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Coronavirus porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric coronavirus that caused severe economic losses worldwide, and more effort is needed to develop economical and efficient vaccines to control or eliminate this disease. The chemokine interleukin-8 (CXCL8/IL-8) is indispensable for the activation and trafficking of inflammatory mediators and tumor progression and metastasis.

Inland waters (rivers, reservoirs, lakes, ponds, streams) and estuaries are significant emitters of methane (CH

International audience; Gaseous reactive nitrogen (Nr) emissions from agricultural soils to the atmosphere constitute an integral part of global N cycle, directly or indirectly causing climate change impacts. The extensive use of N fertilizer in crop production will compromise our efforts to reduce agricultural Nr emissions in China. A national inventory of fertilizer N-induced gaseous Nr emissions from croplands in China remains to be developed to reveal its role in shaping climate change. Here we present a data-driven estimate of fertilizer N-induced soil Nr emissions based on regional and crop-specific emission factors (EFs) compiled from 379 manipulative studies. In China, agricultural soil Nr emissions from the use of synthetic N fertilizer and manure in 2018 are estimated to be 3.81 and 0.73 Tg N yr−1, with a combined contribution of 23%, 20% and 15% to the global agricultural emission total of ammonia (NH3), nitrous oxide (N2O) and nitric oxide (NO), respectively. Over the past three decades, NH3 volatilization from croplands has experienced a shift from a rapid increase to a decline trend, whereas N2O and NO emissions always maintain a strong growth momentum due to a robust and continuous rise of EFs. Regionally, croplands in Central south (1.51 Tg N yr−1) and East (0.99 Tg N yr−1) of China exhibit as hotspots of soil Nr emissions. In terms of crop-specific emissions, rice, maize and vegetable show as three leading Nr emitters, together accounting for 61% of synthetic N fertilizer-induced Nr emissions from croplands. The global warming effect derived from cropland N2O emissions in China was found to dominate over the local cooling effects of NH3 and NO emissions. Our established regional and crop-specific EFs for gaseous Nr forms provide a new benchmark for constraining the IPCC Tier 1 default EF values. The spatio-temporal insight into soil Nr emission data from N fertilizer application in our estimate is expected to advance our efforts towards more accurate global or regional cropland Nr emission inventories and effective mitigation strategies.

African swine fever (ASF) is etiologically an acute, highly contagious and hemorrhagic disease caused by African swine fever virus (ASFV). Due to its genetic variation and phenotypic diversity, until now, no efficient commercial vaccines or therapeutic options are available. The ASFV genome contains a conserved middle region and two flexible ends that code for five multigene families (MGFs), while the biological functions of the MGFs are not fully characterized. Here, ASFV MGF505-2R-deficient mutant ASFV-Δ2R was constructed based on a highly virulent genotype II field isolate ASFV CN/GS/2018 currently circulating in China. Transcriptomic profiling demonstrated that ASFV-Δ2R was capable of inducing a larger number of differentially expressed genes (DEGs) compared with ASFV CN/GS/2018. Hierarchical clustering of up-regulated DEGs revealed that ASFV-Δ2R induced the most dramatic expression of interferon-related genes and inflammatory and innate immune genes, as further validated by RT-qPCR. The GO and KEGG pathway analysis identified significantly enriched pathways involved in pathogen recognition and innate antiviral immunity. Conversely, pharmacological activation of those antiviral immune responses by exogenous cytokines, including type I/II IFNs, TNF-α and IL-1β, exerted combinatory effects and synergized in antiviral capacity against ASFV replication. Collectively, MGF505-2R is a newly identified inhibitor of innate immunity potentially implicated in immune evasion.

The coronavirus disease 2019 (COVID-19) pandemic is caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is spread primary via respiratory droplets and infects the lungs. Currently widely used cell lines and animals are unable to accurately mimic human physiological conditions because of the abnormal status of cell lines (transformed or cancer cells) and species differences between animals and humans. Organoids are stem cell-derived self-organized three-dimensional culture in vitro and model the physiological conditions of natural organs. Here we showed that SARS-CoV-2 infected and extensively replicated in human embryonic stem cells (hESCs)-derived lung organoids, including airway and alveolar organoids which covered the complete infection and spread route for SARS-CoV-2 within lungs. The infected cells were ciliated, club, and alveolar type 2 (AT2) cells, which were sequentially located from the proximal to the distal airway and terminal alveoli, respectively. Additionally, RNA-seq revealed early cell response to virus infection including an unexpected downregulation of the metabolic processes, especially lipid metabolism, in addition to the well-known upregulation of immune response. Further, Remdesivir and a human neutralizing antibody potently inhibited SARS-CoV-2 replication in lung organoids. Therefore, human lung organoids can serve as a pathophysiological model to investigate the underlying mechanism of SARS-CoV-2 infection and to discover and test therapeutic drugs for COVID-19. Electronic supplementary material The online version of this article (10.1007/s13238-020-00811-w) contains supplementary material, which is available to authorized users.

We have surveyed avian influenza virus (AIV) genomes from live poultry markets within China since 2014. Here we present a total of 16,091 samples that were collected from May 2016 to February 2019 in 23 provinces and municipalities in China. We identify 2048 AIV-positive samples and perform next generation sequencing. AIV-positive rates (12.73%) from samples had decreased substantially since 2016, compared to that during 2014–2016 (26.90%). Additionally, H9N2 has replaced H5N6 and H7N9 as the dominant AIV subtype in both chickens and ducks. Notably, novel reassortants and variants continually emerged and disseminated in avian populations, including H7N3, H9N9, H9N6 and H5N6 variants. Importantly, almost all of the H9 AIVs and many H7N9 and H6N2 strains prefer human-type receptors, posing an increased risk for human infections. In summary, our nation-wide surveillance highlights substantial changes in the circulation of AIVs since 2016, which greatly impacts the prevention and control of AIVs in China and worldwide., In this study, the authors present a genomic surveillance of avian influenza genomes sampled from live poultry markets in China. They report that a number of variants have emerged since 2016 that pose an increased risk to humans. They highlight the importance of continuous genome surveillance of circulating influenza strains.

Warming can accelerate the decomposition of soil organic matter and stimulate the release of soil greenhouse gases (GHGs), but to what extent soil release of methane (CH4 ) and nitrous oxide (N2 O) may contribute to soil C loss for driving climate change under warming remains unresolved. By synthesizing 1,845 measurements from 164 peer-reviewed publications, we show that around 1.5°C (1.16-2.01°C) of experimental warming significantly stimulates soil respiration by 12.9%, N2 O emissions by 35.2%, CH4 emissions by 23.4% from rice paddies, and by 37.5% from natural wetlands. Rising temperature increases CH4 uptake of upland soils by 13.8%. Warming-enhanced emission of soil CH4 and N2 O corresponds to an overall source strength of 1.19, 1.84, and 3.12 Pg CO2 -equivalent/year under 1°C, 1.5°C, and 2°C warming scenarios, respectively, interacting with soil C loss of 1.60 Pg CO2 /year in terms of contribution to climate change. The warming-induced rise in soil CH4 and N2 O emissions (1.84 Pg CO2 -equivalent/year) could reduce mitigation potential of terrestrial net ecosystem production by 8.3% (NEP, 22.25 Pg CO2 /year) under warming. Soil respiration and CH4 release are intensified following the mean warming threshold of 1.5°C scenario, as compared to soil CH4 uptake and N2 O release with a reduced and less positive response, respectively. Soil C loss increases to a larger extent under soil warming than under canopy air warming. Warming-raised emission of soil GHG increases with the intensity of temperature rise but decreases with the extension of experimental duration. This synthesis takes the lead to quantify the ecosystem C and N cycling in response to warming and advances our capacity to predict terrestrial feedback to climate change under projected warming scenarios.

With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and growing fear, people have become very concerned about whether this novel coronavirus could be transmitted by mosquitoes. We evaluate the infectivity of SARS-CoV-2 in Aedes albopictus and Aedes aegypti derived cell lines. The results indicated that SARS-CoV-2 could not replicate in both C6/36, Sf9 and Aag2 cells. Further, no SARS-CoV-2 RNA was detected in the field collected Culex, and Anopheles mosquitoes during the months of April and May in Wuhan in 2020. Our findings highlight the restricted replication of SARS-CoV-2 in mosquito cells and field-caught mosquitoes.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), as the pathogen of coronavirus disease 2019 (COVID-19), has infected millions of people and took hundreds of thousands of lives. Unfortunately, there is deficiency of effective medicines to prevent or treat COVID-19. 3C like protease (3CL

MicroRNAs (miRNAs) play an important role in the virus-host interaction. Our previous work has indicated that the expression level of miR-10a increased in porcine alveolar macrophages (PAMs) during porcine reproductive and respiratory syndrome virus (PRRSV) infection and further inhibited viral replication through downregulates the expression of host molecule signal-recognition particle 14 (SRP14) protein. However, the molecular mechanism of miR-10a increased after PRRSV infection remains unknown. In the present study, transcription factor interferon regulatory factor 8 (IRF8) was identified as a negative regulator of miR-10a. PRRSV infection decreases the expression level of IRF8 in PAMs, leading to upregulating miR-10a expression to play an anti-PRRSV role. Meanwhile, this work first proved that IRF8 promoted PRRSV replication in an miR-10a-dependent manner. Further, we explained that SRP14, the target gene of miR-10a, promotes the synthesis of the PRRSV genome by interacting with the viral components Nsp2, thus facilitating PRRSV replication. In conclusion, we identified a novel IRF8-miR-10a-SRP14 regulatory pathway against PRRSV infection, which provides new insights into virus-host interactions and suggests potential new antiviral strategies to control PRRSV. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) has rapidly spread to the global pig industry and caused incalculable economic damage since first discovered in the 1980s. However, conventional vaccines do not provide satisfactory protection. Understanding the molecular mechanisms of host resistance to PRRSV infection is necessary to develop safe and effective strategies to control PRRSV. During viral infection, miRNAs play vital roles in regulating the expression of viral or host genes at the posttranscriptional level. The significance of our study is that we revealed the transcriptional regulation mechanism of the antiviral molecule miR-10a after PRRSV infection. Moreover, our research also explained the mechanism of host molecule SRP14, the target gene of miR-10a regulating PRRSV replication. Thus, we report a novel regulatory pathway of IRF8-miR-10a-SRP14 against PRRSV infection, which provides new insights into virus-host interactions and suggests potential new control measures for future PRRSV outbreaks.

Type I interferons (IFN-I) play a key role in the host defense against virus infection, but porcine reproductive and respiratory syndrome virus (PRRSV) infection does not effectively activate IFN-I response, and the underlying molecular mechanisms are poorly characterized. In this study, a novel transcription factor of the heme oxygenase-1 (HO-1) gene, homeobox A3 (HOXA3), was screened and identified. Here, we found that HOXA3 was significantly increased during PRRSV infection. We demonstrated that HOXA3 promotes PRRSV replication by negatively regulating the HO-1 gene transcription, which is achieved by regulating type I interferons (IFN-I) production. A detailed analysis showed that PRRSV exploits HOXA3 to suppress beta interferon (IFN-β) and IFN-stimulated gene (ISG) expression in host cells. We also provide direct evidence that the activation of IFN-I by HO-1 depends on its interaction with IRF3. Then we further proved that deficiency of HOXA3 promoted the HO-1-IRF3 interaction, and subsequently enhanced IRF3 phosphorylation and nuclear translocation in PRRSV-infected cells. These data suggest that PRRSV uses HOXA3 to negatively regulate the transcription of the HO-1 gene to suppress the IFN-I response for immune evasion. IMPORTANCE Porcine reproductive and respiratory syndrome (PRRS), caused by PRRSV, leads the pork industry worldwide to significant economic losses. HOXA3 is generally considered to be an important molecule in the process of body development and cell differentiation. Here, we found a novel transcription factor of the HO-1 gene, HOXA3, can negatively regulate the transcription of the HO-1 gene and play an important role in the suppression of IFN-I response by PRRSV. PRRSV induces the upregulation of HOXA3, which can negatively regulate HO-1 gene transcription, thereby weakening the interaction between HO-1 and IRF3 for inhibiting the type I IFN response. This study extends the function of HOXA3 to the virus field for the first time and provides new insights into PRRSV immune evasion mechanism.

Background The recent COVID-19 pandemic highlights the need for efficacious virucidal products to limit the spread of SARS-CoV-2. Several studies have suggested that alcohol-based sanitizers and some disinfectants are effective. While virucidal activity data of low-level disinfectants are lacking and some conclusions are not clear yet. Methods We evaluated the virucidal activity of two quaternary ammonium compounds (QAC) disinfectants (MICRO-CHEM PLUS and FWD), W30 (an amphoteric surfactant) and Medical EtOH® against SARS-CoV-2. Suspension tests covering different concentration and contact time were performed using the integrated cell culture-qPCR method. Results Each of disinfectants was effective at inactivating SARS-CoV-2. MCP and FWD are highly effective within 15 seconds. W30 is also efficient within 2 minutes at concentration of 1%. Consistent with previous report, our results also demonstrated that 38% ethanol was sufficient to completely inactivate virus, which proved the method used in this study is feasible. Conclusion and Discussion QAC disinfectants, MCP and FWD, are highly effective for the inactivation of SARS-CoV-2, which making them practical for use in healthcare setting and laboratories where prompt disinfection is important. The low-level disinfectant based on amphoteric surfactant, W30, which may present in commonly available household hygiene agents is also able to inactivate SARS-CoV-2.

The aim of this study was to develop a blocking enzyme-linked immunosorbent assay (bELISA) based on a biotinylated nanobody target the S1 protein of porcine epidemic diarrhea virus (PEDV) for detecting the anti-PEDV antibodies and evaluating the immune effect of the vaccine. The gene encoding the single-domain antibody sdAb3 target the PEDV S1 protein was amplified and the Avitag sequence was fused at its 3'-end. The PCR product was cloned into the expression vector pET-21b for expression and purification of the sdAb3-Avitag protein. The purified sdAb3-Avitag fusion protein was biotinylated and its activity was determined. Using the recombinant S1 protein as a coating antigen, a bELISA was established and optimized. Serum samples were tested in parallel by the bELISA and a commercial kit. The recombinant vector pET21b-sdAb3-Avitag was constructed to express the tagged sdAb3. After induction for expression, the biotin-labeled sdAb3 (sdAb3-Biotin) with high purity and good activity was obtained. For the optimized bELISA, the coating concentration of the S1 protein was 200 ng/well, the serum dilution was 1:2 and incubated for 2 h, the dilution ratio of the biotinylated sdAb3 was 1:8 000 and incubated for 30 min, the dilution of the enzyme-labeled antibody was 1:5 000 and incubated for 30 min. The bELISA had no cross reaction with the sera of major porcine viruses including transmissible gastroenteritis virus, porcine reproductive and respiratory syndrome virus and showed good specificity and reproducibility. For a total of 54 porcine serum samples tested, the overall compliance rate of the bELISA with a commercial kit was 92.56%. This study developed a rapid and reliable bELISA method, which can be used for serosurveillance and vaccine evaluation for PEDV.

In some cases, antibodies can enhance virus entry and replication in cells. This phenomenon is called antibody-dependent infection enhancement (ADE). ADE not only promotes the virus to be recognized by the target cell and enters the target cell, but also affects the signal transmission in the target cell. Early formalin-inactivated virus vaccines such as aluminum adjuvants (RSV and measles) have been shown to induce ADE. Although there is no direct evidence that there is ADE in COVID-19, this potential risk is a huge challenge for prevention and vaccine development. This article focuses on the virus-induced ADE phenomenon and its molecular mechanism. It also summarizes various attempts in vaccine research and development to eliminate the ADE phenomenon, and proposes to avoid ADE in vaccine development from the perspective of antigens and adjuvants.

Non-marine waters (i.e., rivers, reservoirs, lakes, ponds, streams and estuaries) are globally significant emitters of methane (CH4) and nitrous oxide (N2O) to the atmosphere, while global estimates of these emissions have been hampered due to the lack of a worldwide comprehensive database with the collection of complete CH4 and N2O flux components. Here we synthesize 2997 in-situ flux or concentration measurements of CH4 and N2O from 277 peer-reviewed publications to examine the role of non-marine waters in shaping climate change. Here we estimate that inland waters including rivers, reservoirs, lakes and streams together release 94.49 Tg CH4 yr− 1 (ebullition plus diffusion) and 1.52 Tg N2O yr− 1 (diffusion) to the atmosphere, yielding an overall CO2-equivalent emission total of 3.05 Pg CO2 yr− 1, representing roughly 59% of CO2 emissions (5.13 Pg CO2 yr− 1) from these four aquatic ecosystems, with lakes acting as the largest emitter for both trace gases. Ebullition is noticed as a dominant flux component, contributing up to 62–84% of total CH4 fluxes across all inland waters. Chamber-derived CH4 flux rates are significantly greater than those determined by diffusion model-based methods for commonly capturing of both diffusive and ebullitive fluxes. The synthesis of global N2O measurements projected that rivers exhibit the highest indirect N2O emission factor (EF5, 0.028%), while streams have the lowest EF5 value (0.015%). Our study reveals a major oversight in regional and global CH4 budgets from inland waters, caused by neglect of the dominant role of ebullition pathways in those emissions. The indirect EF5 values established in this study generally suggest an order of magnitude downward revision is required in current IPCC default EF5 values for inland waters and estuaries. Our findings further indicate that a comprehensive understanding of the magnitude and patterns of CH4 and N2O emissions from non-marine waters is essential in defining the way that these natural ecosystems shape our climate.

MicroRNAs (miRNAs) play critical roles in the complex networks of virus–host interactions. Our previous research showed that porcine reproductive and respiratory syndrome virus (PRRSV) infection markedly upregulates miR-c89 expression, suggesting that miR-c89 may play an important role in PRRSV infection. The present study sought to determine the function of miR-c89 and its molecular mechanism during PRRSV infection. Using quantitative reverse transcription PCR (RT-qPCR) verification, we demonstrated that both highly pathogenic PRRSV and low-pathogenic PRRSV infection induced miR-c89 expression. The overexpression of miR-c89 significantly suppressed the replication of a variety of PRRSV strains, regardless of the timing of infection. Further, miR-c89 can directly target the 3′UTR of porcine retinoid X receptor β (RXRB) mRNA in a sequence-specific manner. Knockdown affected RXRB expression, as siRNA can suppress the replication of a variety of PRRSV strains. This work not only provides new insights into PRRSV–cell interactions, but also highlights the potential for the use of miR-c89 in the development of new antiviral strategies to combat PRRSV infection.

BackgroundPorcine epidemic diarrhea virus (PEDV), which is characterized by severe watery diarrhea, vomiting, dehydration and a high mortality rate in piglets, leads to enormous economic losses to the pork industry and remains a large challenge worldwide. Thus, a rapid and reliable method is required for epidemiological investigations and to evaluate the effect of immunization. However, the current diagnostic methods for PEDV are time-consuming and very expensive and rarely meet the requirements for clinical application. Nanobodies have been used in the clinic to overcome these problems because of the advantages of their easy expression and high level of stability. In the present work, a novel biotinylated nanobody-based blocking ELISA (bELISA) was developed to detect anti-PEDV antibodies in clinical pig serum.ResultsUsing phage display technology and periplasmic extraction ELISA (PE-ELISA), anti-PEDV N protein nanobodies from three strains of PEDV were successfully isolated after three consecutive rounds of bio-panning from a high quality phage display VHH library. Then, purified Nb2-Avi-tag fusion protein was biotinylated in vitro. A novel bELISA was subsequently developed for the first time with biotinylated Nb2. The cutoff value for bELISA was 29.27%. One hundred and fifty clinical serum samples were tested by both newly developed bELISA and commercial kits. The sensitivity and specificity of bELISA were 100% and 93.18%, respectively, and the coincidence rate between the two methods was 94%.ConclusionsIn brief, bELISA is a rapid, low-cost, reliable and useful nanobody-based tool for the serological evaluation of current PEDV vaccines efficacy and indirect diagnosis of PEDV infection.

Microcystin-LR (MC-LR), a toxin produced by cyanobacteria, is very toxic and poses a threat to public health when entering water treatment works. In this study, UV/chlorine process, as an advanced oxidation process (AOP), has been demonstrated for effective elimination of MC-LR levels and associated toxicity. At a chlorine dose of 3.0 mg L−1 and UV fluence of 125 mJ cm−2, MC-LR (initial concentration 1.0 μM) was reduced by 92.5%, which was much higher than 20.3% removal under UV irradiation alone and 65.1% removal during dark chlorination. Enhanced degradation was attributed by hydroxyl radicals (HO ) and reactive chlorine species (RCS), mainly Cl2 - and ClO . Increasing chlorine doses or lowering pH favored MC-LR removal. Increased bicarbonate and natural organic matter concentrations inhibited MC-LR removal, but bromide ions enhanced MC-LR removal instead. MC-LR elimination rates in natural waters were roughly two times smaller than those in ultrapure water. The reactive radicals promoted hydroxylation of both diene of Adda moiety and double bond of Mdha moiety in MC-LR. UV exposure enhanced the dechlorination of chloro-MC-LR via the cleavage of C Cl bond. The toxicity was evaluated by a protein phosphatase (PP2A) inhibition assay. At a chlorine dose of 3.0 mg L−1 and UV fluence of 125 mJ cm−2, the toxicity of the treated water was reduced by 75.0%, which was also higher than 25.7% and 46.7% removal under UV irradiation alone and during dark chlorination, respectively. These results highlight UV/chlorine is an efficient AOP for MC-LR degradation and detoxification.

Given that ebolavirus causes severe and frequently lethal disease, its rapid and accurate detection using available and validated methods is essential for controlling infection. Real-time reverse-transcription PCR (RT-PCR) has proven to be an invaluable tool for ebolaviruses diagnostics. Many assays with different targets have been developed, but they have not been externally compared or validated, and limits of detection are not uniformly reported. Here we compared and evaluated the sensitivity, reproducibility and specificity of 23 in-house assays under the same conditions. Our results showed that these assays were highly gene- and species- specific when evaluated using in vitro RNA transcripts and viral RNA, and the potential limits of detection were uniformly reported ranging from 102 to 106 in vitro synthesized RNA transcripts copies perμL and 1–100 TCID50/mL. The comparison of these assays indicated that those targeting the more conservative NP gene could be the better option for EVD case definition and quantitative measurement because of its higher sensitivity for the same species. Our analysis could contribute to the standardization of ebolavirus detection and quantification assays, which can offer a better understanding of the meaning of results across laboratories and time points, as well as make them easy to implement, especially under outbreak conditions.

Ebola virus is among the most dangerous viral pathogens, with a case fatality rate of up to 90%. Since 2013, the two largest and most complex Ebola outbreaks in West Africa have revealed the lack of investigation on this notorious virus., Ebola virus (EBOV) is a highly pathogenic negative-stranded RNA virus that has caused several deadly endemics in the past decades. EBOV reverse genetics systems are available for studying live viruses under biosafety level 4 (BSL-4) or subviral particles under BSL-2 conditions. However, these systems all require cotransfection of multiple plasmids expressing viral genome and viral proteins essential for EBOV replication, which is technically challenging and unable to naturally mimic virus propagation using the subviral particle. Here, we established a new EBOV reverse genetics system only requiring transfection of a single viral RNA genome into an engineered cell line that stably expresses viral nucleoprotein (NP), viral protein 35 (VP35), VP30, and large (L) proteins and has been fine-tuned for its superior permissiveness for EBOV replication. Using this system, subviral particles expressing viral VP40, glycoprotein (GP), and VP24 could be produced and continuously propagated and eventually infect the entire cell population. We demonstrated the authentic response of the subviral system to antivirals and uncovered that the VP35 amount is critical for optimal virus replication. Furthermore, we showed that fully infectious virions can be efficiently rescued by delivering the full-length EBOV genome into the same supporting cell, and the efficiency is not affected by genome polarity or virus variant specificity. In summary, our work provides a new tool for studying EBOV under different biosafety levels. IMPORTANCE Ebola virus is among the most dangerous viral pathogens, with a case fatality rate of up to 90%. Since 2013, the two largest and most complex Ebola outbreaks in Africa have revealed the lack of investigation on this notorious virus. A reverse genetics system is an important tool for studying viruses by producing mutant viruses or generating safer and convenient model systems. Here, we developed an EBOV life cycle modeling system in which subviral particles can spontaneously propagate in cell culture. In addition, this system can be employed to rescue infectious virions of homologous or heterologous EBOV isolates using either sense or antisense viral RNA genomes. In summary, we developed a new tool for EBOV research.

Additional file of Aberrant host immune response induced by highly virulent PRRSV identified by digital gene expression tag profiling

Additional file 1: Seven supplementary figures and one supplementary table. Additional file 1 contains seven supplementary figures and supplementary table 1 in PDF format. Figure S1. Saturation of DGE libraries. Figure S2. The positions of tags in the gene. Figure S3. Effect of library size on the number of genes identified. Figure S4. STC (Series Test of Cluster) analysis of DE genes. Figure S5. Biological process GO terms of profiles 6 and 1. Figure S6. Biological process GO terms of profiles 7 and 0. Figure S7. Differential expression of heat shock genes. Table S1. Tissue distribution of H-PRRSV in infected pigs using QPCR assays. (PDF 987 KB)

Objective: Mosquitoes are medically important arthropod vectors that harbor a variety of viruses. Geography and climate are known to be associated with variations in mosquito density, species and viromes. Our study investigated the dynamic changes in mosquito populations, species compositions and viromes in a regularly disinfected environment in Wuhan, China, during 2020. Methods: Traps were set in different mosquito habitats, including an urban residential area, two hospitals, a scenic area and a pig farm in a rural region between April and October of 2020. The collected mosquitoes were subjected to morphological identification, RT-qPCR and metagenomic sequencing. Results: A total of 2345 adult mosquitoes were collected. Culex mosquitoes were dominant in both urban regions (90.32%, 1538/1703) and the pig farm (54.98%, 353/642). In RT-qPCR screening, the prevalence of Banna virus was 15% and 3% in mosquitoes from the urban area and the pig farm, respectively, whereas no Japanese encephalitis virus was detected. Culex viromes showed dynamic changes during the collection period. Several mosquito-specific viruses, such as Culex flavivirus, Alphamesonivirus 1, Hubei mosquito virus 2 and Hubei mosquito virus 4, showed seasonal changes and unimodal increases or declines. Other mosquito-specific viruses, such as Wuhan mosquito virus 6, Hubei virga-like virus 2 and Zhejiang mosquito virus 3, were stable in all collected Culex and are potential members of the core viromes. Conclusion: This study improves understanding of the dynamic composition of mosquito species and the viromes that they carry, and provides useful information for guiding mosquito control and mosquito-borne disease prevention strategies.

In some cases, antibodies can enhance virus entry and replication in cells. This phenomenon is called antibody-dependent infection enhancement (ADE). ADE not only promotes the virus to be recognized by the target cell and enters the target cell, but also affects the signal transmission in the target cell. Early formalin-inactivated virus vaccines such as aluminum adjuvants (RSV and measles) have been shown to induce ADE. Although there is no direct evidence that there is ADE in COVID-19, this potential risk is a huge challenge for prevention and vaccine development. This article focuses on the virus-induced ADE phenomenon and its molecular mechanism. It also summarizes various attempts in vaccine research and development to eliminate the ADE phenomenon, and proposes to avoid ADE in vaccine development from the perspective of antigens and adjuvants.

Hybrid integration of two-dimensional (2D) materials with photonic integrated circuits can enable additional functionality in planar waveguides based on excellent optical and electrical properties of 2D materials. 2D layered palladium diselenide (PdSe2) has a narrow energy bandgap and high carrier mobility, and its stability under normal laboratory environment conditions makes it of interest for use as high-performance infrared photodetectors. In this work, we propose and experimentally demonstrate a high-speed waveguide-integrated photodetector which uses chemical vapor deposition grown PdSe2 transferred onto a silicon waveguide. At 1550 nm wavelength, the photodetector can be operated without external bias with a responsivity of 0.57 mA/W and a responsivity of 20 mA/W at 6 V bias voltage. The detector had an impulse response full-width-half-maximum pulse width of about 11 ps, corresponding to a 3-dB bandwidth of 40 GHz.

The diversity of porcine reproductive and respiratory syndrome virus (PRRSV) in China is increasing rapidly along with mutation and recombination. Recombination could occur between inter- and intra-lineage of PRRSV, which accelerated the complexity of pathogenicity and cell tropism of the recombinant strain. In the present study, a novel PRRSV strain named HN-YL1711 was isolated from a pig farm suffering from severe respiratory difficulty in Henan province, China. The whole genomic sequence analysis indicated that the genome of HN-YL1711 was 15018 nt. It shared 86%, 87.3%, 88.1%, 91.1%, 84.2%, and 84.1% nucleotide similarities with PRRSVs VR2332, CH1a, JXA1, NADC30, QYYZ, and GM2, respectively. Based on phylogenetic analysis of Nsp2, ORF5 and complete genomes, HN-YL1711 was classified into lineage 1 of PRRSV. However, seven genomic break points were detected in recombination analysis, which indicated that the HN-YL1711 originated from multiple recombination among NADC30-like (major parent, lineage 1), JXA1-like (minor parent, lineage 8), and QYYZ-like (minor parent, lineage 3) PRRSV. Porcine alveolar macrophages (PAMs), 3D4/21-CD163 and MARC-145 cells were used to explore the viral adaptation of HN-YL1711. The results indicated that it could infect the PAMs but failed to infect MARC-145 cells. Challenge experiments showed that HN-YL1711 exhibits intermediate virulence in pigs, compared with HP-PRRSV JXA1 and LP-PRRSV CH1a. Taken together, our findings suggest that recombination remains an important factor in PRRSV evolution and that recombination further complicates the cell tropism and pathogenicity of PRRSV.

Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community. Congruently, SARS-CoV-2, the etiologic agent of COVID-19, has been demonstrated to infect the gastrointestinal tissues, and be shed in feces. In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, sediment, and soil samples of municipal and hospital wastewater systems and related environments in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). From the findings of this study, during the middle risk period, one influent sample and three secondary effluents collected from waste water treatment plant 2, as well as two samples from Jinyintan Hospital wastewater system influent were SARS-CoV-2 RNA positive. One sludge sample collected from Guanggu Branch of Tongji Hospital, which was obtained during the low risk period, was also positive for SARS-CoV-2 RNA. These study findings demonstrate the significance of WBE in continuous surveillance of SARS-CoV-2 at the community level, even when the COVID-19 prevalence is low. Overall, this study can be used as an important reference for contingency management of wastewater treatment plants and COVID-19 prevention and control departments of Wuhan.

The coronavirus disease 2019 (COVID-19) pandemic is caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is spread primary via respiratory droplets and infects the lungs. Currently widely used cell lines and animals are unable to accurately mimic human physiological conditions because of the abnormal status of cell lines (transformed or cancer cells) and species differences between animals and humans. Organoids are stem cell-derived self-organized three-dimensional culturein vitroand model the physiological conditions of natural organs. Here we demonstrated that SARS-CoV-2 infected and extensively replicated in human embryonic stem cells (hESCs)-derived lung organoids, including airway and alveolar organoids. Ciliated cells, alveolar type 2 (AT2) cells and rare club cells were virus target cells. Electron microscopy captured typical replication, assembly and release ultrastructures and revealed the presence of viruses within lamellar bodies in AT2 cells. Virus infection induced more severe cell death in alveolar organoids than in airway organoids. Additionally, RNA-seq revealed early cell response to SARS-CoV-2 infection and an unexpected downregulation of ACE2 mRNA. Further, compared to the transmembrane protease, serine 2 (TMPRSS2) inhibitor camostat, the nucleotide analog prodrug Remdesivir potently inhibited SARS-CoV-2 replication in lung organoids. Therefore, human lung organoids can serve as a pathophysiological model for SARS-CoV-2 infection and drug discovery.

Recombination is an important phenomenon that accelerates evolution and enriches the genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV). Recombinant PRRSV isolates sometimes have different genetic backgrounds. In this study, we report a recombinant PRRSV (SD-YL1712) isolated from a pig farm. The genome of SD-YL1712 is 15,014 nucleotides in length, and its nucleotide and amino acid sequence conservation is higher than that of PRRSV strain JXA1 except within the NSP2 region. The NSP2 region of SDYL1712 shares the highest nucleotide (85.9%) and amino acid (84.1%) sequence identity with PRRSV strain NADC30. SD-YL1712 was found to contain a characteristic 131-amino-acid deletion in the NSP2 region. Two recombination breakpoints were detected at nt 2134 and nt 3958 within the NSP2 region, which revealed that SD-YL1712 originated from a recombination event between NADC30-like and HP-PRRSV-derived MLV-like strains. Interestingly, SD-YL1712 had an additional deletion at position 586, similar to that found in strain TJnh1501. Moreover, the pathogenicity of strain SD-YL1712 was found to be similar to that of HP-PRRSV JXA1, which was higher than that of the CH1a strain. Further analysis indicated that SD-YL1712 might be a transitional intermediate in the evolution of TJbd1401 to TJnh1501.

The emerging SARS-CoV-2 infection associated with the outbreak of viral pneumonia in China is ongoing worldwide. There are no approved antiviral therapies to treat this viral disease. Here we examined the antiviral abilities of three broad-spectrum antiviral compounds gemcitabine, lycorine and oxysophoridine against SARS-CoV-2 in cell culture. We found that all three tested compounds inhibited viral replication in Vero-E6 cells at noncytotoxic concentrations. The antiviral effect of gemcitabine was suppressed efficiently by the cytidine nucleosides. Additionally, combination of gemcitabine with oxysophoridine had an additive antiviral effect against SARS-CoV-2. Our results demonstrate that broad-spectrum antiviral compounds may have a priority for the screening of antiviral compounds against newly emerging viruses to control viral infection.

Since the end of 2019, the global COVID-19 outbreak has once again made coronaviruses a hot topic. Vaccines are hoped to be an effective way to stop the spread of the virus. However, there are no clinically approved vaccines available for coronavirus infections. Reverse genetics technology can realize the operation of RNA virus genomes at the DNA level and provide new ideas and strategies for the development of new vaccines. In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. An efficient reverse genetics platform is useful for obtaining the ideal attenuated strain to prepare an attenuated live vaccine.

Since the end of 2019, the global COVID-19 outbreak has once again made coronaviruses a hot topic. Vaccines are hoped to be an effective way to stop the spread of the virus. However, there are no clinically approved vaccines available for coronavirus infections. Reverse genetics technology can realize the operation of RNA virus genomes at the DNA level and provide new ideas and strategies for the development of new vaccines. In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. An efficient reverse genetics platform is useful for obtaining the ideal attenuated strain to prepare an attenuated live vaccine.