Multi-Omics Analysis by Machine Learning Identified Lysophosphatidic Acid as a Biomarker and Therapeutic Target for Porcine Reproductive and Respiratory Syndrome.

As a significant infectious disease in livestock, porcine reproductive and respiratory syndrome (PRRS) imposes substantial economic losses on the swine industry. Identification of diagnostic markers and therapeutic targets has been a focal challenge in PPRS prevention and control. By integrating metabolomic and lipidomic serum analyses of clinical pig cohorts through a machine learning approach with in vivo and in vitro infection models, lysophosphatidic acid (LPA) is discovered as a serum metabolic biomarker for PRRS virus (PRRSV) clinical diagnosis. PRRSV promoted LPA synthesis by upregulating the autotaxin expression, which causes innate immunosuppression by dampening the retinoic acid-inducible gene I (RIG-I) and type I interferon responses, leading to enhanced virus replication. Targeting LPA demonstrated protection against virus infection and associated disease outcomes in infected pigs, indicating that LPA is a novel antiviral target against PRRSV. This study lays a foundation for clinical prevention and control of PRRSV infections.

Isolation, identification, and pathogenicity of a NADC30-like porcine reproductive and respiratory disorder syndrome virus strain affecting sow production.

Since it was first reported in 1987, porcine reproductive and respiratory syndrome virus (PRRSV) has caused several economic crises worldwide. The current prevalence of PRRSV NADC30-like stains causing clinical disease outbreaks in Chain is highly concerning. Immunization against and the prevention of this infection are burdensome for farming organizations as the pathogen frequently mutates and undergoes recombination. Herein, the genetic characterization of a NADC30-like strain (termed BL2019) isolated from a farm in Guangdong Province, China, was analyzed and its pathogenicity for piglets and sows was assessed. Results revealed that BL2019 exhibits a nucleotide homology of 93.7% with NADC30 PRRSV and its NSP2 coding region demonstrates the same 131aa deletion pattern as that of NADC30 and NADC30-like. Furthermore, we identified two recombination breakpoints located nt5804 of the NSP5-coding region and nt6478 of NSP2-coding region, the gene fragment between the two breakpoints showed higher homology to the TJ strain(a representative strain of highly pathogenic PRRSV) compared to the NADC30 strain. In addition, BL2019 infection in piglets caused fever lasting for 1 week, moderate respiratory clinical signs and obvious visual and microscopic lung lesions; infection in gestating sows affected their feed intake and increased body temperature, abortion rates, number of weak fetuses, and other undesirable phenomena. Therefore, we report a NADC30-like PRRSV strain with partial recombination and a representative strain of HP-PRRSV, strain TJ, that can provide early warning and support for PRRS immune prevention and control.

Characterization and Pathogenicity of Two Novel PRRSVs Recombined by NADC30-like and NADC34-like Strains in China.

Porcine reproductive and respiratory syndrome viruses (PRRSVs) pose a serious threat to the swine industry in China, which has caused great difficulties for porcine reproductive and respiratory syndrome (PRRS) immune prevention and control, due to its easily mutable and recombinant nature. In this study, two novel PRRSV strains, which were named GD-H1 and GD-F1, were isolated and fully sequenced from pig farms in Guangdong province, China. The phylogenetic analysis and recombination analysis revealed that the GD-H1 and GD-F1 were generated by the recombination of NADC30-like and NADC34-like strains which were different from the previously prevalent strain. Further pathogenic studies on piglets and sows found that the recombinant strains could cause piglets high fever, loss of appetite and lung lesions, but no piglets died. However, the recombinant strains could cause acute death and abortion in pregnant sow infection models together with average survival rates of 62.5% and 37.5% abortion rates, respectively. These findings indicated that the recombinant strains were extremely pathogenic to sows. Therefore, we report two clinical novel recombinant strains of PRRSV that are different from the traditional epidemic strains in China, which may provide early warning and support for PRRS immune prevention and control.

Epidemiological investigation of duck adenovirus 3 in southern China, during 2018-2020.

RESEARCH HIGHLIGHTSFirst report of the epidemiology of duck adenovirus 3 infection in China.Mutant DAdV-3 strains (truncated ORF67) became predominant.

Characterization and pathogenicity of a novel avian nephritis virus isolated in China.

ABSTRACTAvian nephritis virus infections of chicken flocks cause enteric and kidney disease, uneven growth, and runting stunting syndrome, leading to economic losses in the poultry industry. In this study, one ANV strain, designated as AH202017, was isolated from a diseased broiler flock in Anhui province, China, in 2020. Virus production in LMH cell culture was confirmed by real-time RT-PCR and immunofluorescence assay. The complete genome sequencing analysis indicated that AH202017 shares 77.5-85.5% identity with 12 reference strains in GenBank. Phylogenetic analysis of the capsid protein revealed that AH202017 is more closely related to VIC-6a/Australia/2014 belonging to ANV genotype 2. However, the phylogenetic tree, based on the ORF1a protein and ORF1b protein, indicated that AH202017 manifests a close relationship with GXJL815/China/2017 belonging to genotype 8. In infection experiments, four infected chickens showed depression and one chicken died at 6 days post-infection, corresponding to 5% mortality. The virus was shed daily in the faeces of infected chickens, and was found distributed in multiple organs. Macroscopic and microscopic lesions in the kidneys were observed. This is the first paper that describes the genomic characteristics and pathogenicity of a novel ANV strain in China. RESEARCH HIGHLIGHTSA novel ANV strain was isolated for the first time from diseased broilers in China.The ANV strain caused nephritis and 5% mortality rate in 1-day-old SPF chickens.

Isolation and characterization of a novel chicken astrovirus in China.

Chicken astrovirus (CAstV) is associated with kidney disease and visceral gout, runting and stunting syndrome, and white chick hatchery disease, causing economic losses to the poultry industry worldwide. In this study, 55.6% of 36 clinical samples from Guangdong province in China were positive for CAstV, but negative for other common enteric viruses, including avian nephritis virus, infectious bronchitis virus, fowl adenovirus Group I, Newcastle disease virus, chicken parvovirus, reovirus, and rotavirus by PCRs and RT-PCRs. A CAstV strain, named GD202013, was isolated from Guangdong province in south China, and was identified by CAstV RT-PCR. A whole genome sequence analysis demonstrated that GD202013 shares 76.0 to 88.1% identity with 24 reference strains in GenBank. Phylogenetic analysis, based on whole genome and capsid protein, showed that GD202013 is more closely related to 2 US strains (GA2011/US/2011 and 4175/US/2011) belonging to subgroup Bii. Recombination analysis indicated that GD202013 is a recombinant strain formed by 3 strains: a major parent strain CkP5/US/2016, and 2 minor parent strains (GA2011/US/2011 and G059/PL/2014). In addition, the chicken embryo infection experiment demonstrated that GD202013 causes hatchability reduction, growth depression, and death of embryos. Macroscopic and microscopic lesions in the liver, kidney and small intestine were observed in the dead-in-shell embryos. This is the first report of the novel CAstV infection in China.

Neuropsychiatric Adverse Events During 12 Months of Treatment With Efavirenz in Treatment-Naïve HIV-Infected Patients in China: A Prospective Cohort Study.

Background: Efavirenz (EFV) is widely used in antiretroviral therapy (ART), but the incidence and risk factors of neuropsychiatric adverse events (NPAEs) after EFV treatment have rarely been studied in Chinese ART naïve patients. Methods: This prospective cohort study assessed HIV-infected patients initiating antiretroviral treatment with EFV to determine prevalence of and factors associated with NPAEs over a 12-month follow-up period using the Hospital Anxiety and Depression Scale (HADS) and the Pittsburgh Sleep Quality Index (PSQI). Results: A total of 546 patients were enrolled. Prevalence of anxiety, depression, and sleep disturbances at baseline were 30.4, 22.7, and 68.1%, respectively. Six patients discontinued treatment due to drug related NPAEs. Treatment was associated with improvements in HADS-A, HADS-D, and PSQI scores over the 12-month follow-up, and the frequencies of patients with anxiety, depression, and sleep disturbances significantly decreased after 12 months. Abnormal baseline HADS-A, HADS-D, and PSQI scores and other factors, including high school education or lower income, unemployment, divorce, and WHO III/IV stages, were associated with severe neuropsychiatric disorders over the 12 months. Conclusions: These findings suggested EFV discontinuation due to NAPEs was low, and the HADS-A, HADS-D, and PSQI scores after 12 months of EFV treatment were associated with several risk factors. The clinicians should keep in mind and routinely screen for the risk factors associated with neuropsychiatric disorders in HIV-infected patients.

Isolation and characterization of a recombinant Muscovy duck parvovirus circulating in Muscovy ducks in South China.

In 2019, flocks of Muscovy ducks presented with clinical signs typical of MDPV infection. The MDPV GD201911 strain was isolated by inoculating samples from positive birds into Muscovy duck embryos. Challenge with the isolate GD201911 caused typical MDPV disease symptoms and resulted in 25%-40% mortality, depending on the challenge dose, indicating the high pathogenicity of GD201911 for Muscovy ducks. Genome sequencing and phylogenetic analysis demonstrated that GD201911 clustered with recombinant MDPV strains, indicating that recombinant MDPV is circulating in China. Epidemiological monitoring should be performed continuously to assist with decision making for disease control.

Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain.

BACKGROUND: Porcine epidemic diarrhea virus (PEDV) has caused enormous economic losses to the global pig industry. Currently available PEDV vaccine strains have limited protective effects against PEDV variant strains. METHODS: In this study, the highly virulent epidemic virus strain CT was serially passaged in Vero cells for up to 120 generations (P120). Characterization of the different passages revealed that compared with P10 and P64, P120 had a higher viral titer and more obvious cytopathic effects, thereby demonstrating better cell adaptability. RESULTS: Pathogenicity experiments using P120 in piglets revealed significant reductions in clinical symptoms, histopathological lesions, and intestinal PEDV antigen distribution; the piglet survival rate in the P120 group was 100%. Furthermore, whole-genome sequencing identified 13 amino acid changes in P120, which might be responsible for the attenuated virulence of P120. CONCLUSIONS: Thus, an attenuated strain was obtained via cell passaging and that this strain could be used in preparing attenuated vaccines.

Attenuation of duck Tembusu virus ZJSBL01 strain following serial passage in BHK-21 cells supplied with 5-Fluorouracil.

Duck Tembusu virus (DTMUV) is a new pathogen that produces an acute and potent disease in ducks which has caused serious economic losses in China. In this study, a virulent strain of DTMUV, designated as ZJSBL01, was attenuated by serial passages in BHK-21 cells supplied with 5-Fluorouracil (5-FU) for 50 passages to induce mutation and attenuation. Growth kinetics of different passages of ZJSBL01 strain in BHK-21 cells show that these viruses have similar replication characteristics. The virus was highly attenuated after 40 passages in BHK-21 cells supplied with 5-FU, based on mortality, morbidity, and viral load in inoculated Sheldrake ducklings. In addition, all of the ducklings immunized with ZJSBL01-P40, the virus obtained at passage 40 of ZJSBL01, showed seroconversion on day 14 post inoculation. Moreover, P40 did not cause clinical symptom for layding ducks. Immunization with ZJSBL01-P40 could provide effective protection against the virulent parental ZJSBL01 strain. Seventeen amino acid substitutions were observed in the polyprotein of ZJSBL01-P40 compared with parental ZJSBL01. These results indicate that ZJSBL01-P40 may be a live vaccine candidate for prevention of DTMUV-disease.

Recombinant fiber-2 protein protects Muscovy ducks against duck adenovirus 3 (DAdV-3).

As a novel duck adenovirus 3 (DAdV-3) infection caused significant economic losses to the poultry industry in China, there is an urgent need to develop a safe and effective vaccine. In the research, fiber-1 and fiber-2 proteins were expressed and purified, respectively. To evaluate the immunogenicity of the two recombinant proteins, we investigated the IgY antibodies and virus-neutralizing antibodies in duck sera. The protective efficacy was evaluated by mortality, virus shedding and histopathological examinations after challenged with the DAdV-3. Results showed that the IgY antibody levels of the fiber-2 group was significantly higher than that of the fiber-1 group and inactivated vaccine group. Ducks vaccinated with fiber-2 group provided full protection with no mortality, no virus shedding and no histological lesions, superior to other groups. These results suggest that the fiber-2 protein can be an ideal candidate for subunit vaccine against the disease.

Detection of three novel atypical porcine pestivirus strains in newborn piglets with congenital tremor in southern China.

Atypical porcine pestivirus (APPV) have been discovered in swine herds from three provinces in China, suggesting a wide distribution in China. This study reports the occurrence of three novel APPV strains in China. They were detected from newborn piglets with clinical signs of congenital tremors (CT) in Guangdong Province, China. The complete genomic sequences of three novel APPV strains exhibited only 80.5%-84.1% nucleotide sequences homology with other APPV reference sequences available in GenBank. Phylogenetic analysis showed that these novel APPV strains formed independent branch from the American, German, Netherlandish, Australian and other Chinese strains. These results will help us better understand the epidemiology and genetic characteristics of APPV in China.

T160A mutation-induced deglycosylation at site 158 in hemagglutinin is a critical determinant of the dual receptor binding properties of clade 2.3.4.4 H5NX subtype avian influenza viruses.

Most clade 2.3.4.4 H5NX subtype avian influenza viruses possess a T160A amino acid substitution in the hemagglutinin (HA) protein that has been shown to affect the receptor binding properties of a clade 2.3.4 H5N1 virus. However, the effect of this single site mutation on the HA backbone of clade 2.3.4.4 H5NX viruses remains unclear. In this study, two H5N6 field isolates possessing HA-160A with dual α-2,3 and α-2,6 receptor binding properties (Y6 virus) and HA-160T with α-2,3 receptor binding affinity (HX virus), respectively, were selected to generate HA mutants containing all of the internal genes from A/PR8/H1N1 virus for comparative investigation. We found that the Y6-P-160A and RHX-P-160A viruses each with 160A in the HA resulting in loss of glycosylation at site 158 exhibited binding to the two receptor types, whereas the RY6-P-160T and HX-P-160T viruses each with 160T in the HA displayed selective binding to α-2,3 receptors only. In addition, differences were noted in the replication of these four H5N6 recombinants in avian and mammalian cells, as well as in their pathogenicity in mice. The contribution of deglycosylation at site 158 to the acquisition of human-like receptors was further verified in H5N2, H5N5 and H5N8 reassortants. Therefore, we conclude that the lack of glycosylation at site 158 induced by the T160A mutation in HA is a critical determinant for the dual receptor binding properties of clade 2.3.4.4 H5NX viruses. This new insight may be helpful in assessing the pandemic potential of novel H5 isolates.

Immunogenicity and protective efficacy of recombinant fiber-2 protein in protecting SPF chickens against fowl adenovirus 4.

Since a novel hyper-virulent fowl adenovirus serotype 4 (FAdV-4) infection occurred in 2015, the novel FAdV-4 has been widely spreading across China, causing significant economic losses to the poultry industry. As the urgency of the issue calls for effective and efficient solutions, the present study investigated the possibility of the fiber-2 protein of the FAdV-4 to serve as a vaccine candidate against the novel FAdV-4. In the research, fiber-2 proteins were expressed in Escherichia coli, and then purified. To evaluate the immunogenicity of the recombinant fiber-2 protein, we investigated both the humoral and cellular immune responses in chickens immunized with fiber-2. The humoral immunity was assessed by detecting IgY antibodies and virus-neutralizing antibodies in chicken serum at 7, 14, 21 days post-immunization (dpi). We examined cellular immune responses by detecting CD3+CD4+ and CD3+CD8+ changes in chickens' peripheral blood through using flow cytometry at 7, 14, 21 dpi. The cytokine production in the serum of the immunized chickens was detected by ELISA at 7, 14, 21 dpi to further explore the impact of the recombinant protein on the regulation of cytokines. The protective efficacy was determined by the survival rate of the immunized chickens challenged with the novel FAdV-4. The results show that the level of IgY antibodies of the chickens immunized with fiber-2 protein was significantly higher than that of the chickens immunized with an inactivated vaccine against FAdV-4. Moreover, 7 days after immunization, the CD4+ T-cell proliferative response of the chickens immunized with fiber-2 was significantly higher than that of the chickens immunized with the inactivated vaccine. Challenge experiment showed that the fiber-2 protein could provide full protection and the inactivated vaccine could provide 90 percent protection against the FAdV-4. These results suggest that the recombinant fiber-2 protein can be an ideal candidate for subunit vaccines against the disease.

Asymptomatic Meningitis and Lung Cavity in a Case of Cryptococcosis.

BACKGROUND Cryptococcus neoformans (C. neoformans) infection is one of the most common opportunistic infections in AIDS patients. C. neoformans usually infects the central nervous system (CNS) and/or lungs with typical clinical manifestation. CASE REPORT Here, we report the case of a 52-year-old HIV-1-infected man with disseminated cryptococcosis, including subacute meningitis, pulmonary, and cutaneous cryptococcosis, but only skin lesion served as the chief complaint. Moreover, the results of cerebrospinal fluid (CSF) tests and lung computed tomography (CT) scan were atypical. CONCLUSIONS We present the clinical characteristics of this case and discuss the diagnostic procedure, which will likely help clinicians in making a timely definitive diagnosis of this disease.

Fast-Growing Subcutaneous Tumors with Lower-Extremity Edema and Rib Lesions: A Case of Non-Hodgkin's Lymphoma in an HIV-1-Infected Patient.

BACKGROUND Diffuse large B-cell lymphoma (DLBCL) accounts for the large majority of AIDS-related non-Hodgkin's lymphoma (NHL). DLBCL usually arises in lymph nodes, presenting as a painless rapid swelling mass in the neck, armpit, or groin. CASE REPORT Here, we report a case of DLBCL that needed only 3 months to develop a tumor 20×15 cm in diameter in the right groin and even caused scrotum swelling and lower-extremity edema. Furthermore, this case of DLBCL had developed other 3 subcutaneous tumors in the chest wall and their diameters were 16×9 cm, 7×7 cm, and 3×3 cm. A thoracic computed tomography (CT) scan presented with bilateral pleural effusion and the chest wall tumors with rib lesions. CONCLUSIONS It is rare that a DLBCL needed only 3 months to develop a tumor 20×15 cm in diameter and even caused scrotum swelling and unilateral lower-extremity edema due to the large mass located in the right groin. Furthermore, it is extremely rare that this lymphoma infiltrated the chest wall and even resulted in rib lesions.

The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs.

We generated and characterized site-directed HA mutants on the genetic backbone of H5N1 clade 2.3.4 virus preferentially binding to α-2,3 receptors in order to identify the key determinants in hemagglutinin rendering the dual affinity to both α-2,3 (avian-type) and α-2,6 (human-type) linked sialic acid receptors of the current clade 2.3.4.4 H5NX subtype avian influenza reassortants. The results show that the T160A substitution resulted in the loss of a glycosylation site at 158N and led not only to enhanced binding specificity for human-type receptors but also transmissibility among guinea pigs, which could be considered as an important molecular marker for assessing pandemic potential of H5 subtype avian influenza isolates.

Reassortant H5N1 avian influenza viruses containing PA or NP gene from an H9N2 virus significantly increase the pathogenicity in mice.

Reassortment between different influenza viruses is a crucial way to generate novel influenza viruses with unpredictable virulence and transmissibility, which may threaten the public health. As currently in China, avian influenza viruses (AIVs) of H9N2 and H5N1 subtypes are endemic in poultry in many areas, while they are prone to reassort with each other naturally. In order to evaluate the risk of the reassortment to public health, A/Goose/Jiangsu/k0403/2010 [GS/10(H5N1)] virus was used as a backbone to generate a series of reassortants, each contained a single internal gene derived from the predominant S genotype of the A/Chicken/Jiangsu/WJ57/2012 [WJ/57(H9N2)]. We next assessed the biological characteristics of these assortments, including pathogenicity, replication efficiency and polymerase activity. We found that the parental WJ/57(H9N2) and GS/10(H5N1) viruses displayed high genetic compatibility. Notably, the H5N1 reassortants containing the PA or NP gene from WJ/57(H9N2) virus significantly increased virulence and replication ability in mice, as well as markedly enhanced polymerase activity. Our results indicate that the endemicity of H9N2 and H5N1 in domestic poultry greatly increases the possibility of generating new viruses by reassortment that may pose a great threat to poultry industry and public health.

Preferential loss of gut-homing α4ß7 CD4+ T cells and their circulating functional subsets in acute HIV-1 infection.

Preferential infection and depletion of gut-homing α4ß7 CD4+ T cells in the blood are observed in chronic HIV/SIV infection. The dynamic change in gut-homing α4ß7 CD4+ T cells and their functional subsets during the acute stages of HIV-1 infection are less documented. Therefore, we conducted a cohort study to investigate whether acute HIV-1 infection induced abnormalities in gut-homing α4ß7 CD4+ T cells and their functional subsets. We examined the frequency, absolute number, and functionality of gut-homing α4ß7 CD4+ T cells in 26 acute HIV-1-infected patients compared with 20 healthy individuals. We found that circulating gut-homing α4ß7 CD4+ T cells were preferentially depleted during acute HIV-1 infection and were positively correlated with absolute CD4+ T-cell count in blood. Notably, Th17 and Th1 cell subsets of gut-homing CD4+ T cells were also decreased, which resulted in an imbalance of T helper cells (Th1):regulatory T cells (Treg) and Treg:Th17 ratios. Gut-homing Th17 and Th1 cells were also positively correlated with the absolute number of total CD4+ T cells and gut-homing CD4+ T cells. The gut-homing Treg:Th17 ratio was inversely correlated with the CD4+ T-cell count. Taken together, the analyses of our acute HIV-1 cohort demonstrate that gut-homing α4ß7 CD4+ T cells and their functional subsets were profoundly depleted during acute HIV-1 infection, which may have resulted in the persistent loss of circulating CD4+ T cells and an imbalance of Th1:Treg and Treg:Th17 ratios and contribute to HIV-1 disease pathogenesis.

[Functional Analyses of HIV-1 Specific Cytotoxic T Lymphocyte Clones].

Human immunodeficiency virus type 1(HIV-1)-specific CD8 cytotoxic T-lymphocytes(CTL)are essential components of the protective immunity against HIV-1infection.However,due to heterogeneous responses of CTL to HIV-1,our general understanding of CTL efficacy in the context of HIV-1infection remains limited. To better understand the factors that determine the potency of HIV-1specific CTL responses, this study directly investigated the relationship between different functional attributes associated with CTL response at the single cell level by using HIV-1specific CTL clones isolated in vitro. Twelve selected HIV-1CTL clones with various HLA restriction and specific antigen epitopes were comprehensively evaluated by several functional assays(e.g., killing capacity, degranulation, production of multiple cytokines and polyfunctionality, as well as the expression of lytic granule components and exhaustion molecules).Our principal findings were that the killing capacity of the CTL response was most closely associated with their degranulation capacity. Additionally, the killing and the degranulation capacity of CTL was associated with the levels and polyfunctionality of the cytokines secreted later. These findings implicate that multiple functional CTL responses are coordinately regulated and determined.