 proteins to support pluripotency originated in the gnathostome lineage, prior to the generation of two paralogues, Pou5f1 and Pou5f3 via gene duplication. In osteichthyans, retaining both genes, the paralogues differ in their support of naïve and primed pluripotency. The specialization of these duplicates enables the diversification of function in self-renewal and differentiation. By integrating sequence evolution, cell phenotypes, developmental contexts and structural modelling, we pinpoint OCT4 regions sufficient for naïve pluripotency and describe their adaptation over evolutionary time.

Toward the Complete Functional Characterization of a Minimal Bacterial Proteome.

Recently, we presented a whole-cell kinetic model of the genetically minimal bacterium JCVI-syn3A that described the coupled metabolic and genetic information processes and predicted behaviors emerging from the interactions among these networks. JCVI-syn3A is a genetically reduced bacterial cell that has the fewest number and smallest fraction of genes of unclear function, with approximately 90 of its 452 protein-coding genes (that is less than 20%) unannotated. Further characterization of unclear JCVI-syn3A genes strengthens the robustness and predictive power of cell modeling efforts and can lead to a deeper understanding of biophysical processes and pathways at the cell scale. Here, we apply computational analyses to elucidate the functions of the products of several essential but previously uncharacterized genes involved in integral cellular processes, particularly those directly affecting cell growth, division, and morphology. We also suggest directed wet-lab experiments informed by our analyses to further understand these “missing puzzle pieces” that are an essential part of the mosaic of biological interactions present in JCVI-syn3A. Our workflow leverages evolutionary sequence analysis, protein structure prediction, interactomics, and genome architecture to determine upgraded annotations. Additionally, we apply the structure prediction analysis component of our work to all 452 protein coding genes in JCVI-syn3A to expedite future functional annotation studies as well as the inverse mapping of the cell state to more physical models requiring all-atom or coarse-grained representations for all JCVI-syn3A proteins.

A novel 4-hydroxyacetophenone monooxygenase featuring aromatic substrates preference for enantioselective access to sulfoxides

Baeyer-Villiger monooxygenases are recognized as valuable tools for biooxidative synthesis of chiral sulfoxides. In this work, a novel HAPMO ortholog from Pseudomonas fluorescens (HAPMOPf) was identified by genome mining. Evolutionary relationship and sequence analysis revealed that HAPMOPf belongs to the family of typical type I BVMOs. HAPMOPf has a low KM value (0.025 mM) toward 4-hydroxyacetophenone, and a half-life of 24 h at 30 °C and pH 9.0. HAPMOPf exhibited distinct activity toward aromatic ketones as well as various thioethers, such as methyl phenyl sulfide and bromo‑methyl phenyl sulfide. The highest activities of HAPMOPf was 1.47 U·mg−1 toward 4-hydroxyacetophenone among tested ketone and thioether substrates. Furthermore, over 95% enantioselectivity was determined toward methyl phenyl sulfides with ortho, meta, and para-substituents (Cl, Br, CHO, NH2). Therefore, HAPMOPf is a promising biocatalyst for the synthesis of aromatic esters and chiral sulfoxides.

Genetic characterization of hepatitis E virus from wild boar in China.

Hepatitis E virus (HEV), the causative agent of hepatitis E (HE), is classified into four major genotypes (1-4), with wild boar being the main natural reservoir for genotypes 3 and 4. However, little is known about the prevalence of HEV infection in wild boars in China. In this study, RT-nested PCR and RT-quantitative PCR were used to detect the HEV RNA in tissue samples taken from 331 free-ranging wild boars collected between 2018 and 2020 from 24 regions across China, and the partial ORF2 genes or complete genomes of the positive samples were sequenced. Furthermore, antibodies against HEV in 216 serum samples from wild boars were tested by ELISA. As a result, HEV RNA was detected in nine out of 331 liver samples of wild boars (2.72%), which were distributed in eight regions. Genetic and evolutionary analysis of partial ORF2 sequences indicated that the HEV strains identified in this study share 83.9%-100% nucleotide sequence identity and belong to subtypes 4d (n=6), 4g (n=2), and 4h (n=1), and similar phylogeny was obtained using the complete genome sequences of seven wild boar HEV strains. Additionally, the HEV viral loads were higher in the liver than in other tissues and blood. Moreover, 61 out of 216 sera (28.2%) from wild boars tested positive for anti-HEV antibodies. To our knowledge, this is the first study to report the epidemiological situations of HEV infections in free-ranging wild boars in China, and the obtained data are valuable for prevention and control of HE.

Phylogenetic study to analyse the evolutionary relationship of taxonomically diverse α-amylases

Microbial α-amylases have been identified and characterized to understand their progressive role in industrial applications. Computational biology tools are employed in various in-silico studies for finding out the ways to improve the titre of this enzyme with improved stability and specificity. This study includes detailed evolutionary analysis and comparison of α-amylase amino acid sequences found in a wide spectrum of microorganisms like algae, bacteria, fungi, cyanobacteria, and plants. We analysed the conservation patterns and signature modules in molecular architectures to study the phylogenetic relationship among various microbial and plant taxa. Additionally, efforts were made to identify signal peptides responsible for the secretion of α-amylase protein outside the cell. Our results concluded the presence of different types of domains with their single or multiple copies, and distinct signal peptides which may alter the overall functioning and secretion efficiency of enzyme. Collectively, overall molecular diversity leads to adaptive evolution of α-amylase in different microbes and plants.

Identification and evolutionary analysis of papillomavirus sequences in New World monkeys (genera Sapajus and Alouatta) from Argentina.

In this study, we investigated the occurrence of papillomavirus (PV) infection in non-human primates (NHPs) in northeastern Argentina. We also explored their evolutionary history and evaluated the co-speciation hypothesis in the context of primate evolution. We obtained DNA samples from 57 individuals belonging to wild and captive populations of Alouatta caraya, Sapajus nigritus, and Sapajus cay. We assessed PV infection by PCR amplification with the CUT primer system and sequencing of 337 bp (112 amino acids) of the L1 gene. The viral sequences were analyzed by phylogenetic and Bayesian coalescence methods to estimate the time to the most common recent ancestor (tMRCA) using BEAST, v1.4.8 software. We evaluated viral/host tree congruence with TreeMap v3.0. We identified two novel putative PV sequences of the genus Gammapapillomavirus in Sapajus spp. and Alouatta caraya (SPV1 and AcPV1, respectively). The tMRCA of SPV1 was estimated to be 11,941,682 years before present (ybp), and that of AcPV1 was 46,638,071 ybp, both before the coalescence times of their hosts (6.4 million years ago [MYA] and 6.8 MYA, respectively). Based on the comparison of primate and viral phylogenies, we found that the PV tree was no more congruent with the host tree than a random tree would be (P > 0.05), thus allowing us to reject the model of virus-host coevolution. This study presents the first evidence of PV infection in platyrrhine species from Argentina, expands the range of described hosts for these viruses, and suggests new scenarios for their origin and dispersal.

A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events.

Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.