Interspecies Recombination Events Research Articles

First report of Tomato interveinal chlorosis virus infecting Rhynchosia minima plants in Brazil.

Tomato interveinal chlorosis virus (ToICV; Begomovirus solanumintervenae, genus Begomovirus, family Geminiviridae) has been described infecting tomato (Solanum lycopersicum) and Macroptilium lathyroides in Northeastern (NE) Brazil for more than a decade (Albuquerque et al., 2012; Silva et al., 2012). During a survey in 2020, plants of the leguminous weed Rhynchosia minima exhibiting virus-like symptoms such as mosaic and interveinal chlorosis were observed in the state of Alagoas, NE Brazil. Symptomatic leaf samples of R. minima were randomly collected (n=15; supplementary figure 1). Total DNA from each sample was used as a template for PCR amplification of partial begomoviral DNA-A sequences using the degenerate primer pair PAL1v1978 and PAR1c496, universal for geminiviruses (Rojas et al., 1993). Amplicons of ~1.2 kbp were observed from 12 samples, although this should not be considered as incidence since only symptomatic plants were collected. To identify the begomovirus associated with R. minima, viral genomes were amplified from PCR-positive samples using rolling circle amplification (RCA) (Inoue-Nagata et al., 2004). The RCA products were digested with HindIII, cloned into the pBluescript II KS+ plasmid vector and bidirectionally Sanger-sequenced (Macrogen Inc., Seoul). BLASTn searches indicated that the clones (n=4) reported here corresponded to a begomovirus DNA-A component, and pairwise comparisons showed that they shared the highest identity with ToICV, at 92.4-94.7% nucleotide sequence identity. Based on the species demarcation criteria of ≥91% nucleotide identity for the genus Begomovirus (Brown et al., 2015), the begomoviruses obtained from R. minima are new isolates of ToICV. The new DNA-A sequences of 2,619-2,623 nt in length were deposited in GenBank under accession numbers PP639092 to PP639095. Multiple nucleotide sequence alignments were prepared using the MUSCLE algorithm implemented in MEGA v.11 (Kumar et al., 2018), and a maximum likelihood (ML) tree was reconstructed in RaxML-NG (Kozlov et al., 2019), assuming a general time reversible (GTR) nucleotide substitution model with a gamma (G) model of rate heterogeneity and 1,000 bootstrap replicates. The DNA-A-based tree showed that the ToICV sequences clustered into a monophyletic group, additionally supporting these isolates as members of the species Begomovirus solanumintervenae. At least two independent interspecies recombination events were predicted among the ToICV isolates, with breakpoints located in the Rep-encoding region and ToICV (GenBank Accession JF803253), tomato mottle leaf curl virus (JF803248) and soybean blistering mosaic virus (MN486865) detected as putative parents. To the best of our knowledge, this is the first report of ToICV infecting R. minima worldwide, expanding the host range of this begomovirus. Non-cultivated plants such as R. minima play a crucial role as reservoirs and sources of inoculum for begomoviruses (Paz-Carrasco et al., 2014), reinforcing their relevance to socioeconomically important crops.

Recombination and selection trajectory of the monkeypox virus during its adaptation in the human population.

Monkeypox, caused by the monkeypox virus (MPXV), was historically confined to West and Central Africa but has now spread globally. Recombination and selection play crucial roles in the evolutionary adaptation of MPXV; however, the evolution of MPXV and its relationship with the recent, ground-breaking monkeypox epidemic remains poorly understood. To gain insights into the evolutionary dynamics of MPXV, comprehensive in silico recombination and selection analyses were conducted based on MPXV whole genome sequence data. Three types of recombination were identified: five ancestor-sharing interspecies recombination events, six specific interspecies recombination events and four intraspecies recombination events. The results highlight the prevalent occurrence of recombination in MPXV, with 73.3% occurring in variable regions of the genome. Selection analysis was performed from three dimensions: proteins around recombination regions, proteins from recombinant ancestors and MPXV branches, and whole-genome gene analysis. Results revealed 2 and 7 proteins under positive selection in the first two dimensions, respectively. These proteins are mainly involved in infection immunity, apoptosis regulation and viral virulence. Whole-genome analysis detected 25 genes under positive selection, mainly associated with immune response and viral regulation. Understanding their evolutionary patterns will help predict and prevent cross-species transmission, zoonotic outbreaks and potential human epidemics.

Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates.

Haemophilus influenzae (Hi) was long known as an easy-to-treat bacterium, but increasing resistance against beta-lactams and other critically important antibiotics is now a growing concern. We describe here the whole-genome sequencing (WGS) analysis of three non-typeable Hi isolates received in 2018-2019 by the Belgian National Reference Centre (NRC) for Haemophilus influenzae, as they presented an unusual multi-resistant profile. All three isolates were sequenced by WGS and mapped to the reference isolate Hi Rd KW20. Shorten uptake signal sequences (USSs) known to be associated with homologous recombination were sought in ftsI, murE and murF genes, and inner partial sequences were compared against the blast nucleotide database to look for similarity with other Haemophilus species. Their antimicrobial resistance (AMR) genotype was studied. Core-genome multilocus sequence typing (MLST) was performed on the NTHi database pubMLST to place our isolates in the actual worldwide epidemiology. The isolates also harboured interspecies recombination patterns in the murF-murE-ftsI region involved in cell wall synthesis. The three isolates were multidrug resistant and two of them were also resistant to amoxicillin-clavulanic acid and showed a reduced susceptibility to meropenem. All three isolates belonged to the MLST clonal complex (CC) 422, and WGS revealed that the three were very similar. They harboured mobile genetic elements (carrying blaTEM-1B, mefA and msrD genes associated with resistance), mutations in gyrA and parC linked to fluoroquinolone resistance as well as remodelling events in ompP2 that might be related to lower carbapenem susceptibility. The Hi evolution towards antimicrobial multiresistance (AMR) is a complex and poorly understood phenomenon, although probably linked to a large degree to the presence of USSs and exchange within the family Pasteurellaceae. To better understand the respective roles of clonal expansion, horizontal gene transfers, spontaneous mutations and interspecies genetic rearrangements in shaping Hi AMR, both analysis of Hi communities over time within individuals and worldwide monitoring of non-typeable Hi causing infections should be conducted.

Genome analyses ofspecies A rotavirus isolated from various mammalian hosts inNorthern Ireland during 2013-2016.

Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted.

Exploring the third-generation tetracycline resistance of multidrug-resistant livestock-associated methicillin-resistant Staphylococcus aureus ST9 across healthcare settings in China.

The overuse of antibiotics in livestock is contributing to the burden of antimicrobial resistance in humans, representing a One Health challenge. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has recently become a growing concern, and ST9 is the major LA-MRSA lineage in China and has emerged in clinical settings. Antimicrobial susceptibility testing was used to evaluate the tetracycline resistance of ST9 MRSA collections, and gene cloning experiments were performed to explore the resistance mechanisms. Whole-genome sequencing and comparative genomics were used to analyse the genetic features of clinical ST9 isolates. A phylogenetic tree was constructed to investigate the relationship of human- and livestock-derived ST9 isolates. Clinical ST9 isolates were found to possess several types of resistance genes and resistance-related mutations and were multidrug-resistant. Notably, all clinical ST9 isolates were resistant to third-generation tetracyclines. Cloning experiments showed that both the acquisition of the tetracycline resistance gene tet(L)/tet(63) and a mutation in the rpsJ gene contributed to third-generation tetracycline resistance. Phylogenetic analysis showed that the ST9 isolates collected in healthcare systems were probably transmitted from livestock. The ST9 lineage underwent multiple interspecies recombination events and gained many resistance elements. Furthermore, the resistance to third-generation tetracyclines may have evolved under tetracycline pressure in livestock. The evolution of ST9 MRSA in livestock and transmission of this clone between humans and livestock highlight the importance of establishing control strategies with the One Health approach to reduce the burden of antibiotic resistance.

Evolution of cucurbit-infecting tobamoviruses: Recombination and codon usage bias

Currently, there are seven cucurbit-infecting tobamoviruses comprising cucumber green mottle mosaic virus (CGMMV), Kyuri green mottle mosaic virus (KGMMV), cucumber fruit mottle mosaic virus (CFMMV), zucchini green mottle mosaic virus (ZGMMV), cucumber mottle virus (CMoV), watermelon green mottle mosaic virus (WGMMV), and Trichosanthes mottle mosaic virus (TrMMV). To gain more insights into their evolution, recombination analyses were conducted. Four CGMMV isolates and one KGMMV isolate were suggested to be recombinants. And there was an interspecies recombination event between CGMMV and ZGMMV. Phylogenetic incongruence was also observed for CGMMV and KGMMV. A probable ancestral pattern was inferred for the gene junction region between RdRp and MP. Codon usage bias analysis revealed that the viral genes had additional influence independent of compositional constraint. In codon preference, the seven viruses were both similar to and different from the host cucumber (Cucumis sativus). Moreover, the viruses were not deficient in CpG and UpA dinucleotides.

Recombination and darwinian selection as drivers of genetic diversity and evolution of sweet potato leaf curl viruses in Tanzania

Using High-throughput Sequencing (HTS) and Sanger sequencing techniques, we detected sweet potato leaf curl viruses (SPLCVs; Genus Begomovirus) and determined their genetic diversities, recombination, and evolutionary selection pressure imposed on their genes. Eleven complete (2767–2824 nucleotides) and fifty partial (V1 and C1 proteins) sequences of SPLCVs were generated, and one complete genome of sweet potato pakakuyu virus was also generated. The detected SPLCVs were genetically diverse, with complete nucleotide sequence identities ranging from 78.7 to 100%. These sequences were closely related (>89% identical) to the sweet potato leaf curl virus, the sweet potato Sao Paulo virus, and the sweet potato leaf curl Uganda virus. The diversity of SPLCVs indicated the occurrence of their strains and variants in Tanzania. Intra- and interspecies recombination events were detected in four and two complete and partial sequences of SPLCVs, respectively. The genes of SPLCVs, except the C4 gene, are evolving under purifying selection pressure. In the C4 gene, numerous codon sites are evolving under positive selection pressure. High genetic diversity and diversifying selection imply an increased chance of SPLCVs to interact and adapt to diverse sweet potato genotypes and their wild relatives in Tanzania.

Isolation and Identification of Inter-Species Enterovirus Recombinant Genomes.

Positive-strand RNA virus evolution is partly attributed to the process of recombination. Although common between closely genetically related viruses, such as within species of the Enterovirus genus of the Picornaviridae family, inter-species recombination is rarely observed in nature. Recent studies have shown recombination is a ubiquitous process, resulting in a wide range of recombinant genomes and progeny viruses. While not all recombinant genomes yield infectious progeny virus, their existence and continued evolution during replication have critical implications for the evolution of the virus population. In this study, we utilised an in vitro recombination assay to demonstrate inter-species recombination events between viruses from four enterovirus species, A-D. We show that inter-species recombinant genomes are generated in vitro with polymerase template-switching events occurring within the virus polyprotein coding region. However, these genomes did not yield infectious progeny virus. Analysis and attempted recovery of a constructed recombinant cDNA revealed a restriction in positive-strand but not negative-strand RNA synthesis, indicating a significant block in replication. This study demonstrates the propensity for inter-species recombination at the genome level but suggests that significant sequence plasticity would be required in order to overcome blocks in the virus life cycle and allow for the production of infectious viruses.

Herpes Simplex Virus Mistyping due to HSV-1 × HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B.

Human herpes simplex viruses (HSV) 1 and 2 are extremely common human pathogens with overlapping disease spectra. Infections due to HSV-1 and HSV-2 are distinguished in clinical settings using sequence-based “typing” assays. Here we describe a case of HSV mistyping caused by a previously undescribed HSV-1 × HSV-2 recombination event in UL27, the HSV gene that encodes glycoprotein B. This is the first documented case of HSV mistyping caused by an HSV-1 × HSV-2 recombination event and the first description of an HSV interspecies recombination event in UL27, which is frequently used as a target for diagnostics and experimental therapeutics. We also review the primer and probe target sequences for a commonly used HSV typing assay from nearly 700 HSV-1 and HSV-2 samples and find that about 4% of HSV-1 samples have a single nucleotide change in at least one of these loci, which could impact assay performance. Our findings illustrate how knowledge of naturally occurring genomic variation in HSV-1 and HSV-2 is essential for the design and interpretation of molecular diagnostics for these viruses.

Recombination of B- and T-cell epitope-rich loci from Aedes- and Culex-borne flaviviruses shapes Zika virus epidemiology

Sporadic human Zika virus (ZIKV) infections have been recorded in Africa and Asia since the 1950s. Major epidemics occurred only after ZIKV emerged in the Pacific islands and spread to the Americas. Specific biological determinants of the explosive epidemic nature of ZIKV have not been identified. Phylogenetic studies revealed incongruence in ZIKV placement in relation to Aedes-borne dengue viruses (DENV) and Culex-borne flaviviruses. We hypothesized that this incongruence reflects interspecies recombination resulting in ZIKV evasion of cross-protective T-cell immunity. We investigated ZIKV phylogenetic incongruence in relation to: DENV T-cell epitope maps experimentally identified ex vivo, published B-cell epitope loci, and CD8+ T-cell epitopes predicted in silico for mosquito-borne flaviviruses. Our findings demonstrate that the ZIKV proteome is a hybrid of Aedes-borne DENV proteins interspersed amongst Culex-borne flavivirus proteins derived through independent interspecies recombination events. These analyses infer that DENV-associated proteins in the ZIKV hybrid proteome generated immunodominant human B-cell responses, whereas ZIKV recombinant derived Culex-borne flavivirus-associated proteins generated immunodominant CD8+ and/or CD4+ T-cell responses. In silico CD8+ T-cell epitope ZIKV cross-reactive prediction analyses verified this observation. We propose that by acquiring cytotoxic T-cell epitope-rich regions from Culex-borne flaviviruses, ZIKV evaded DENV-generated T-cell immune cross-protection. Thus, Culex-borne flaviviruses, including West Nile virus and Japanese encephalitis virus, might induce cross-protective T-cell responses against ZIKV. This would explain why explosive ZIKV epidemics occurred in DENV-endemic regions of Micronesia, Polynesia and the Americas where Culex-borne flavivirus outbreaks are infrequent and why ZIKV did not cause major epidemics in Asia where Culex-borne flaviviruses are widespread.

Large, Stable, Contemporary Interspecies Recombination Events in Circulating Human Herpes Simplex Viruses.

The ubiquitous human pathogens, herpes simplex virus (HSV)-1 and HSV-2, are distinct viral species that diverged approximately 6 million years ago. At least 4 small, ancient HSV-1 × HSV-2 interspecies recombination events have affected the HSV-2 genome, with recombinants and nonrecombinants at each locus circulating today. However, it is unknown whether interspecies recombination can affect other loci and whether new recombinants continue to be generated. Using 255 newly sequenced and 230 existing HSV genome sequences, we comprehensively assessed interspecies recombination in HSV. Our findings show that the sizes and locations of interspecies recombination events in HSV-2 are significantly more variable than previously appreciated and that they can impact species-specific T-cell recognition of HSV. We describe 2 large (>5 kb) recombination events, one of which arose in its current host, demonstrating that interspecies recombination continues to occur today. These results raise concerns about the use of live-attenuated HSV-2 vaccines in high HSV-1 prevalence areas.

Detection by high-throughput sequencing and molecular characterization of complexes of fabaviruses infecting ‘Staccato(R)’ sweet cherry (Prunus avium) in Canada

High throughput sequencing (HTS) revealed the existence of complexes of fabaviruses infecting two ‘Staccato(R) ’ sweet cherry plants (Prunus avium). Species classified as members of the genus Fabavirus are positive sense RNA viruses that possess bipartite genomes. The cherry plants Stac-3B (symptomatic) and Stac-4B (asymptomatic) were each determined to be infected with multiple RNA1 and RNA2 segments of Prunus virus F (PrVF) and the putative cherry virus F (CVF). The RNA1 and RNA2 segments Stac-3B_C3 and Stac-3B_c11, respectively, are proposed to represent an isolate identified as PrVF-CP1; while the RNA1 and RNA2 segments Stac-3B_C4 and Stac-3B_c7 are proposed to represent an isolate CVF-CC1. The termini of these four RNA segments were confirmed by RACE revealing that the first 28 nucleotides of the 5ʹuntranslated region (UTR) of all four RNA segments is conserved and is predicted to form a hairpin structure. The 3ʹUTRs possess various repeat sequences. Very interestingly, a group of PrVF sequences, exemplified by SwC 74_2c, were identified as the products of an interspecies recombination event, with PrVF 8816_s1 as a possible major parent and an isolate of CVF being the minor parent. This was supported by all methods in the RDP4 program. No association was made of any of the fabavirus complexes with any disease symptoms. This is the first description of the detection of CVF in Canada.

The possible origin of human adenovirus type 3: Evidence of natural genetic recombination between human and simian adenovirus

We determined a complete genome sequence of the Korean field strain, KUMC-62, of human adenovirus type 3 (HAdV-3) and performed comparative genome analyses. Interestingly HAdV-3 has a distinct genomic sequence for the fiber CDS region on average 62.46% of nucleotide sequence identity to other types of HAdV-B1, while remaining genomic region of HAdV-3 is very similar (on average 95.71% of nucleotide sequence identity) to other types of HAdV-B1. The blast results showed that the fiber CDS region of HAdV-3 exhibited the highest nucleotide sequence identity with that of simian adenovirus type 32 (SAdV-32), except other strains of HAdV-3. In the Simplot analysis, a potential recombination event was detected between HAdV-7 and SAdV-32, which might have created HAdV-3 in the past. These findings suggest that HAdV-3 highly likely was created by a natural inter-species recombination event between human and non-human primate AdVs.

CHARACTERIZATION OF GRAPEVINE LEAFROLL-ASSOCIATED VIRUS 4 FROM INDIAN VINEYARDS

In a 2013-15 survey, typical symptoms of grapevine leafroll disease were observed in vineyards of Western and North-Eastern India. Twelve grapevine cultivars were infected with Grapevine leafroll-associated virus 4 (GLRaV-4), as shown by ELISA. The coat protein (CP), heat shock protein 70 homologue (HSP70h) and p23 genes of GLRaV-4 isolates from India were characterized by RT-PCR and sequencing. A phylogenetic analysis of the CP gene showed that the Indian isolates clustered with GLRaV-4 isolates Y252-IL (AM162279) from Israel, Y253-TK (AM176759) from Turkey, and LR106 (FJ467503) from USA with a maximum identity of 98% at the amino acid level. Sequences analysis revealed intra- and inter-species recombination events within CP and p23 genes of GLRaV-4 isolates. Indian isolates GRP-G (KT759152) and GDR-I (KT759153) diverged from other GLRaV-4 isolates in their p23 gene. This is the first report of the occurrence of GLRaV-4 in Indian vineyards and of recombination in the GLRaV-4 genome.

Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.

Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5' and 3' ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.

Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages.

Streptomyces species produce many important antibiotics and have a crucial role in soil nutrient cycling. However, their evolutionary history remains poorly characterized. We have evaluated the impact of homologous recombination on the evolution of Streptomyces using multi-locus sequence analysis of 234 strains that represent at least 11 species clusters. Evidence of inter-species recombination is widespread but not uniform within the genus and levels of mosaicism vary between species clusters. Most phylogenetically incongruent loci are monophyletic at the scale of species clusters and their subclades, suggesting that these recombination events occurred in shared ancestral lineages. Further investigation of two mosaic species clusters suggests that genes acquired by inter-species recombination may have become fixed in these lineages during periods of demographic expansion; implicating a role for phylogeography in determining contemporary patterns of genetic diversity. Only by examining the phylogeny at the scale of the genus is apparent that widespread phylogenetically incongruent loci in Streptomyces are derived from a far smaller number of ancestral inter-species recombination events.

Occurrence and molecular characterization of Tomato common mosaic virus (ToCmMV) in tomato fields in Espírito Santo state, Brazil

Here, we report for the first time the complete molecular characterization of a begomovirus infecting tomato crops in Espirito Santo state, Brazil. Based on the analysis of partial nucleotide sequences of isolates obtained from 20 samples, collected from 2007 to 2011, all isolates were preliminary classified as Tomato commom mosaic virus (ToCmMV). Complete nucleotide sequences of the DNA-A and DNA-B components of one isolate were determined. The DNA-A sequence shares 97.5 % identity with that of ToCmMV-[BR:Coi22:07], thus confirming it to be an isolate of ToCmMV. In addition, recombination analysis showed that this ToCmMV isolate probably evolved from an inter-species recombination event and likely contributed to the emergence of the weed-infecting begomovirus, Sida yellow leaf curl virus (SiYLCV).

A novel astrovirus species in the gut of yaks with diarrhoea in the Qinghai–Tibetan Plateau, 2013.

The yak (Bos grunniens) is an iconic symbol in the high-altitude region of the Qinghai–Tibetan Plateau. Diarrhoea is a common disease in yaks, resulting in major economic losses. To investigate the diversity of viral species, we reported the metagenomics-derived virome in a pooled faecal sample of 20 diarrhoeic yaks. The nine viruses found in the pooled diarrhoeic samples, in order of abundance of nucleic acid sequence, were influenza A virus, bovine viral diarrhoea virus (BVDV), rotavirus, ungulate tetraparvovirus 1 (bovine hokovirus), astrovirus (AstV), bovine enterovirus, hepatitis E virus, kobuvirus and woodchuck hepatitis virus. Compared with healthy yaks, only AstV had a significantly higher prevalence rate in diarrhoeal samples, indicating a correlation with the clinical symptoms of diarrhoea in yaks. To further investigate the molecular characterization of yak AstV, a near-full genome was obtained from a diarrhoeic sample. It was 6243 bp in length and shared 46.4–66.2 % similarity with other related bovine AstVs from faeces. Phylogenetic analysis of the genome demonstrated that the yak AstV fell within the bovine AstVs cluster, but was located in a unique lineage, suggesting a novel AstV species was identified in yaks. Interestingly, the ORF2 region of yak AstV had closer similarity and genetically relationship with deer AstV strain CcAstV-2 than that of the bovine AstVs. Further analysis showed that one possible interspecies recombination event occurred in ORF2. In summary, this study expanded our understanding of the viral communities of diarrhoeal yaks and identified a novel AstV that was associated with diarrhoea in yaks.

Contrasting inter- and intraspecies recombination patterns in the "Harveyi clade" vibrio collected over large spatial and temporal scales.

Recombination plays an important role in the divergence of bacteria, but the frequency of interspecies and intraspecies recombination events remains poorly understood. We investigated recombination events that occurred within core genomes of 35 Vibrio strains (family Vibrionaceae, Gammaproteobacteria), from six closely related species in the so-called “Harveyi clade.” The strains were selected from a collection of strains isolated in the last 90 years, from various environments worldwide. We found a close relationship between the number of interspecies recombination events within core genomes of the 35 strains and the overall genomic identity, as inferred from calculations of the average nucleotide identity. The relationship between the overall nucleotide identity and the number of detected interspecies recombination events was comparable when analyzing strains isolated over 80 years apart, from different hemispheres, or from different ecologies, as well as in strains isolated from the same geographic location within a short time frame. We further applied the same method of detecting recombination events to analyze 11 strains of Vibrio campbellii, and identified disproportionally high number of intraspecies recombination events within the core genomes of some, but not all, strains. The high number of recombination events was detected between V. campbellii strains that have significant temporal (over 18 years) and geographical (over 10,000 km) differences in their origins of isolation. Results of this study reveal a remarkable stability of Harveyi clade species, and give clues about the origins and persistence of species in the clade.

Mapping of the exchangeable and dispensable domains of the RNA 2-encoded 2AHP protein of arabis mosaic nepovirus

The N-terminal domains of the RNA 2-encoded 2AHP proteins of the arabis mosaic (ArMV) and grapevine fanleaf (GFLV) nepoviruses were shown to be highly variable and a hotspot for intra- and inter-species recombination events. Chimeric ArMV-NW clones in which the N-terminal domain of 2AHP or the entire 2AHP of GFLV isolates replaced the corresponding domains of ArMV retained their infectivity, showing that the 2AHP proteins of ArMV-NW and GFLV are exchangeable. ArMN-NW clones with deletions of the N-terminal, core, or C-terminal domains of the ArMV-NW 2AHP were infectious in Chenopodium quinoa although viral RNA (especially RNA 2) accumulated at reduced levels. In contrast, deletion of the entire 2AHP protein or of the C-terminal two thirds of the protein abolished infectivity of the ArMV-NW clones. These results suggest that multiple functional domains are distributed throughout the 2AHP protein and are essential for the accumulation of viral RNA 2.