Intrasegmental recombination as an evolutionary force of Lassa fever virus.

Lassa fever (LF), caused by Lassa virus (LASV), is one of the most dangerous diseases to public health. Homologous recombination (HR) is a basic genetic power driving biological evolution. However, as a negative-stranded RNA virus, it is unknown whether HR occurs between LASVs and its influence on the outbreak of LF. In this study, after analyzing 575 S and 433 L segments of LASV collected in Africa, we found that LASV can achieve HR in both of its segments. Interestingly, although the length of S segment is less than half of the L segment, the proportion of LASVs with S recombinants is significantly higher than that with L recombinants. These results suggest that HR may be a feature of LASV, which can be set by natural selection to produce beneficial or eliminate harmful mutations for the virus, so it plays a role in LASV evolution during the outbreak of LF.

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.

Discovery of vaccine-like recombinant SARS-CoV-2 circulating in human.

For viral diseases, vaccination with live attenuated vaccine (LAV) is one of the most effective means for fighting the diseases. However, LAV occasionally overflows from vaccinated individuals circulate in the population with unforeseen consequences. Currently, SARS-CoV-2 LAVs are undergoing clinical trials. In this study, we found that the viruses isolated from Indian SARS CoV-2 infected persons may be candidate LAV-derived strains, indicating the risk of SARS-CoV-2 LAV spillover from vaccinated persons, increasing the complexity of SARS-CoV-2 detection. In addition, the property of frequent recombination of SARS-CoV-2 increases the chance of LAV virulence reversion. Therefore, how to distinguish the LAV viruses from the wild strain and how to avoid the recombination of the circulating vaccine strain and the wild strain are the challenges currently faced by SARS CoV-2 LAV development.

Evolution of Potato virus X.

Potato virus X (PVX) is the type potexvirus of economic significance. The pathogen is distributed worldwide, threatening solanaceous plants in particular. Based on the coat protein (CP) gene, PVX isolates are classified into two major genotypes (I and II). To gain more insights into the molecular epidemiology and evolution of PVX, recombination analyses were conducted and significant signals were detected. Bayesian coalescent method was then applied to the time-stamped entire CP sequences. According to the estimates, the global subtype I-1 went into expansion in the 20th century and was evolving at a moderate rate. Based on the CP phylogenies, a divergence scenario was proposed for PVX. Surveys of codon usage variation showed that PVX genes had additional bias independent of compositional constraint. In codon preference, PVX was both similar to and different from the three major hosts, potato (Solanum tuberosum), tobacco (Nicotiana tabacum), and tomato (S. lycopersicum). Moreover, the suppression of CpG and UpA dinucleotide frequencies was observed in PVX.

YY1 and RTCB in mouse uterine decidualization and embryo implantation.

As a multifunctional transcription factor, YY1 regulates the expression of many genes essential for early embryonic development. RTCB is an RNA ligase that plays a role in tRNA maturation and Xbp1 mRNA splicing. YY1 can bind in vitro to the response element in the proximal promoter of Rtcb and regulate Rtcb promoter activity. However, the in vivo regulation and whether these two genes are involved in the mother-fetal dialogue during early pregnancy remain unclear. In this study, we validated that YY1 bound in vivo to the proximal promoter of Rtcb in mouse uterus of early pregnancy. Moreover, via building a variety of animal models, our study suggested that both YY1 and RTCB might play a role in mouse uterus decidualization and embryo implantation during early pregnancy.

The dominant strain of SARS-CoV-2 is a mosaicism.

COVID-19 is seriously threatening human health all over the world. A comprehensive understanding of the genetic mechanisms driving the rapid evolution of its pathogen (SARS-CoV-2) is the key to controlling this pandemic. In this study, by comparing the entire genome sequences of SARS-CoV-2 isolates from Asia, Europe and America, and analyzing their phylogenetic histories, we found a lineage derived from a recombination event that likely occurred before March 2020. More importantly, the recombinant offspring has become the dominant strain responsible for more than one-third of the global cases in the pandemic. These results indicated that the recombination might have played a key role in the pandemic of the virus.

Novirhabdoviruses versus fish innate immunity: A review.

Novirhabdoviruses belong to the Rhabdoviridae family of RNA viruses. All of the four members are pathogenic for bony fish. Particularly, Infectious hematopoietic necrosis virus (IHNV) and Viral hemorrhagic septicemia virus (VHSV) often cause mass animal deaths and huge economic losses, representing major obstacles to fish farming industry worldwide. The interactions between fish and novirhabdoviruses are becoming better understood. In this review, we will present our current knowledge of fish innate immunity, particularly type I interferon (IFN-I) response, against novirhabdoviral infection, and the evasion strategies exploited by novirhabdoviruses. Members of Toll-like receptors (TLRs) and RIG-I-like receptors (RLRs) appear to be involved in novirhabdovirus surveillance. NF-κB activation and IFN-I induction are primarily triggered for antiviral defense. Autophagy can also be induced by viral glycoprotein (G). Although sensitive to IFN-I, novirhabdoviruses have nucleoprotein (N), matrix protein (M), and non-virion protein (NV) to interfere with host signal transduction and gene expression steps toward antiviral state establishment. Moreover, novirhabdoviruses may exploit some microRNAs for immunosuppression.

[Expression and regulation of XBP1 in mouse uterus during early pregnancy].

The transcription factor X-box binding protein-1 (XBP1) plays a key role in unfolded protein reaction. This study was aimed to investigate the expression pattern and regulation of XBP1 in the mouse uterus during early pregnancy. The methods of immunohistochemistry (IHC) and real time quantitative RT-PCR were used to test XBP1 expression in early pregnancy, artificial decidualization, oestrous cycle and hormone-regulated mouse models. The results showed that XBP1 was spatiotemporally expressed in mouse uterus during early pregnancy. The XBP1 protein was mainly detected in the luminal and glandular epithelia on days 1-4 of pregnancy, and was strongly detected in the decidual area on days 5-8 of pregnancy. Similarly, XBP1 expression was also mainly expressed in decidual cells following artificial decidualization. During the oestrous cycle, Xbp1, Xbp1u, and Xbp1s mRNA was predominantly present in proestrus. In the ovariectomized uterus, the expression of XBP1 in luminal and glandular epithelia was up-regulated after estrogen treatment. These results suggest that XBP1 is associated with embryo implantation and decidualization during early pregnancy in mice, and the expression of XBP1 in luminal and glandular epithelia may be regulated by estrogen.

The matrix segment of the "Spanish flu" virus originated from intragenic recombination between avian and human influenza A viruses.

The 1918 Spanish flu virus has claimed more than 50 million lives. However, the mechanism of its high pathogenicity remains elusive; and the origin of the virus is controversial. The matrix (M) segment regulates the replication of influenza A virus, thereby affecting its virulence and pathogenicity. This study found that the M segment of the Spanish flu virus is a recombinant chimera originating from avian influenza virus and human influenza virus. The unique mosaic M segment might confer the virus high replication capacity, showing that the recombination might play an important role in inducing high pathogenicity of the virus. In addition, this study also suggested that the NA and NS segments of the virus were generated by reassortment between mammalian and avian viruses. Direct phylogenetic evidence was also provided for its avian origin.

Abiotic Stresses: General Defenses of Land Plants and Chances for Engineering Multistress Tolerance.

Abiotic stresses, such as low or high temperature, deficient or excessive water, high salinity, heavy metals, and ultraviolet radiation, are hostile to plant growth and development, leading to great crop yield penalty worldwide. It is getting imperative to equip crops with multistress tolerance to relieve the pressure of environmental changes and to meet the demand of population growth, as different abiotic stresses usually arise together in the field. The feasibility is raised as land plants actually have established more generalized defenses against abiotic stresses, including the cuticle outside plants, together with unsaturated fatty acids, reactive species scavengers, molecular chaperones, and compatible solutes inside cells. In stress response, they are orchestrated by a complex regulatory network involving upstream signaling molecules including stress hormones, reactive oxygen species, gasotransmitters, polyamines, phytochromes, and calcium, as well as downstream gene regulation factors, particularly transcription factors. In this review, we aimed at presenting an overview of these defensive systems and the regulatory network, with an eye to their practical potential via genetic engineering and/or exogenous application.

Rapid detection of foot-and-mouth disease virus using reverse transcription recombinase polymerase amplification combined with a lateral flow dipstick.

Foot-and-mouth disease caused by foot-and-mouth disease virus (FMDV) is one of the most highly contagious diseases of domestic animals, and leads to enormous economic loss. Currently there are two main prevention and control strategies for the disease: eradication of the infected animals in FMDV free countries, and vaccination of the susceptible animals in countries with endemic FMDV infection. Early discovery and diagnosis of the source of infection is therefore integral to the containment of FMDV. In this study, a two-step reverse transcription recombinase polymerase amplification assay combined with lateral flow detection (RPA-LFD) was developed to detect FMDV. With incubation at 38 °C, a region of the 2B gene on the FMDV genome was successfully amplified within 20 min using specific primers and a probe. The amplified RPA product can be visualized on a lateral flow dipstick. The RPA-LFD assay was highly sensitive, detecting down to 10 copies of plasmid DNA. There was no cross-reactivity with other pathogens causing vesicular lesions. In addition, 143 clinical samples were used to compare RPA-LFD with real-time PCR, with 98.6% concordance between the assays. Therefore, the developed RPA-LFD assay provides a rapid, simple, highly promising approach to be used as point-of-care diagnostics in the field.

Cellular prion protein is involved in decidualization of mouse uterus.

Prion protein (PrP) is encoded by a single copy gene Prnp in many cell and tissue types. PrP is very famous for its infectious conformers (PrPSC) resulting in transmissible spongiform encephalopathies. At present, physiological functions of its cellular isoform (PrPC) remain ambiguous. Although PrPC expression has been found in uterus, whether it functions in maternal-fetal dialogue during early pregnant is unknown. In this study, we examined PrPC mRNA and protein in the uterus of peri-implantation mice, and found that they were expressed with a spatiotemporal dynamic pattern. Interestingly, PrPC was significantly increased in the decidual zones around the implanting embryos at the implantation window stage. To further demonstrate that PrPC is involved in the decidualization of mouse uterus during embryo implantation, we constructed the artificial decidualization models and the delayed implantation models. Once the pseudopregnant mice were artificially induced to decidualization, the PrPC expression then increased significantly in the decidua zone. And also, if the delayed implantation embryos were allowed to implant, PrPC protein was also simultaneously improved in stromal cells surrounding the implanting embryos. Moreover, PrPC expression can be inhibited by progesterone but upregulated by estrogen in mouse uterus. These results suggest that PrPC may play an important role in embryo implantation and decidualization.

A permanent host shift of rabies virus from Chiroptera to Carnivora associated with recombination.

Bat virus host shifts can result in the spread of diseases with significant effects. The rabies virus (RABV) is able to infect almost all mammals and is therefore a useful model for the study of host shift mechanisms. Carnivore RABVs originated from two historical host shifts from bat viruses. To reveal the genetic pathways by which bat RABVs changed their host tropism from bats to carnivores, we investigated the second permanent bat-to-carnivore shift resulting in two carnivore variants, known as raccoon RABV (RRV) and south-central skunk RABV (SCSKV). We found that their glycoprotein (G) genes are the result of recombination between an American bat virus and a carnivore virus. This recombination allowed the bat RABV to acquire the head of the G-protein ectodomain of the carnivore virus. This region is involved in receptor recognition and binding, response to changes in the pH microenvironment, trimerization of G proteins, and cell-to-cell transmission during the viral infection. Therefore, this recombination event may have significantly improved the variant's adaptability to carnivores, altering its host tropism and thus leading to large-scale epidemics in striped skunk and raccoon.

Evolution of rice stripe virus.

Rice stripe virus (RSV) is an insect-borne tenuivirus of economical significance. It is endemic to the rice-growing regions of East Asia and exhibits more genetic diversity in Yunnan Province of China. To gain more insights into the molecular epidemiology and evolution of RSV, recombination analyses were conducted and potential events were detected in each of the four RNA segments of RSV. Bayesian coalescent method was then applied to the time-stamped coding sequences of the CP gene. The nucleotide substitution rate and the divergence time were estimated. Age calculations suggested that the first diversification event of the RSV isolates analyzed might take place in the early 20th century, and RSV has existed in Yunnan long before notice. Surveys of codon usage variation showed that the RSV genes had influences other than mutational bias. In codon choice, RSV conformed to neither vector small brown planthopper nor host rice, although the former exerted a more dominant influence on shaping codon usage pattern of RSV. In addition, CpG dinucleotide deficiency was observed in RSV.

New genetic mechanism, origin and population dynamic of bovine ephemeral fever virus.

Bovine ephemeral fever virus (BEFV) is a typical species of the genusEphemerovirus in the family Rhabdoviridae. Today, prevailing BEFV can be divided into three phylogeographic lineages, East Asia, Mideast, and Australia. In this study, we provide evidence that the whole East Asia lineage originates from a homologous recombination (HR) between the Mideast and Australia lineages that probably occurred in the 1940s. To our knowledge, HR has not been proposed before as the genetic mechanism of BEFV. According to the HR event and Bayesian estimation, the three BEFV lineages might originate from Africa, and may have spread to Asia and Australia through the Mideast. In addition, the population of the virus may have augmented significantly in the 2000s, suggesting that the risk for outbreaks of BEFV may be high at present.

Studying classical swine fever virus: making the best of a bad virus.

Classical swine fever (CSF) is a highly contagious and often fatal disease that affects domestic pigs and wild boars. Outbreak of CSF can cause heavy economic losses to the pig industry. The strategies to prevent, control and eradicate CSF disease are based on containing the disease through a systematic prophylactic vaccination policy and a non-vaccination stamping-out policy. The quest for prevention, control and eradication of CSF has moved research forward in academia and industry, and has produced noticeable advances in understanding fundamental aspects of the virus replication mechanisms, virulence, and led to the development of new vaccines. In this review we summarize recent progress in CSFV epidemiology, molecular features of the genome and proteome, the molecular basis of virulence, and the development of anti-virus technologies.

Vaccination influences the evolution of classical swine fever virus.

Classical swine fever is a serious, economically damaging disease caused by classical swine fever virus (CSFV). The CSFV is composed of two clades, according to phylogenetic estimates. Attenuated live vaccine such as HCLV, has been widely used to protect pigs from CSFV, but the influence of vaccination on the evolution of CSFV has not been studied. We conducted a systemic analysis of the impact of vaccination on the evolution of CSFV by comparing vaccine-related and non-vaccine-related CSFV groups. We found that vaccination may affect strain diversity and immune escape through recombination and point mutation. We also found that vaccination may influence the population dynamics, evolutionary rate and adaptive evolution of classical swine fever virus. Our evidence suggests that the vaccination might also change host adaptation through influencing codon usage of the virus in swine. These findings suggest that it is necessary to avoid excessive use of CSFV attenuated vaccines.

Identification of two severe fever with thrombocytopenia syndrome virus strains originating from reassortment.

Recently, a novel bunyavirus, severe fever with thrombocytopenia syndrome virus (SFTSV), was isolated in central China. The virus can cause multi-clinical symptoms: severe fever, thrombocytopenia, leukocytopenia, with a mortality rate of ~10%. Several studies show that SFTSV could undergo rapid evolution via gene mutation and homologous recombination. However, as an important evolutionary force for segmented-genome viruses, reassortment has not been reported in SFTSV. In this study, we identified two SFTSV strains of which the S segment has different origin from M and L, suggesting that reassortment might be potential force driving rapid change of SFTSV. This result might shed new light on the evolutionary behavior of the novel virus.

Dating the divergence of the infectious hematopoietic necrosis virus.

Infectious hematopoietic necrosis virus (IHNV) is an economically significant rhabdovirus that can cause severe disease to most salmonid fish. Phylogenetic analyses of worldwide IHNV isolates have defined five major genogroups. Herein, to further the understanding of the molecular epidemiology and evolution of IHNV, Bayesian coalescent analyses were conducted to the time-stamped coding sequences of the N, G and NV genes. The nucleotide substitution rates and the divergence times were assessed. Among the three genes, NV, the smallest one coding for a non-virion protein, was conferred the highest mean rate. Estimates for the G subsets based upon the five genogroups indicated that L and U evolved much slower than the others. Age calculations suggested that the first diversification event of the IHNV isolates analyzed might have happened before the notification of the disease during the early 1950s. Selection analyses suggested that the three genes were mainly subject to purifying selection. In addition, surveys of codon usage variation showed that the three genes had influences other than mutational bias.

Isolation and identification of a novel rabies virus lineage in China with natural recombinant nucleoprotein gene.

Rabies virus (RABV) causes severe neurological disease and death. As an important mechanism for generating genetic diversity in viruses, homologous recombination can lead to the emergence of novel virus strains with increased virulence and changed host tropism. However, it is still unclear whether recombination plays a role in the evolution of RABV. In this study, we isolated and sequenced four circulating RABV strains in China. Phylogenetic analyses identified a novel lineage of hybrid origin that comprises two different strains, J and CQ92. Analyses revealed that the virus 3' untranslated region (UTR) and part of the N gene (approximate 500 nt in length) were likely derived from Chinese lineage I while the other part of the genomic sequence was homologous to Chinese lineage II. Our findings reveal that homologous recombination can occur naturally in the field and shape the genetic structure of RABV populations.