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Zika virus (ZIKV) is one of the arboviruses implicated in febrile illness, microcephaly and other neurological disorders in babies whose mothers were infected during pregnancy. Information on ZIKV in Nigeria is limited. Hence, this study was aimed at investigating the seroprevalence of Zika virus among pregnant women in Lagos State. In a cross-sectional study, blood samples collected from 352 randomly selected pregnant women in four hospitals in Lagos State were separated and plasma analyzed using Zika virus IgG and IgM capture Enzyme-linked immunosorbent assay (Demeditec Diagnostics, Germany). The optical densities were read using Precision Microplate reader (Molecular devices) and cut-off calculated according to manufacturer’s guide. Parameters and symptoms such as history of fever, rashes on the body, exposure to mosquito were extracted from the questionnaire and analyzed. IgM seropositive samples were screened for ZIKV RNA on RT-qPCR. Out of 352 samples screened, 7(2.0%) and 5(1.4%) of the pregnant women tested positive for IgG and IgM respectively. None tested positive for both IgG and IgM markers. Statistical analysis showed that there is no significant relationship between the symptoms analyzed in this study at 95% Confidence interval except conjunctivitis. None of the ZIKV IgM seropositive samples tested positive for ZIKV RNA on RT-qPCR. The results show that there is evidence of exposure to Zika virus among the population studied in Lagos, Nigeria. Also, the low level seroprevalence of the virus in the population studied indicates that there is lack of herd immunity of Zika virus infection in Lagos, Nigeria.

SFTS virus (SFTSV) is a novel bunyavirus, which was discovered as the etiological agent of severe fever with thrombocytopenia syndrome (SFTS) in China in 2009, and was now prevalent in at least 25 provinces in China. SFTS was subsequently identified in South Korea and Japan in 2012. To explore the molecular evolution and genetic characteristics of this newly identified pathogen, we reported 72 whole genome sequences of SFTSV, and built a dataset of SFTSV genome sequences containing 292 L-segment, 302 M-segment and 502 S-segment. We clearly divided SFTSV into six genotypes, Genotype A-F. It was found that genotype F was the dominant epidemic genotype of Japan, South Korea, and Zhejiang province of China. The coalescent analysis supported that SFTSV originated in the early 18th century from Zhejiang province, and Genotype F was the most primitive one. Henan, Hubei, and Anhui provinces which are located in Dabie Mountain area were mainly epidemic of Genotype A, which emerged relatively late but distributed widely. A total of 37 recombination events were identified, making SFTSV with a high recombination frequency (L segment 5.1%, M segment 3.6%, S segment 0.8%) among negative-strand segmented RNA viruses. It was identified that 19 reassortant strains belonged to 12 reassortment forms of SFTSV genome containing 6 newly identified forms. The reassortment virus and recombination in tick were both found for the first time. We also found many of genotype-specific mutation sites, 7 of which could be considered as potential molecular marker for genotype classification. This study promoted a more comprehensive understanding of the phylogeny and origin, and the genetic diversity of SFTSV, and it could help the studies of other newly discovered tick-borne bunyavirus as reference data and research ideas.

Over one million people are living with cystic echinococcosis (CE) and alveolar echinococcosis (AE). For CE, long-term albendazole treatment is often needed, which requires regular follow-up. Follow-up is mainly through imaging which is insensitive to subtle changes and subjective to experience. We investigated the changes of Echinococcus granulosus (Eg) cell-free DNA (cfDNA) in plasma of CE patients before and after albendazole treatment to evaluate its potential as an objective marker for treatment follow-up. Plasma samples of nine CE patients were collected before and after treatment. We identified Eg cfDNA from every sample through high-throughput sequencing. Eg cfDNA concentration and fragment length increased significantly after the treatment period. Ultrasound examination before and after the treatment initiation reflected the drug effects to a certain extent, as the cyst size of four patients reduced. Our findings indicated that Eg cfDNA from plasma could be a potential marker in the monitoring of CE treatment.

Gallbladder cancer is the most common malignant tumor of the biliary system and is characterized by difficulty to diagnose in early stages, a high degree of malignancy, and poor prognosis. Finding new drugs may improve the prognosis for this dismal cancer. Herein, we investigated the potential application of pterostilbene (PTS) against gallbladder cancer in vivo and in vitro. PTS potently inhibited cell proliferation, migration and invasion of gallbladder cancer cells. Moreover, PTS also had a function of inducing apoptosis in vitro. Meanwhile, PTS reversed EMT with a correlated inhibition of PI3K/Akt activation. Tumor xenograft models showed that PTS inhibited tumor growth and had low toxicity in vivo, which were consistent with the in vitro data. These findings indicate that PTS arrests cell growth through inhibition of PI3K/AKT signaling and is a potential drug for the therapy of gallbladder cancer.

What is already known about this topic? Dengue fever (DF) outbreaks affect hundreds of millions of people worldwide and have increased significantly in Guangdong Province in 2019. What is added by this report? This paper described briefly DF outbreaks were attributed to several types of dengue virus (DENV) including DENV-1, DENV-2, and DENV-3 in 2019 in Guangdong, tracked the sources of viruses through phylogenetic analysis and epidemiological investigation, and primarily revealed the epidemiological links among the outbreaks. What are the implications for public health practice? The introduction of DENV from DF endemic areas increased pressure on the prevention and control of DF in Guangdong. Early detection of suspected cases and typing and genotyping of circulating viruses should be prioritized and enhanced to promptly assess the likelihood of local transmission, of introduction, and of subsequent sustained local transmission of the virus to implement optimal prevention and control strategies and measures.

What is known about this topic? Dengue fever is an acute febrile illness caused by four types of dengue virus (DENV 1–4), and is a mosquito-borne infectious disease. The incidence of dengue has increased dramatically around the world in recent decades. An estimated of 3.9 billion people in 128 countries are at risk of infection with dengue viruses, 70% of whom are in Asia. In 2017, the first local infections of dengue virus (DENV-2) in Jiangxi Province was reported in Zhanggong District, Ganzhou City. What is added by this report? From August to September 2019, the first dengue outbreak happened in Xin’gan County, where 81 local dengue fever cases were reported, 35 were laboratory-confirmed cases, and 46 were clinically-diagnosed cases; all cases were dengue virus type 1. The DENV-virus strains isolated from the cases of Xin’gan County were close to the strains isolated in Singapore (MF033254|25657|Singapore|2016) and Henan (MK905537|Henan201903|China: Henan Province|2019). What are the implications for public health practice? The outbreak might have been caused by imported cases or covert infections. The outbreak in Xin’gan County indicated that more proactive countermeasures should be taken during the dengue epidemic period such as intensifying surveillance for dengue cases, virus serotype, and Aedes vector density and strengthening cooperation with customs and tourism departments. Moreover, the outbreak should prompt training in medical institutions and improved ability for doctor’s to diagnose dengue fever, which is very important for early detection of dengue cases and taking preventive measures.

Here, we report the identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana. In March 2019, 14 employees of Chongqing Bosai Mining Company, China, working in a manganese mining of Guyana, had unexplained fever, and two of them died. We obtained lung and brain tissues as well as the blood samples from the two deceased cases (patient No. 1 and 2), and bronchoscopy lavages and cerebrospinal fluid samples from one severe case (patient No. 3), respectively. All samples were tested by pathological examination, high-throughput sequencing, and real-time PCR. Pathological detection showed the presence of spore-like structures in the lung tissue of patient No. 1, indicating a fungal infection in this patient. Nanopore sequencing identified the existing of H. capsulatum in the lung tissue sample within 13 h. Next-generation sequencing identified specific fragments of H. capsulatum in all of the samples tested (lung, brain and blood serum from the deceased cases, and plasma from the severe case). Real-time PCR assays did not reveal any viral infection related to transmission from bat feces. We conclude that H. capsulatum was the causative pathogen of this disease cluster based on epidemiologic, clinical, pathological and nucleic acid evidence., Highlights • Scientific question This study reported the identification of Histoplasma as the cause of an unexplained disease cluster in Matthews Ridge, Guyana. • Evidence before this study In March 2019, 14 Chinese employees from Chongqing Bosai Mining Company, China, were engaged in manganese mining in Guyana and presented with unexplained fever. Two of them died. After preliminary examination by the local hospital, some potential infectious pathogens were excluded, including Leptospira, HIV, influenza H1N1, Zika virus, Chikungunya virus, Dengue virus, and Influenza A and B viruses. Histoplasmosis is a fungal disease caused by members of the genus Histoplasma and is mainly prevalent in the American continents. Histoplasma is capable of survival in moist soils and can often be isolated from soils containing decaying feces of bats and birds. Human activities in the surface soil produce aerosols, which in turn are inhaled to cause infection. • New findings In response to the unexplained disease cluster, pathological examination, high through-put sequencing and real-time PCR were implemented. A TGS platform found Histoplasma within 13 hours. NGS was also successfully applied in response to this event. Compared with NGS, the main features of nanopore sequencing are long sequencing ability, simplicity of use, the fastest turn-around time, high portability and real-time analysis of sequencing data. Though NGS had a longer turnaround time (24 hours), it worked well with different sample types (lung tissue, brain tissue and serum from deceased cases and plasma from a severe case) and was more sensitive than nanopore sequencing. Real-time PCR assays did not reveal any infection by viruses related to bat feces transmission. Pathological detection results showed the presence of spore-like structures, indicating fungus infection in this patient. All the results were consistent with the NGS analysis, supporting the fungus infection. • Significance of the study We concluded that H. capsulatum is the causative pathogen for this disease cluster based on epidemiologic, clinical, pathological and nucleic acid supportive evidence.

This paper aims at shedding light on the impact of unsaturated traffic on the performance of uplink non-orthogonal multiple access (NOMA) transmissions. Nevertheless, the unsaturated traffic gives rise to the discontinuous interference and the inherent interaction of queues, which in turn highly complicates the performance evaluation. By utilizing tools from queuing theory, we first explicitly characterize the stable throughput region, which represents the region of traffic arrival rates on the condition that the queuing delay converges in distribution to a bounded random variable. In light of this, the critical condition under which NOMA can extend the stable throughput region of orthogonal multiple access (OMA) is derived. Then, we propose an algorithmic solution to evaluate the average delay incurred from both queuing and transmission. It is interestingly found that the superiority of NOMA over OMA in terms of average delay heavily hinges on the temporal traffic dynamics of each user. In particular, NOMA enjoys a clear advantage when the traffic arrival rate of the user with stronger channel condition considerably exceeds the traffic arrival rate of the user with weaker channel condition. The derived results can provide helpful guidance to fully leverage the comparative advantages of NOMA under various traffic conditions.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, the microbial composition of the respiratory tract and other infected tissues as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Between 27 January and 26 February 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients in Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. We identified distinct signatures of microbial dysbiosis among severely ill COVID-19 patients on broad spectrum antimicrobial therapy. Co-detection of other human respiratory viruses (including human alphaherpesvirus 1, rhinovirus B, and human orthopneumovirus) was demonstrated in 30.8% (4/13) of the severely ill patients, but not in any of the mildly affected patients. Notably, the predominant respiratory microbial taxa of severely ill patients were Burkholderia cepacia complex (BCC), Staphylococcus epidermidis, or Mycoplasma spp. (including M. hominis and M. orale). The presence of the former two bacterial taxa was also confirmed by clinical cultures of respiratory specimens (expectorated sputum or nasal secretions) in 23.1% (3/13) of the severe cases. Finally, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes was demonstrated in one severely ill patient, which might accelerate his disease deterioration and death occurring one month after ICU admission. Our findings point to SARS-CoV-2-related microbial dysbiosis and various antibiotic-resistant respiratory microbes/pathogens in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking strategies are needed to prevent the spread of antimicrobial resistance, improve the treatment regimen and clinical outcomes of hospitalized, severely ill COVID-19 patients.

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a highly pathogenic tick-borne bunyavirus that causes lethal infectious disease and severe fever with thrombocytopenia syndrome (SFTS) in humans. The molecular mechanisms and host cellular factors required for SFTSV infection remain uncharacterized. Using a genome-wide CRISPR-based screening strategy, we identified a host cellular protein, sorting nexin 11 (SNX11) which is involved in the intracellular endosomal trafficking pathway, as an essential cell factor for SFTSV infection. An SNX11-KO HeLa cell line was established, and SFTSV replication was significantly reduced. The glycoproteins of SFTSV were detected and remained in later endosomal compartments but were not detectable in the endoplasmic reticulum (ER) or Golgi apparatus. pH values in the endosomal compartments of the SNX11-KO cells increased compared with the pH of normal HeLa cells, and lysosomal-associated membrane protein 1 (LAMP1) expression was significantly elevated in the SNX11-KO cells. Overall, these results indicated that penetration of SFTSV from the endolysosomes into the cytoplasm of host cells was blocked in the cells lacking SNX11. Our study for the first time provides insight into the important role of the SNX11 as an essential host factor in the intracellular trafficking and penetrating process of SFTSV infection via potential regulation of viral protein sorting, membrane fusion, and other endocytic machinery. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-019-00141-0) contains supplementary material, which is available to authorized users.

What is already known on this topic? Cases of histoplasmosis have been reported in every continent except Antarctica but are fairly rare in China. High prevalence of histoplasmosis has been observed in Central America, Caribbean, and South America. Infections of Histoplasma are acquired through a respiratory route, particularly inhalation of aerosols from disturbed soils enriched with excreta from birds and bats. These infections are most common in persons involved with removing soil, visiting caves, cleaning old houses, or felling trees, etc. What is added by this report? This is the first report of cluster infections of Histoplasma among overseas Chinese workers. A strong dose-dependent association of illness onset and disease severity with the exposure intensity to the soils and wastes possibly contaminated by the Histoplasma has been proposed. Long labor times, repeated entering of contaminated tunnels, working in high-dust environments are likely to result in earlier illness onsets, more severe clinical courses, and even fatal outcomes. More importantly, none of the patients used reliable personal protection equipment (PPE), such as common masks while working, that would prevent the inhalation of more Histoplasma spores. What are the implications for public health practice? The epidemiological findings of this outbreak investigation highlight a probable risk of infection with Histoplasma when entering without PPE into the environment with bats living around, such as caves or mines. Effective education and communication might be needed among residents and travelers. This outbreak expands our knowledge of the control and prevention of fungal disease in China.

BACKGROUNDCoronavirus disease 2019 (COVID-19) triggers distinct patterns of pneumonia progression with multiorgan disease, calling for cell- and/or tissue-type specific host injury markers.METHODSAn integrated hypothesis-free single biomarker analysis framework was performed on nasal swabs (n = 484) from patients with COVID-19 in GSE152075. The origin of candidate biomarker was assessed in single-cell RNA data (GSE145926). The candidate biomarker was validated in a cross-sectional cohort (n = 564) at both nucleotide and protein levels.RESULTSPhospholipase A2 group VII (PLA2G7) was identified as a candidate biomarker in COVID-19. PLA2G7 was predominantly expressed by proinflammatory macrophages in lungs emerging with progression of COVID-19. In the validation stage, PLA2G7 was found in patients with COVID-19 and pneumonia, especially in severe pneumonia, rather than patients suffered mild H1N1 influenza infection. Up to 100% positive rates of PLA2G7 were positively correlated with not only viral loads in patients with COVID-19 but also severity of pneumonia in non-COVID-19 patients. Although Ct values of PLA2G7 in severe pneumonia was significantly lower than that in moderate pneumonia (P = 7.2e-11), no differences were observed in moderate pneumonia with COVID-19 between severe pneumonia without COVID-19 (P = 0.81). Serum protein levels of PLA2G7, also known as lipoprotein-associated phospholipase A2 (Lp-PLA2), were further found to be elevated and beyond the upper limit of normal in patients with COVID-19, especially among the re-positive patients.CONCLUSIONSWe firstly identified and validated PLA2G7, a biomarker for cardiovascular diseases (CVDs), was abnormally enhanced in COVID-19 patients at both nucleotide and protein aspects. These findings provided indications into the prevalence of cardiovascular involvements seen in COVID-19 patients. PLA2G7 could be a hallmark of COVID-19 for monitoring disease progress and therapeutic response.FUNDINGThis study was supported by grants from China Mega-Projects for Infectious Disease (2018ZX10711001), National Natural Science Foundation of China (82041023).

We gratefully acknowledge China National GeneBank at Shenzhen, China for the sequencing strategy and capacity support. We also gratefully acknowledge the laboratories that have contributed publicly available genomes via GISAID: The Public Health Agency of Sweden, Sweden; Public Health Ontario Laboratories, Canada; Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, United States; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, United State; Alaska State Virology Laboratory, United States; Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, United Kingdom; Laboratory for Functional Genome Analysis, Dept. Genomics, Gene Center of the LMU Munich, Germany; Michigan Department of Health and Human Services, Bureau of Laboratories, United State; National Public Health Laboratory, National Centre for Infectious Diseases, Singapore; BGI-shenzhen & The First Affiliated Hospital of Guangzhou Medical University, China; NSW Health Pathology - Institute of Clinical Pathology and Medical Research; Westmead Hospital; University of Sydney, Australia; BCCDC Public Health Laboratory, Canada; COVID-19 Genomics UK (COG-UK) Consortium, United Kingdom; Guangdong Provincial Institution of Public Health, China; Department of Microbiology, Guangdong Provincial Center for Diseases Control and Prevention, China; Department of Health Technology and Informatics, Faculty of Health and Social Science, The Hong Kong Polytechnic University, Hong Kong; School of Public Health, The University of Hong Kong, Hong Kong; Pathogen Genomics Center, National Institute of Infectious Diseases, Japan; National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine & Shanghai Public Health Clinical Center, China; Seattle Flu Study, United States; UW Virology Lab, United States; National Institute for Viral Disease Control & Prevention, CCDC, China; Beijing Institute of Microbiology and Epidemiology, China; National Institute for Viral Disease Control and Prevention, China CDC, China; Inspection Center of Hangzhou Center for Disease Control and Prevention, China; Pathogen Genomics Lab King Abdullah University of Science and Technology (KAUST), Saudi Arabia; Chinese PLA Institute for Disease Control and Prevention, China; National Institute of Health. Department of medical Sciences, Ministry of Public Health, Thailand; Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Greece; Wellcome Sanger Institute for the COVID-19 Genomics UK Consortium, United Kingdom; State Key Laboratory of Biotherapy of Sichuan University, China; SeqCOVID-SPAIN consortium/IBV(CSIC), Spain; Oxford University Clinical Research Unit, Hanoi, Vietnam; Institute of Environmental Science and Research (ESR), New Zealand; Erasmus Medical Center, Netherlands.

Severe cholestatic liver injury diseases, such as obstructive jaundice and the subsequent acute obstructive cholangitis, are induced by biliary tract occlusion. Heat shock protein 90 (HSP90) inhibitors have been demonstrated to be protective for various organs. The potential of HSP90 inhibitors in the treatment of cholestatic liver injury, however, remains unclear. In the present study, rat models of bile duct ligation (BDL) were established, the HSP90 inhibitor 17-dimethylamino-ethylamino-17-demethoxygeldanamycin (17-DMAG) was administered, and its ability to ameliorate the cholestasis-induced liver injuries was evaluated. In the BDL rat models and clinical samples, increased HSP90 expression was observed to be associated with cholestatic liver injury. Furthermore, 17-DMAG alleviated cholestasis-induced liver injury in the rat models, as revealed by the assessment of pathological changes and liver function. In addition, 17-DMAG protected hepatocytes against cholestatic injury in vitro. Further assays indicated that 17-DMAG administration prevented cholestasis-induced liver injury in the rats by decreasing the expression of interleukin (IL)-1β and IL-18. Moreover, 17-DMAG also decreased the cholestasis-induced upregulation of IL-1β and IL-18 in liver sinusoidal endothelial cells in vitro. In conclusion, the HSP90 inhibitor 17-DMAG is able to prevent liver injury in rats with biliary obstruction, and this phenomenon is associated with the reduction of IL-1β and IL-18 expression.

A large amount of protein impurity severely restricts the application of polysaccharides of Ruditapes philippinarum (PRP) in food and medicine. Moreover, the traditional Sevag deproteinization method always involves organic reagents. The purpose of this paper was to develop an effective, green and mild deproteinization method from PRP by attapulgite-based silk fibroin composite aerogel (ASA). Firstly, ASA was synthesized and applied to remove protein from PRP. Secondly, the deproteinization parameters were optimized with selectivity coefficient as index as follows: dose of ASA 1% and pH 7.0. Under these conditions, deproteinization ratio (Dr%), polysaccharide recovery ratio (Rr%) and selectivity coefficient (Kc) reached 79.44 ± 1.87%, 95.81 ± 2.95% and 18.95 ± 1.55, respectively. Next, the feasibility of ASA method was evaluated. As a result, ASA method not only achieved higher deproteinization efficiency in less time compared with Sevag method, but also retained structure and antioxidant activity of polysaccharides. ASA was also proven with recycling ability and could be reused more than five times. Furthermore, it was found that protein adsorption on ASA was better fitted by pseudo second-order kinetic and Freundlich model. Taking together, the data implied that ASA method would be promising of deproteinization from PRP suitable for polysaccharides processing.

We studied the effects of wolfberry and astragalus extract on the growth performance, carcass traits, and meat quality of Tibetan fragrant pigs, and we want to explain the mechanism of the difference from the level of RNA Seq. Twelve healthy 120-day-old Tibetan fragrant pigs weighing 35 ± 2 kg were divided randomly into two groups, each with six pigs. The control group was fed a basal diet, and the wolfberry and astragalus extract (WAE) group was fed a basal diet +1‰ of WAE. The experimental period was 90 days. Compared with the control group, the growth performance of the WAE group was significantly improved (p < .05), pork marble score significantly improved (p < .05), vitamin E content significantly increased (p < .05), unsaturated fatty acid content significantly increased (p < .05). A total of 256 differentially expressed genes were obtained by transcriptome sequencing, among which 114 were up-regulated and 142 were down-regulated. GO analysis showed that the differentially expressed genes were related to biological functions, such as monounsaturated fatty acid biosynthesis, fatty acid metabolism, lipoprotein decomposition, and lipase activity. Pathway analysis showed that these differentially expressed genes were mainly involved in unsaturated fatty acid biosynthesis regulation, glycerin metabolism, and lipopolysaccharide regulation in fat. WAE improved Tibetan fragrant pigs growth performance. By intervening in key genes related to fatty acid metabolism, the unsaturated fatty acid contents in pork were regulated, which improved the nutritional value of the pork.

The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.Author summaryIn this study, we compared SARS-CoV-2 populations of 13 Chinese COVID-19 patients. Those viral populations contained a considerable proportion of viral sub-genomic messenger RNAs (sgmRNA), reflecting an active viral replication activity in the respiratory tract tissues. The comparison of 66 identified intra-host variants further showed a low viral genetic distance between intra-household patients and a narrow transmission bottleneck size. Despite the co-existence of genetically distinct viruses within the same host, most intra-host minor variants were not shared between transmission pairs, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Furthermore, the narrow bottleneck and active viral activity in the respiratory tract show that the passage of a small number of virions can cause infection. Our data have therefore delivered a key genomic resource for the SARS-CoV-2 transmission research and enhanced our understanding of the evolutionary dynamics of SARS-CoV-2.

The H7 subtype avian influenza viruses (AIV) have a much longer history and their adaptation through evolution pose continuous threat to humans 1. Since 2013 March, the novel reasserted H7N9 subtype have transmitted to humans through their repeated assertion in the poultry market. Through repeated transmission, H7N9 gradually became the second AIV subtype posing greater public health risk after H5N1 2,3. After infection, how the virus tunes its genome to adapt and evolve in humans remains unknown. Through direct amplification of H7N9 and high throughput (HT) sequencing of full genomes from the swabs and lower respiratory tract samples collected from infected patients in Shenzhen, China, we have analyzed the in vivo H7N9 mutations at the level of whole genomes and have compared with the genomes derived by in vitro cultures. These comparisons and frequency analysis against the H7N9 genomes in the public database, 40 amino acids were identified that play potential roles in virus adaptation during H7N9 infection in humans. Various synonymous mutations were also identified that might be crucial to H7N9 adaptation in humans. The mechanism of these mutations occurred in a single infection are discussed in this study.

Jiandong Li, Xiaohu Xu, Dandan Zhang, Han Lv, Xin Lei Department of Stomatology, Shenzhen Longhua District Central Hospital, Shenzhen, 518000, People’s Republic of ChinaCorrespondence: Jiandong LiDepartment of Stomatology, Shenzhen Longhua District Central Hospital, Shenzhen, 518000, People’s Republic of ChinaEmail lijiandong00111@163.comBackground: Oral squamous cell carcinoma (OSCC) is a common oral cancer. The current study aims to elucidate the potential roles of long noncoding RNA (lncRNA) LHFPL3-AS1 in OSCC development.Methods: Gene expression was measured by qRT-PCR in tumor tissues and cell lines. Loss-of-function assays were performed to analyze the effects of LHFPL3-AS1 on malignant behaviors. Bioinformatics analysis was conducted to explore the downstream signaling pathway of LHFPL3-AS1 in OSCC.Results: LHFPL3-AS1 was highly expressed in OSCC tissues and cell lines. LHFPL3-AS1 was upregulated in cisplatin-resistant tumor cell lines. LHFPL3-AS1 level was correlated with survival rate. LHFPL3-AS1 knockdown suppressed OSCC proliferation, migration and invasion. LHFPL3-AS1 downregulation reduced cisplatin resistance of OSCC cells. LHFPL3-AS1 was the competing endogenous RNA (ceRNA) for miR-194-5p to enhance CHSY1 expression.Conclusion: LHFPL3-AS1/miR-362-5p/CHSY1 signaling pathway plays essential roles in regulating OSCC development and cisplatin resistance.Keywords: oral squamous cell carcinoma, LHFPL3-AS1, miR-362-5p, CHSY1

Hepatocellular carcinoma and intrahepatic cholangiocarcinoma cells are common primary hepatic tumor cells in the liver. Combined hepatocellular cholangiocarcinoma (CHC) contains both hepatocellular carcinoma cells and intrahepatic cholangiocarcinoma cells in one tumor lesion and these tumors show poor prognosis. Here we examined the potential interaction between hepatocellular carcinoma cells and intrahepatic cholangiocarcinoma cells using cell culture studies. The results showed that culture supernatant from intrahepatic cholangiocarcinoma cells induced endothelial-mesenchymal transition and facilitated the migration and invasion of hepatocellular carcinoma cells, although it did not accelerate the proliferation of hepatocellular carcinoma cells. Furthermore, culture supernatant from intrahepatic cholangiocarcinoma cells increased the chemoresistance of hepatocellular carcinoma cells. Laminin subunit gamma 2 (LAMC2) was detected in the culture supernatant of intrahepatic cholangiocarcinoma cells but not in that of hepatocellular carcinoma cells. Using established LAMC2 knockout intrahepatic cholangiocarcinoma cells, our results demonstrated that intrahepatic cholangiocarcinoma cells promoted the epithelial-mesenchymal transition of hepatocellular carcinoma cells through secreting LAMC2. Our results have revealed a novel mechanism of interaction between intrahepatic cholangiocarcinoma cells and hepatocellular carcinoma cells, which may provide new insight into developing effective treatments for CHC.

As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 million people with more than 300 thousand death as official reports1,2. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we achieved and characterized consensus genomes and intra-host genomic variants from 32 serial samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the coexistence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity within GIT, showing an increased population with accumulated mutations developed in the tissue-specific environments. The iSNVs identified here not only show spatial divergence of intra-host viral populations, but also provide new insights into the complex virus-host interactions.

Background To investigate the efficacy and safety of aerosol inhalation of recombinant human interferon α1b (IFNα1b) injection for noninfluenza viral pneumonia. Methods One hundred sixty-four patients with noninfluenza viral pneumonia were divided into IFNα1b and control groups. The IFNα1b group received routine treatment + aerosol inhalation of recombinant human IFNα1b injection (50 μg × 2 injections, bid). The control group received routine treatment + IFN analog (two injections, bid). Overall response rate (ORR) of five kinds clinical symptoms. Further outcomes were daily average score and the response rate of each of the symptoms above. Results A total of 163 patients were included in the full analysis set (FAS) and 151 patients were included in the per-protocol set (PPS). After 7 days of treatment, ORR of clinical symptoms was higher in IFNα1b group than that in control group for both the FAS and PPS. Moreover, after 7 days of treatment, the daily score of three efficacy indexes including expectoration, respiratory rate, and pulmonary rales were improved. The ORRs for expectoration and pulmonary rales were higher in the IFNα1b group than in the control group (P 0.05). The incidence of adverse events was 6.5% (n = 5) in IFNα1b group and 3.5% (n = 3) in control group (P > 0.05). Conclusion Aerosol inhalation of recombinant human IFNα1b is safe and it can improve the clinical symptoms of noninfluenza viral pneumonia.

ARAF is a member of the RAF kinase family that is necessary for mitogen-activated protein kinase (MAPK) activation in various malignancies, including lung, colorectal, pancreatic, and breast cancers. As the most common biliary tract tumor, gallbladder cancer (GBC) seriously harms human health while the function of ARAF in GBC remains elusive. Here, we found that ARAF expression was upregulated in gallbladder cancer tissues. In vitro, ARAF silencing mediated by RNA interference effectively inhibited cell proliferation, colony formation, migration, and invasion of GBC cells. Moreover, knocking down ARAF suppressed tumor growth in vivo. Our results indicated that ARAF functions as an oncogene in GBC and, thus, could be a potential therapeutic target for GBC.

What is already known on this topic? Hemorrhagic fever with renal syndrome (HFRS) is endemic in Liaoning Province. Both Seoul and Hantaan virus are circulating in rodents, and epidemic outbreaks and sporadic cases have been recorded every year since the disease was recognized. What is added by this report? The epidemic trend of HFRS over the past 20 years (1999–2018) in Liaoning was analyzed, which showed both regional complexity and consistence with the epidemic in China. Genetic and antigenic stability of the circulating hantavirus were demonstrated, which suggested the effectiveness of the approved inactivated vaccine currently used in China. What are the implications for public health practice? Precise risk-based strategic practices that are integrated and regional are required for further improvement of the prevention and control of HFRS.

Bearing stiffness exhibits non-linear characteristic when the bearing is subjected to a certain external load, which will inevitably cause changes in the spindle stiffness, since bearing stiffness has a decisive impact on the spindle stiffness. In this paper, the axial stiffness softening and hardening characteristics of machine tool spindle were studied. A novel spindle axial load automatic applying device and the spindle stiffness test bench were proposed. Meantime, an axial stiffness model for the experimental spindle was established based on the bearing load–displacement model and mechanical analysis of spindle. Then, the axial stiffness of fixed position preload spindle under different preload was measured experimentally and the evolution mechanism was analyzed. The results show that when bearing preload reaches a certain relatively large threshold, a “sag” shape occurs in the axial stiffness curve, indicating the “stiffness hardening” characteristic of the spindle. On the other hand, for a small preload, no “sag” shape occurs in spindle stiffness curve, indicating the “stiffness softening” characteristic of the spindle. This phenomenon is of great significance for the acquisition of the excellent spindle stiffness properties.

This study aimed to investigate the serological characteristics of Ebola virus (EBOV) infection during the late phase of the Ebola outbreak in Sierra Leone. In total, 877 blood samples from 694 suspected Ebola virus disease (EVD) cases assessed from March to December 2015, were analyzed via real-time reverse transcription polymerase chain reaction (RT-PCR) for viral RNA and enzyme-linked immunosorbent assay (ELISA) and Luminex to detect antibodies against EBOV. Viral load and EBOV-specific IgM/IgG titers displayed a declining trend during March to December 2015. Viral RNA load decreased rapidly at earlier stages after disease onset, while EBOV-specific IgM and IgG still persisted in 58.1% (18/31) and 93.5% (29/31) of the confirmed EVD patients and in 3.8% (25/663) and 17.8% (118/663) of the RNA-negative suspected patients in the later phase, respectively. Dynamic analysis of longitudinally collected samples from eight EVD patients revealed typically reversed trends of declining viral load and increasing IgM and/or IgG titers in response to the EBOV infection. The present results indicate that certain populations of Sierra Leone developed immunity to an EBOV infection in the late phase of the outbreak, providing novel insights into the risk assessment of EBOV infections among human populations.

Lipopolysaccharide (LPS) causes an inflammatory response, and α-mangostin (α-MG) is an ingredient of a Chinese herbal medicine with anti-inflammatory effects. We investigated the mechanism by which α-MG reduces LPS-stimulated IEC-6 cells inflammation. A genome-wide examination of control, LPS-stimulated, and α-MG-pretreated cells was performed with the Illumina Hiseq sequencing platform, and gene expression was verified with quantitative real-time PCR (qPCR). Among the 37,199 genes profiled, 2014 genes were regulated in the LPS group, and 475 genes were regulated in the α-MG group. GO enrichment and KEGG pathway analyses of the differentially expressed genes (DEGs) showed that they were mainly related to inflammation and oxidative stress. Based on the transcriptomic results, we constructed a rat model of inflammatory bowel disease (IBD) with LPS and investigated the effects of α-MG on NLRP3 inflammasomes. After LPS stimulation, the rat intestinal villi were significantly detached, with congestion and hemorrhage; the intestinal epithelial cell nuclei were deformed; and the mitochondria were swollen. However, after pretreatment with α-MG, the intestinal villus congestion and hemorrhage were reduced, the epithelial nuclei were rounded, and the mitochondrial morphology was intact. qPCR and western blotting were used to detect NLRP3, caspase 1, interleukin (IL)-18, and IL-1β expression at the gene and protein levels. Their expression increased at both the transcript and protein levels after LPS stimulation, whereas it decreased after pretreatment with α-MG. This study provides new methods and ideas for the treatment of inflammation. α-MG may have utility as a drug for intestinal inflammation.

The efficiency of immune responses and host defense against pathogens largely depends on the function of dendritic cells (DCs). Porcine circovirus type 2 (PCV2) infection causes viremia and extensive modulation of immune activities in the blood. The objective of the present study was to investigate the effects of PCV2 infection in vivo on the immunological function of DCs induced from peripheral blood monocytes (MoDCs). At different points after infection with PCV2, peripheral blood monocytes from PCV2-infected pigs were used to induce differentiation of DCs in vitro. Flow cytometry and quantitative real-time reverse transcription PCR were conducted to detect mRNA expression of surface markers related to antigen presentation and inflammatory/immunosuppressive cytokines of the induced MoDCs. The ability of induced MoDCs to stimulate T cells was measured using an MTS assay. In the early phase of infection at 3 days post-inoculation (DPI), IL-10, IL-8 and MIP-1β in MoDCs were upregulated significantly. By the peak of virus proliferation at 7 DPI, antigen presentation molecules SLA-DR (MHC II) and CD80/86 together with cytokines IL-12 and IL-10 had decreased, accompanied by a rapid reduction of IL-8 and MIP-1β. The T cell stimulation index of induced MoDCs in PCV2 groups after different infection times declined to some extent, with a significant difference at 7 DPI. PCV2 infection in vivo functionally reduced the antigen presentation capability of induced MoDCs from peripheral blood and modified expression of inflammatory/immunosuppressive cytokines that may be related to PCV2-induced immunosuppression.

The health impact of changes in particulate matter with an aerodynamic diameter, Graphical abstract Image 1

Background Hantaan and Seoul viruses, in the Hantavirus genus, are known to cause hemorrhagic fever with renal syndrome (HFRS). The plaque reduction neutralization test (PRNT), as conventional neutralization test for hantaviruses, is laborious and time-consuming. Alternatives to PRNT for hantaviruses are required. Methods In this study, the methods for Hantaan and Seoul viruses serological typing including microneutralization test (MNT), pseudoparticle neutralization test (PPNT) and immunofluorescence assay based on viral glycoproteins (IFA-GP) were developed and compared with PRNT using a panel of 74 sera including 44 convalescent sera of laboratory confirmed HFRS patients and 30 patients sera of non-hantavirus infection. Antibody titres and serotyping obtained with different methods above were analyzed by paired-t, linear correlation, McNemar χ2 and Kappa agreement tests. Results Antibody titres obtained with MNT50, PPNT50 and IFA-GP were significantly correlated with that obtained with PRNT50 (p 0.05) and less than (p 0.05). IFA-GP was less sensitive than PRNT50 and MNT50 for serotyping of hantaviruses infection (p

Objectives We aimed to evaluate the association of genes of peroxisome proliferator-activated receptor-γ (PPARγ), adiponectin (APM1) and apolipoprotein E (APOC1) polymorphisms with metabolic syndrome (MS) in children. Methods A matched case-control study was conducted with 114 MS cases and 114 controls. Anthropometric measurements and a questionnaire survey were conducted in all subjects. The polymerase chain reaction method and DNA sequencing were used for genotyping of single nucleotide polymorphism for PPARγ (rs1801282), APM1 (rs266729) and APOC1 (rs4420638). Results After adjustments for sex, age, educational level of parents, physical activity, dietary patterns, pubertal development and household income, there were significant associations between rs266729 (OR = 1.91, 95% CI: 1.01–3.62), rs4420638 (OR = 2.21, 95%CI: 1.19–4.10) polymorphisms and the risk of MS in children. However, no association was found between rs1801282 polymorphism and MS. Conclusion The results showed that the genetic variants of the APM1 and the APOC1 were associated with MS in children.

Infections of the human immunodeficiency virus (HIV) trigger host immune responses, but the virus can destroy the immune system and cause acquired immune deficiency syndrome (AIDS). Highly active antiretroviral therapy (HAART) can suppress viral replication and restore the impaired immune function. To understand HIV interactions with host immune cells during HAART, the transcriptomes of peripheral blood mononuclear cells (PBMC) from HIV patients and HIV negative volunteers before and two weeks after HAART initiation were analyzed using RNA sequencing (RNA-Seq) technology. Differentially expressed genes (DEGs) in response to HAART were firstly identified for each individual, then common features were extracted by comparing DEGs among individuals and finally HIV-related DEGs were obtained by comparing DEGs between the HIV patients and HIV negative volunteers. To demonstrate the power of this approach, minimum numbers of patients (one HIV alone; one HIV + tuberculosis, TB; one HIV + TB with immune reconstitution inflammatory syndrome during HAART) and two HIV negative volunteers were used. More than 15,000 gene transcripts were detected in each individual sample. Fourteen HAART up-regulated and eleven down-regulated DEGs were specifically identified in the HIV patients. Among them, nine up-regulated (CXCL1, S100P, AQP9, BASP1, MMP9, SOD2, LIMK2, IL1R2 and BCL2A1) and nine down-regulated DEGs (CD160, CD244, CX3CR1, IFIT1, IFI27, IFI44, IFI44L, MX1 and SIGLEC1) have already been reported as relevant to HIV infections in the literature, which demonstrates the credibility of the method. The newly identified HIV-related genes (up-regulated: ACSL1, GPR84, GPR97, ADM, LRG1; down-regulated: RASSF1, PATL2) were empirically validated using qRT-PCR. The Gene Set Enrichment Analysis (GSEA) was also used to determine pathways significantly affected by HAART. GSEA further confirmed the HAART relevance of five genes (ADM, AQP9, BASP1, IL1R2 and MMP9). The newly identified HIV-related genes, ADM (which encodes Adrenomedullin), a peptide hormone in circulation control, may contribute to HIV-associated hypertensions, providing new insights into HIV pathology and novel strategies for developing anti-HIV target. More importantly, we demonstrated that comparative transcriptome analysis is a very powerful tool to identify infection related DEGs using a very small number of samples. This approach could be easily applied to improve the understanding of pathogen-host interactions in many infections and anti-infection treatments.

This study uses 2001–2014 satellite observations and reanalyses to investigate the seasonal characteristics of Cloud Radiative Effects (CREs) and their associations with cloud fraction (CF) and precipitation over the Asian monsoon region (AMR) covering Eastern China (EC) and South Asia (SA). The CREs exhibit strong seasonal variations but show distinctly different relationships with CFs and precipitation over the two regions. For EC, the CREs is dominated by shortwave (SW) cooling, with an annual mean value of − 40 W m− 2 for net CRE, and peak in summer while the presence of extensive and opaque low-level clouds contributes to large Top-Of-Atmosphere (TOA) albedo (>0.5) in winter. For SA, a weak net CRE exists throughout the year due to in-phase compensation of SWCRE by longwave (LW) CRE associated with the frequent occurrence of high clouds. For the entire AMR, SWCRE strongly correlates with the dominant types of CFs, although the cloud vertical structure plays important role particularly in summer. The relationships between CREs and precipitation are stronger in SA than in EC, indicating the dominant effect of monsoon circulation in the former region. SWCRE over EC is only partly related to precipitation and shows distinctive regional variations. Further studies need to pay more attention to vertical distributions of cloud micro- and macro-physical properties, and associated precipitation systems over the AMR.