Recombination Breakpoints Research Articles

Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023.

Recombination plays a crucial role in the evolution of SARS-CoV-2. The Omicron XBB* recombinant lineages are a noteworthy example, as they have been the dominant SARS-CoV-2 variant worldwide in the first half of 2023. Since November 2023, a new recombinant lineage between Omicron subvariants XBB and BA.2.86, designated XDR, has been detected mainly in Brazil. In this study, we reconstructed the spatiotemporal dynamics and estimated the absolute and relative transmissibility of the XDR lineage. The XDR lineage displayed a recombination breakpoint in the ORF1a-coding region, and the most closely related sequences to the 5' and 3' ends of the recombinant correspond to JD.1.1 and JN.1.1 lineages, respectively. The first XDR sequences were detected in November 2023 in the Northeastern Brazilian region, and their prevalence rapidly surged from <1% to 25% by February 2024. The Bayesian phylogeographic analysis supports that the XDR lineage likely emerged in the Northeastern Brazilian region around late October 2023 and rapidly disseminated within and outside Brazilian borders from mid-November onward. The median effective reproductive number of the XDR lineage in Brazil during the initial expansion phase was estimated to be around 1.5, and the average relative instantaneous reproduction numbers of XDR and JN* lineages were estimated to be 1.37 and 1.29 higher than that of co-circulating XBB* lineages. In summary, these findings support that the recombinant lineage XDR arose in the Northeastern Brazilian region in October 2023, shortly after the first detection of JN.1 sequences in the country. In Brazil, the XDR lineage exhibited a higher transmissibility level than its parental XBB.* lineages and is spreading at a rate similar to or slightly faster than the JN.1* lineages.IMPORTANCEThis study highlights the emergence and rapid dissemination of the recombinant SARS-CoV-2 XDR lineage, derived from the Omicron lineages JD.1.1 and JN.1.1. The XDR lineage exhibited equivalent transmissibility to its JN.1* parental lineages and quickly spread across Brazil in late 2023. The findings underscore the critical role of real-time genomic surveillance in detecting novel variants with higher transmission potential. By utilizing phylogenetic and epidemiological methods, this research provides important insights into the molecular dynamics of XDR, which could inform public health responses and vaccine composition updates. The study's significance lies in its ability to document the impact of recombination on viral evolution, offering valuable information to the field of virology and pandemic preparedness.

Molecular characterization of doublesex and Mab-3 (DMRT) gene family in Ctenopharyngodon idella (grass carp).

Doublesex and Mab-3 (DMRT) gene family is a diverse group of transcriptional factors crucially involved in sex differentiation and biological processes such as body growth and differentiation in vertebrates. In this study, we analyzed DMRT genes structural characterization and physiochemical properties, and elucidated their functional role as a ligand of different gonadal receptors including androgen (AR), estrogen β (ER-β), estrogen γ (ER-γ), and progesterone (PR). All six genes of the DMRT gene family in grass carp (Ctenopharyngodon Idella Valenciennes, 1844) exhibited an acidic nature. These DMRT genes are primarily localized in the nucleus, where they play a role in DNA binding via doublesex DNA binding motif. All the DMRT gene pairsare under strong purifying selection with two segmental duplications envisaged about 18.30 (DMRT3a/DMRTA2) and 24.90 (DMRT2b/DMRT2a) million years ago (MYA). Recombination analysis revealed six potential recombinant breakpoints posing substantial evolutionary pressure for diverse cellular functioning of DMRT isoforms. Moreover, the DMRTA1 protein had a highest binding affinity of - 270.42 and - 267.16 for androgen receptors (AR) and progesterone receptors (PR), whereas, for estrogen receptors ER-β and ER-γ, the maximum binding affinity was observed with DMRT2a and DMRT2b proteins showing a docking score of - 254.22 and - 261.71, respectively. First time we studied the binding scores and interface residues of the DMRT genes as a ligand of gonadal receptors that play a crucial role in fish growth, sex development and differentiation, and spermatogenesis and oocyte maturation. The present study provides a molecular basis for DMRT genes in grass carp that may serve as a reference for in-depth phylogenomic study in other species.

Multiple third-generation recombinants formed by CRF55_01B and CRF07_BC in newly diagnosed HIV-1 infected patients in Shenzhen city, China

In the evolution landscape of HIV, the coexistence of multiple subtypes has led to new, complex recombinants, posing public health challenges. CRF55_01B, first identified among MSM in Shenzhen, China, has spread rapidly across China. In this study, 47 plasma samples from newly diagnosed HIV-1 CRF55_01B patients in Shenzhen, of which the genotype was only identified by the routine HIV drug resistance test, were collected. Multiple gene regions were acquired using Sanger and next-generation sequencing methods, followed by the phylogenetic reconstruction, recombination breakpoint scanning, Bayesian molecular clock, and the prediction of coreceptors. From 47 samples, we found seven new unique recombinants formed by CRF55_01B and CRF07_BC, which shared similar breakpoints in certain gene regions and primarily utilized CCR5 receptors. All of the most recent common ancestors of subregions for these recombinants were estimated to be later than CRF55_01B and CRF07_BC, potentially suggesting they are the third-generation recombinants formed by CRF55_01B and CRF07_BC as parents. The continuous emergence of new recombinants highlights the increasing complexity of circulating strains in Shenzhen, and also suggests that subtype analysis using partial pol gene may lead to an overestimation of the major subtype strains and an underestimation of new complex HIV recombinants. Consequently, to effectively address and mitigate the complex HIV epidemic, there is an urgent need for expanded monitoring and the optimization of testing methodologies.

Long-Read Sequencing Identifying the Genetic Complexity of Congenital Adrenal Hyperplasia in the Pedigree.

High sequence homology between CYP21A2 and CYP21A1P poses challenges to genetic diagnosis of congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21-OHD). Traditional genetic testing is unable to provide an accurate diagnosis due to the genetic complexity of CAH. Deletions, duplications, and recombination breakpoints were precisely identified by long-read sequencing (LRS). This study presented a pregnant woman, a 21-OHD carrier detected by MLPA, and her husband, a normal subject also detected by MLPA. The fetus was suspected of having 21-OHD based on clinical presentations such as enlarged adrenal glands, atypical external genitalia and karyotyping of 46, XX. LRS further identified the fetus as having the most severe salt-wasting (SW) form of 21-OHD with a compound heterozygote genotype. One allele was TNXA/TNXB CH-2, while the other allele was CYP21A1P/CYP21A2 CH-8. LRS precisely determined the genotypes of the fetus's father and grandmother with duplications, which misdiagnosed by MLPA. The multidisciplinary team recommended immediate glucocorticoid and mineralocorticoid treatment for the child after birth to prevent life-threatening adrenal crisis. LRS provides precise diagnosis for family members with CYP21A2 deletion or duplication, improving disease management and preventing potential adrenal crises. When used in pre-pregnancy genetic testing, LRS can indicate high genetic risk and guide the appropriate therapy during pregnancy and immediately after birth.

Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India.

Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.

Evidence of circulating recombinants between deformed wing virus and Varroa destructor virus-1 in honey bee colonies in Türkiye.

Deformed wing virus (DWV), which is an important honey bee virus transmitted by Varroa destructor (V. destructor), causes colony losses in honey bee colonies. This study aimed to investigate the prevalence and genetic diversity of DWV in honey bees in Türkiye and to determine the role of V. destructor in the transmission of the genetic variants of DWV. Honey bee samples were collected from 62 apiaries, by simple random sampling, during March 2022 and April 2023. The presence of V. destructor in collected bee samples was examined using a stereo microscope. Real-time RT-PCR was used for the detection of DWV-A and DWV-B (Varroa destructor virus-1 (VDV-1)) viruses. Genetic characterisation of the positive samples was conducted by sequencing polyprotein genomic region. Considering the V. destructor infestation rate of 3% as relevant, out of the 62 apiaries examined, 17 (27.4%) were positive. However, DWV-A and VDV-1 specific RNA was not detected in V. destructor samples. VDV-1 specific RNA was detected in 6.5% (4/62) of the apiaries, whereas DWV-A was not detected in the sampled apiaries. Phylogenetic analysis showed that isolates detected in this study were located in a separate cluster from previously characterised DWV-A and VDV-1 isolates. According to RDP4 and GARD analyses, DWV-VDV-1 recombination breakpoints were detected in field isolates. To the best our knowledge, this is the first report of the presence of VDV-1-DWV recombinants in Türkiye. Further studies are needed to determine the impact of VDV-1-DWV recombinants and their virological and antigenic properties.

Feline bocaviruses found in Thailand have undergone genetic recombination for their evolutions

Feline bocaviruses (FBoVs) have been discovered for a decade and are often detected in feces, possibly associated with diarrhea in cats. Studies on FBoV evolution remain limited and have mainly focused on prevalence and genetic characterization. Although genetic recombination serves as a potential mechanism in bocavirus evolution, research on this process for FBoVs has been scarce. In this study, we characterized 19 complete coding sequences of FBoVs obtained from Thai cats, revealing that FBoV-1, -2, and -3 were endemic in Thailand. Genetic characterizations showed that most Thai FBoVs were closely related to previously detected strains in Thailand and China. Recombination analyses indicated intragenic, intraspecies recombination in all FBoV species, with recombination breakpoints commonly found in the NP1 and VP1/2 genes, highlighting these genes may be hotspots for FBoV recombination. However, no interspecies recombination was detected. Selective pressure analysis of various FBoV genes revealed that these viruses underwent purifying selection. Although the VP1/2 gene of all FBoV species was under the strongest negative selection pressure, positive selection sites were only found in FBoV-1 and FBoV-3. This study is the first to identify natural recombination in FBoV-2 and FBoV-3 and provides evidence that genetic recombination is a potential driver of FBoV evolutions. Additionally, this study offers up-to-date information on the genetic characteristics, evolutionary dynamics, and selective pressure status of FBoVs, which should be continuously monitored.

Characterization of Two Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Among Men Who Have Sex with Men and Mother-to-Child Transmission Cases in Baoding City, China.

CRF01_AE and CRF07_BC are predominant circulating HIV-1 subtypes in China. In this study, we report two novel HIV-1 CRF01_AE/CRF07_BC recombinant forms isolated from one man who has sex with men (MSM) (BDD027) and one mother-to-child transmission (MTCT) case (BDL123) in Baoding City, Hebei Province, China. The recombination breakpoint analysis showed that the recombination pattern of the near-full-length genome of BDD027 consisted of two CRF07_BC fragments inserted into a CRF01_AE backbone, while the recombination pattern of the near-full-length genome of BDL123 consisted of one CRF01_AE fragment inserted into a CRF07_BC backbone. This study demonstrates the importance of strengthening the monitoring of HIV-1 molecular epidemiological characteristics and emphasizes the urgent need to reduce the HIV-1 epidemic among MSM and MTCT populations in China.

In Silico Analysis: Molecular Characterization and Evolutionary Study of CLCN Gene Family in Buffalo.

Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating the electrolytes' balance in kidneys and other organs. In order to define the chloride voltage-gated channel (CLCN) gene family in buffalo, this study used in silico analyses to examine physicochemical properties, evolutionary patterns, and genome-wide identification. We identified eight CLCN genes in buffalo. The ProtParam tool analysis identified a number of important physicochemical properties of these proteins, including hydrophilicity, thermostability, in vitro instability, and basic nature. Based on their evolutionary relationships, a phylogenetic analysis divided the eight discovered genes into three subfamilies. Furthermore, a gene structure analysis, motif patterns, and conserved domains using TBtool demonstrated the significant conservation of this gene family among selected species over the course of evolution. A comparative amino acid analysis using ClustalW revealed similarities and differences between buffalo and cattle CLCN proteins. Three duplicated gene pairs were identified, all of which were segmental duplications except for CLCN4-CLCN5, which was a tandem duplication in buffalo. For each gene pair, the Ka/Ks test ratio findings showed that none of the ratios was more than one, indicating that these proteins were likely subject to positive selection. A synteny analysis confirmed a conserved pattern of genomic blocks between buffalo and cattle. Transcriptional control in cells relies on the binding of transcription factors to specific sites in the genome. The number of transcription factor binding sites (TFBSs) was higher in cattle compared to buffalo. Five main recombination breakpoints were identified at various places in the recombination analysis. The outcomes of our study provide new knowledge about the CLCN gene family in buffalo and open the door for further research on candidate genes in vertebrates through genome-wide studies.

Identification of Two HIV-1 CRF01_AE/B Recombinant Forms and a CRF01_AE/B/C Recombinant Form in Hebei Province, China.

In the Hebei province, Human Immunodeficiency Virus type one (HIV-1) recombinant strains of subtypes B, C, and CRF01_AE are emerging very rapidly and diversely. In order to confirm the characteristics of novel recombination forms, we aimed to analyze HIV-1 Near-full-length Genome sequences (NFLGs) obtained from three Men who have Sex with Men (MSM) in this study. Phylogenetic trees were constructed and breakpoints analysis was performed based on the NFLGs and each gene fragment to examine the gene recombination patterns of three new HIV-1 NFLGs. HIV-1 subtypes CRF01_AE and B were combined to generate the recombinant structures of the NFLGs 610 and 687. CRF01_AE, B, and C were combined to generate the recombinant structures of the NFLG 825. According to the NFLG phylogenetic tree, the NFLG 825 clustered with CRF65_cpx and the NFLGs 610 and 687 clustered with CRF68_01B. The recombination breakpoints analysis revealed that the recombination pattern of the NFLGs 610 and 687 was the insertion of subtype B fragment into the CRF01_AE backbone. Subregions I, II, and III were derived from CRF01_AE, subtype B, and CRF01_AE, respectively. The recombination pattern of the NFLG 825 contained ten fragments of subtypes CRF01_AE, C, and B. Finally, the above factors were formed using phylogenetic trees and breakpoints analysis, which were combined to get two CRF68_01B forms and one CRF65_cpx form. Our findings have suggested that it is crucial to keep an eye on the genetic diversity of HIV-1 in Hebei province.

Novel pathogenic adenovirus in Timneh grey parrot (Psittacus timneh) unveils distinct lineage within Aviadenovirus

Wild birds harbour a vast diversity of adenoviruses that remain uncharacterised with respect to their genome organisation and evolutionary relatedness within complex host ecosystems. Here, we characterise a novel adenovirus type within Aviadenovirus genus associated with severe necrotising hepatitis in a captive Timneh grey parrot, tentatively named as Timneh grey parrot adenovirus 1 (TpAdV-1). The TpAdV-1 genome is 39,867 bp and encodes 46 putative genes with seven hitherto not described ones. Comparative genomics and phylogenetic analyses revealed highest nucleotide identity with psittacine adenovirus 1 and psittacine adenovirus 4 that formed a discrete monophyletic clade within Aviadenovirus lineage suggesting a deep host co-divergent lineage within Psittaciformes hosts. Several recombination breakpoints were identified within the TpAdV-1 genome, which highlighted an ancient evolutionary relationship across the genera Aviadenovirus, Mastadenovirus and Atadenovirus. This study hints towards a host-adapted sub-lineage of avian adenovirus capable of having significant host virulence in Psittaciformes birds augmented with ecological opportunity.

Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints.

Phylogenetic methods are widely used to reconstruct the evolutionary relationships among species and individuals. However, recombination can obscure ancestral relationships as individuals may inherit different regions of their genome from different ancestors. It is, therefore, often necessary to detect recombination events, locate recombination breakpoints, and select recombination-free alignments prior to reconstructing phylogenetic trees. While many earlier studies have examined the power of different methods to detect recombination, very few have examined the ability of these methods to accurately locate recombination breakpoints. In this study, we simulated genome sequences based on ancestral recombination graphs and explored the accuracy of three popular recombination detection methods: MaxChi, 3SEQ, and Genetic Algorithm Recombination Detection. The accuracy of inferred breakpoint locations was evaluated along with the key factors contributing to variation in accuracy across datasets. While many different genomic features contribute to the variation in performance across methods, the number of informative sites consistent with the pattern of inheritance between parent and recombinant child sequences always has the greatest contribution to accuracy. While partitioning sequence alignments based on identified recombination breakpoints can greatly decrease phylogenetic error, the quality of phylogenetic reconstructions depends very little on how breakpoints are chosen to partition the alignment. Our work sheds light on how different features of recombinant genomes affect the performance of recombination detection methods and suggests best practices for reconstructing phylogenies based on recombination-free alignments.

Recombination of Porcine Reproductive and Respiratory Syndrome Virus: Features, Possible Mechanisms, and Future Directions.

Recombination is a pervasive phenomenon in RNA viruses and an important strategy for accelerating the evolution of RNA virus populations. Recombination in the porcine reproductive and respiratory syndrome virus (PRRSV) was first reported in 1999, and many case reports have been published in recent years. In this review, all the existing reports on PRRSV recombination events were collected, and the genotypes, parental strains, and locations of the recombination breakpoints have been summarized and analyzed. The results showed that the recombination pattern constantly changes; whether inter- or intra-lineage recombination, the recombination hotspots vary in different recombination patterns. The virulence of recombinant PRRSVs was higher than that of the parental strains, and the emergence of virulence reversion was caused by recombination after using MLV vaccines. This could be attributed to the enhanced adaptability of recombinant PRRSV for entry and replication, facilitating their rapid propagation. The aim of this paper was to identify common features of recombinant PRRSV strains, reduce the recombination risk, and provide a foundation for future research into the mechanism of PRRSV recombination.

First report of PST-producing Microseira wollei from China reveals its novel toxin profile

Microseira wollei, a globally distributed freshwater bloom-forming benthic cyanobacterium, is known for its production of cyanotoxins and taste and odor (T&O). While CYN (Cylindrospermopsin)-producing populations of M. wollei are confined to Australia, PST (Paralytic shellfish toxins)-producing populations have been exclusively documented in North America. In this study, four benthic cyanobacterial strains, isolated from West Lake in China, were identified as M. wollei based on morphological and phylogenetic analyses. Detection of sxtA gene and UPLC-MS/MS analysis conclusively confirmed the PST-producing capability of M. wollei CHAB5998. In the phylogenetic tree of 16S rDNA, M. wollei strains formed a monophyletic group with two subclades. Notably, non-PST-producing Chinese strains clustered with Australian strains in Clade II, while all other strains, including PST-producing ones, clustered in Clade I. Additionally, CHAB5998 contains ten PST variants, of which STX, NEO, GTX2, GTX3, GTX5 and C1 were identified for the first time in M. wollei. Sequence analysis of PST biosynthetic gene cluster (sxt) genes indicated potential base variations, gene rearrangements, insertions, and deletions in the strain CHAB5998. Also, sxt gene has a longer evolutionary history in M. wollei than that in cyanobacteria from Nostocales. Multiple recombination breakpoints detected in sxt genes and the inconsistency in the topology of the phylogenetic trees between sxt and 16S rDNA suggested that multiple horizontal gene transfers (HGT) have occurred. Overall, the present study marks the first documented occurrence of PST-producing M. wollei outside of North America and identifies it as the first toxic freshwater benthic cyanobacterium in China. This revelation implies that benthic cyanobacteria may pose a higher environmental risk in China than previously acknowledged.

SIMULATING PEDIGREES ASCERTAINED ON THE BASIS OF OBSERVED IBD SHARING.

In large genotyping datasets, individuals often have thousands of distant cousins with whom they share detectable segments of DNA identically by descent (IBD). The ability to simulate these distant relationships is important for developing and testing methods, carrying out power analyses, and performing population genetic analyses. Because distant relatives are unlikely to share detectable IBD segments by chance, many simulation replicates are needed to sample IBD between any given pair of distant relatives. Exponentially more samples are needed to simulate observable segments of IBD simultaneously among multiple pairs of distant relatives in a single pedigree. Using existing pedigree simulation methods that do not condition on the event that IBD is observed among certain pairs of relatives, the chances of sampling shared IBD patterns that reflect those observed in real data ascertained from large genotyping datasets are vanishingly small, even for pedigrees of modest size. Here, we show how to sample recombination breakpoints on a fixed pedigree while conditioning on the event that specified pairs of individuals share at least one observed segment of IBD. The resulting simulator makes it possible to sample genotypes and IBD segments on pedigrees that reflect those ascertained from biobank scale data.

Precision mapping and expression analysis of recessive bacterial blight resistance gene xa-45(t) from Oryza glaberrima.

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of rice leading to huge yield losses in Southeast Asia. The recessive resistance gene xa-45(t) from Oryza glaberrima IRGC102600B, mapped on rice chromosome 8, spans 80Kb with 9 candidate genes on Nipponbare reference genome IRGSP-1.0. The xa-45(t) gene provides durable resistance against all the ten Xanthomonas pathotypes of Northern India, thus aiding in the expansion of recessive bacterial blight resistance gene pool. Punjab Rice PR127, carrying xa-45(t), was released for wider use in breeding programs. This study aims to precisely locate the target gene among the 9 candidates conferring resistance to bacterial blight disease. Sanger sequencing of all nine candidate genes revealed seven SNPs and an Indel between the susceptible parent Pusa 44 and the resistant introgression line IL274. The genotyping with polymorphic markers identified three recombinant breakpoints for LOC_Os08g42370, and LOC_Os08g42400, 15 recombinants for LOC_Os08g423420 and 26 for LOC_Os08g42440 out of 190 individuals. Relative expression analysis across six time intervals (0, 8, 24, 48, 72, and 96h) after bacterial blight infection showed over expression of LOC_Os08g42410-specific transcripts in IL274 compared to Pusa 44, with a significant 4.46-fold increase observed at 72h post-inoculation. The Indel marker at the locus LOC_Os08g42410 was found co-segregating with the phenotype, suggesting its candidacy towards xa-45(t). The transcript abundance assay provides strong evidence for the involvement of LOC_Os08g42410 in the resistance conferred by the bacterial blight gene xa-45(t).

Molecular genetic characterization analysis of a novel HIV-1 circulating recombinant form (CRF156_0755) in Guangdong, China.

The characteristic of human immunodeficiency virus type 1 (HIV-1) is its susceptibility to erroneous replication and recombination, which plays a crucial role in the diverse and dynamic variation of HIV-1. The spread of different subtypes in the same population often leads to the emergence of circulating recombination forms (CRFs). At present, the main recombinant subtypes of HIV-1 in China are CRF07_BC, CRF01_AE, CRF08_BC and B' subtypes, while CRF55_01B has become the fifth major epidemic strain in China after rapid growth in recent years since it was first reported in 2013. In this study, we obtained five nearly full-length genomes (NFLGs) and one half-length genome from five different cities in Guangdong. Here, we focused on analyzing their characteristics, parental origin and drug resistance. Plasma samples were collected from six HIV-1 infected patients in Guangdong Province who had no epidemiological association with each other. The NFLGs of HIV-1 were amplified in two overlapping segments by the near-terminal dilution method. The positive products were sequenced directly to obtain genomic sequences. The recombinant patterns and breakpoints of the NFLGs were determined using the Simplot software and confirmed by the maximum likelihood trees for segments using the IQ-TREE and BEAST software. The genotypic resistance profiles of the protease reverse transcriptase and integrase were resolved by the Stanford HIV drug resistance database. The six genomes shared highly similar recombinant pattern, with the CRF55_01B backbone substituted by CRF07_BC segments, therefore assigned as CRF156_0755. The evolutionary analysis of the segments showed that CRF07_BC segments were not clustered with the Chinese MSM variants in the CRF07_BC lineage. All the five NFLGs were identified with the non-nucleoside reverse-transcription inhibitors (NNRTIs) resistance mutation V179E. With the accumulation and evolution of recombination between CRF55_01B and CRF 07_BC, the prevalence of more recombinant strains of CRF55_01B and CRF 07_BC may occur. Therefore, it is necessary to strengthen the identification and monitoring of the recombination of CRF55_01B and CRF 07_BC.

Complete genome characterization of chilli veinal mottle virus associated with mosaic and mottling disease of tomato and development of LAMP assay for quick detection.

Chilli veinal mottle virus (ChiVMV) is a potyvirus known to cause havoc in many solanaceous crops. Samples from tomato plants exhibiting typical mosaic and mottling symptoms in two locations from farmers' fields were collected and tested using DAC ELISA for the presence of ChiVMV and other viruses known to infect tomato. ChiVMV Gauribidanur isolate from infected tomato was mechanically inoculated to Datura metel, Nicotiana tabacum, Nicotiana benthamiana, Nicotiana glutinosa, chilli, and tomato plants which exhibited systemic mosaic and mottling symptoms 10days post-inoculation. This results were further confirmed by RT-PCR and DAC ELISA using CP gene-specific primers and ChiVMV antisera, respectively. Transmission electron microscopy revealed the presence of long filamentous particles (800×11nm) resembling viruses in the Potyviridae family. The complete genome of ChiVMV comprised 9716 nucleotides except for poly A tail, with a predicted open reading frame spanning 9270 nucleotides encoding polyproteins of 3089 amino acids. Comparative analysis revealed that ChiVMV-tomato isolates reported across the world shared maximum nucleotide identity (93-96.7%) with chilli isolates from India and Pakistan. These results were well supported by sequence demarcation analysis. Further, the Neibhor-Net network analysis of the complete genome of ChiVMV-tomato, along with other host isolates, formed a reticular network phylogenetic tree suggesting recombination events. Subsequently, RDP5 detected intra-specific recombination breakpoints at the positions 1656-5666 nucleotides with major parent ChiVMV (MN508960) Uravakonda and minor parent ChiVMV (MN508956) with a significant average p value of 1.905×10-22. The LAMP assay using ChiVMV-specific primers resulted in ladder-like amplified products on electrophoresed gel and a distinct red colour pattern with hydroxy naphthalene blue, indicating a positive reaction for the presence of ChiVMV in infected tomato samples. To validate LAMP-designed primers, RNA extracted from ChiVMV-infected tomato, chilli, datura, and tobacco samples were subjected to LAMP assay and it accurately detected the presence of ChiVMV in infected plant samples. Overall, this study provides holistic information of ChiVMV infecting tomato, spanning diagnosis, transmission, genetic characterization, and detection of recombination events, which collectively contribute to effective disease management, crop protection, and informed decision-making in agricultural practices.

Comparing the molecular evolution and recombination patterns of predominant PRRSV-2 lineages co-circulating in China.

Porcine reproductive and respiratory syndrome virus (PRRSV) poses widespread epidemics in swine herds, yet the drivers underlying lineage replacements/fitness dynamics remain unclear. To delineate the evolutionary trajectories of PRRSV-2 lineages prevalent in China, we performed a comprehensive longitudinal phylodynamic analysis of 822 viral sequences spanning 1991-2022. The objectives encompassed evaluating lineage dynamics, genetic diversity, recombination patterns and glycosylation profiles. A significant shift in the dominance of PRRSV-2 sub-lineages has been observed over the past 3 decades, transitioning from sub-lineage 8.7 to sub-lineage 1.8, followed by extensive diversification. The analysis revealed discordant recombination patterns between the two dominant viral sub-lineages 1.8 and 8.7, underscoring that modular genetic exchanges contribute significantly to their evolutionary shaping. Additionally, a strong association was found between recombination breakpoint locations and transcriptional regulatory sequences (TRSs). Glycosylation patterns also demonstrated considerable variability across sub-lineages and temporally, providing evidence for immune-driven viral evolution. Furthermore, we quantified different evolutionary rates across sub-lineages, with sub-lineage 1.8 uniquely displaying the highest nucleotide substitution rates. Taken together, these findings provide refined insight into the evolutionary mechanisms underpinning cyclic shifts in dominance among regionally circulating PRRSV sub-lineages.

Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses.

Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002-2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.