Temporal dynamics in viral shedding and transmissibility of COVID-19

We report temporal patterns of viral shedding in 94 patients with laboratory-confirmed COVID-19 and modeled COVID-19 infectiousness profiles from a separate sample of 77 infector-infectee transmission pairs. We observed the highest viral load in throat swabs at the time of symptom onset, and inferred that infectiousness peaked on or before symptom onset. We estimated that 44% (95% confidence interval, 25-69%) of secondary cases were infected during the index cases' presymptomatic stage, in settings with substantial household clustering, active case finding and quarantine outside the home. Disease control measures should be adjusted to account for probable substantial presymptomatic transmission.

Evidence that the second human pegivirus (HPgV-2) is primarily a lymphotropic virus and can replicate independent of HCV replication

The second human pegivirus HPgV-2 is a novel blood-borne virus that is strongly associated with the hepatitis C virus (HCV) infection. However, the molecular evidence for their association as well as the natural history and tissue tropism of HPgV-2 remain to be elucidated. In this longitudinal study, a total of 753 patients including 512 HIV-1 and HCV co-infected patients were enrolled to characterize the natural history of HPgV-2 infection. Peripheral blood mononuclear cells (PBMCs) and liver biopsies were collected to determine the tissue tropism of HPgV-2 using immunohistochemical staining of the HPgV-2 antigen and in situ hybridization of HPgV-2 RNA. We documented both persistent HPgV-2 infection with the presence of HPgV-2 viral RNA and antibodies up to 4.6 years and resolved HPgV-2 infection, accompanied by a simultaneous decline of anti-HPgV-2 antibodies and clearance of HPgV-2 viremia. Furthermore, we observed the clearance of HCV, but not HPgV-2, by treatment with direct-acting antivirals (DAAs). Biochemical tests and pathological analyses did not reveal any indication of hepatic impairment caused by HPgV-2. HPgV-2 RNA and nonstructural antigen were detected in the lymphocytes, but not in the hepatocytes present in the liver biopsy samples. In addition, both positive- and negative-strand HPgV-2 RNAs were detected in PBMCs, especially in B cells. The present study is the first to provide evidence that HPgV-2 is a lymphotropic, but not a hepatotropic virus and that HPgV-2 replication is independent of HCV viremia. These new findings let us gain insights into the evolution and persistent infection of RNA viruses in humans.

Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity

The novel coronavirus (2019-nCoV) infection caused pneumonia. we retrospectively analyzed the virus presence in the pharyngeal swab, blood, and the anal swab detected by real-time PCR in the clinical lab. Unexpectedly, the 2109-nCoV RNA was readily detected in the blood (6 of 57 patients) and the anal swabs (11 of 28 patients). Importantly, all of the 6 patients with detectable viral RNA in the blood cohort progressed to severe symptom stage, indicating a strong correlation of serum viral RNA with the disease severity (p-value = 0.0001). Meanwhile, 8 of the 11 patients with annal swab virus-positive was in severe clinical stage. However, the concentration of viral RNA in the anal swab (Ct value = 24 + 39) was higher than in the blood (Ct value = 34 + 39) from patient 2, suggesting that the virus might replicate in the digestive tract. Altogether, our results confirmed the presence of virus RNA in extra-pulmonary sites.

Antibodies against carbamylated vimentin exist in systemic lupus erythematosus and correlate with disease activity

OBJECTIVES

Antibodies against carbamylated protein (anti-CarP) were found to be a promising marker to evaluate joint damage and disease activity in patients with rheumatoid arthritis (RA). However, whether anti-CarP antibodies were present in systemic lupus erythematosus (SLE) remained ambiguous. We have therefore undertaken this study to assess the levels of serum anti-CarP antibodies and to evaluate their clinical value in SLE.

METHODS

Serum levels of antibodies against carbamylated-vimentin (anti-Carp) were measured by enzyme immunosorbent assay in 100 patients with SLE, 76 with RA, 17 with primary Sjögren syndrome (pSS), and 68 healthy controls. Data analyses between anti-Carp antibodies and other laboratory measures were performed using SPSS 24 software for Windows.

RESULTS

The levels of serum anti-CarP antibodies in patients with SLE were significantly higher than those in healthy controls. In addition, anti-CarP antibodies were present in SLE patients lacking the disease-specific antibodies, including anti-Smith-negative patients (24.4%, 21/86), anti-dsDNA-negative patients (29.3%, 12/41), anti-nucleosome-negative patients (21.4%, 9/42), and antiribosomal P protein antibody-negative patients (23.7%, 18/76). There were significant differences between the anti-CarP-positive and anti-CarP-negative SLE patients in clinical and laboratory features, such as age, erythrocyte sedimentation rate (ESR), C-reactive protein, rheumatoid factor, third-generation cyclic citrullinated peptide (CCP3), anticardiolipin, D-dipolymer, complement 3, immunoglobulin G (IgG), red blood cell count (RBC) and hemoglobin. After adjusting for age and disease duration, the high levels of anti-CarP antibodies were still correlated with low RBC, hemoglobin and high ESR, IgG and CCP3. Active SLE patients demonstrated higher anti-CarP IgG than inactive patients. Moreover, the levels of anti-CarP were significantly higher in SLE patients with arthralgia and/or arthritis than in those without joint involvement.

CONCLUSIONS

Anti-CarP antibodies were present in SLE patients and associated with the disease severity. These might provide a potential supplement to other specific autoantibodies for diagnosis of SLE and serve as a promising marker for measuring joint damage in the disease.

Cell Culture Models and Animal Models for HBV Study

Highly representative and relevant cell and mouse models are required for HBV study, including uncovering its lifecycle, investigation of the viral-host interaction, and development and evaluation of the novel antiviral therapy. During the past 40 years, both HBV cell culture models and animal models have evolved over several generations, each with significant improvement for specific purposes. In one aspect, HBV cell culture models experienced the original noninfection model including HBV plasmid DNA transfection and HBV genome integrated stable cells such as HepG2.2.15 which constitutively produces HBV virus and HepAD38 cells and its derivatives which drug-regulated HBV production. As for HBV infection models, HepaRG cells once dominated the HBV infection field for over a decade, but its complicated and labor-extensive cell differentiation procedures discouraged primary researchers from stepping in the field. The identification of human NTCP as HBV receptor evoked great enthusiasm of the whole HBV field, and its readily adaptive characteristic makes it popular in many HBV laboratories. Recombinant cccDNA (rc-cccDNA) emerged recently aiming to tackle the very basic question of how to eventually eradicate cccDNA without HBV real virus infection. In the other aspect, HBV transgenic mouse was firstly generated in the 1990s, which was helpful to decipher HBV production in vivo. However, the HBV transgenic mice were naturally immune tolerant to HBV viral products. Subsequently, a series of nonintegrated HBV mouse models were generated through plasmid hydrodynamic tail vein injection and viral vector-mediated delivery approaches, and HBV full life cycle was incomplete as cccDNA was not formed from HBV relaxed circular DNA (rcDNA). Human NTCP transgenic mouse still could not support productive HBV infection, and humanized mouse liver with human hepatocytes which supported whole HBV life cycle still dominates HBV infection in vivo, a value but expensive model until now. Other methods to empower mouse to carry HBV cccDNA were also exploited. In this chapter, we summarized the advantages and disadvantages of each model historically and provided protocols for HBV infection in HepG2-NTCP cells, HBV rc-cccDNA transfection in HepG2 cells, and HBV infection in NRG-Fah-/- liver humanized mouse.

[Analysis of differences in epidemiology and clinical features of Guillain-Barré syndrome between rural and urban areas of southern China]

Objective: To explore the differences in epidemiology and clinical features of Guillain- Barré syndrome (GBS) between rural and urban areas of southern China. Methods: The clinical data of 759 hospitalized GBS patients from 31 hospitals of 13 provinces/cities in southern China, between January 1st, 2013 and September 30th, 2016, were collected and analyzed retrospectively. Results: The risk of GBS was higher for males than females in rural and urban areas and the median age was 49 and 48 years, respectively. Seasonal clustering in winter and spring was noted in both rural and urban areas, and the seasonal trend was more markedly in rural areas, but the differences showed no statistical significance. There were 70.37% of patients in rural areas and 73.69% in urban areas who had antecedent respiratory infection. The median time from onset to nadir was 7 days, and Hughes Disability Scale at admission, nadir and discharge were (2.95±1.10 vs 2.84±1.15), (3.25±1.11 vs 3.14±1.21), (2.02±1.24 vs 2.00±1.31) in rural and urban areas respectively. Albuminocytologic dissociation was present in 84.34% of patients in rural areas and 84.62% of cases in urban areas. There were 8.65% and 10.94% of cases in rural and urban areas who required mechanical ventilation during hospitalization, respectively. Demyelinating GBS accounted for 53.29% and 48.77%, respectively, in patients with findings of nerve conduction studies available in rural and urban areas. Conclusions: GBS in rural areas of southern China showed male predominance and a peak of spring and winter occurrence, with respiratory infection as the predominated preceding events and demyelinating GBS being main clinical subtype. Winter and spring showed a higher incidence of GBS in rural and urban areas. There were no significant differences of sex, age, preceding events, season trend, progression of disease, clinical subtypes and cerebrospinal fluid investigations in GBS patients between rural and urban areas.

[Survey of Schistosoma japonicum infections in wild animals in hilly transmission-controlled areas of Jiangxi Province]

OBJECTIVE

To understand the situation of Schistosoma japonicum infections in wild animals in transmission-controlled schistosomiasis-endemic areas in Jiangxi Province, so as to provide scientific evidence for implementing precision control interventions and achieving the goal of transmission interruption and elimination of schistosomiasis.

METHODS

Five endemic villages from Ruichang City and Pengze County that were heavily endemic for schistosomiasis in Jiangxi Province, were selected as the study villages. Wild animals like wild mice were captured, and the livers of wild animals were purchased from the snail habitats in the study villages for detection of S. japonicum infections. In the study villages, S. japonicum human infections were screened using indirect hemagglutination assay (IHA) followed by parasitological examinations with miracidial hatching test and Kato-Katz method, and the S. japonicum infection in livestock was tested using a miracidial hatching test with a plastic tube. In addition, snail survey was conducted in the study villages by means of systematic sampling combined with environmental sampling, and the S. japonicum infection in snails was detected using a loop-mediated isothermal amplification (LAMP) assay.

RESULTS

A total of 240 liver specimens were sampled or purchased from 5 species of wild animals in the study villages, including wild mice, weasels, pigs, deer and rabbits. A total of 172 wild mice were captured, with a 2.91% rate of S. japonicum infection, and there was no S. japonicum infection detected in other wild animals. The prevalence of Capillaria hepatica infection was 12.21%, 1.96% and 12.50% in wild mice, deer and pigs, respectively. In addition, there was no S. japonicum infection found in either humans or livestock in the study villages, and the mean snail density varied from 0.13 to 0.80 snails/0.1 m² in the study villages. LAMP assay detected S. japonicum infection in 2 tubes in a study village.

CONCLUSIONS

The role of wild animals in schistosomiasis transmission and their potential risks can not be neglected in hilly schistosomiasis-endemic areas of Jiangsu Province after transmission control. Intensified surveillance and targeted control measures should be implemented to consolidate schistosomiasis control achievements.

A rare case of association between Budd-Chiari syndrome and sea-blue histiocytosis

Budd-Chiari syndrome (BCS) is a rare disease characterized by obstruction of hepatic venous outflow tract with diversified etiologies. Sea-blue histiocytosis (SBH) is a kind of storage diseases defined by the deposition of abundant sea-blue histiocytes in various organs and can lead to hepatosplenomegaly, cirrhosis, or even liver failure. The association between BCS and SBH has never been reported before. Here, we report a patient with BCS presenting with hepatosplenomegaly, portal hypertension, and pancytopenia who was later confirmed to also have SBH.

Tailored Plasmons in Pentacene/Graphene Heterostructures with Interlayer Electron Transfer

van der Waals (vdW) heterostructures, which are produced by the precise assemblies of varieties of two-dimensional (2D) materials, have demonstrated many novel properties and functionalities. Here we report a nanoplasmonic study of vdW heterostructures that were produced by depositing ordered molecular layers of pentacene on top of graphene. We find through nanoinfrared (IR) imaging that surface plasmons formed due to the collective oscillations of Dirac Fermions in graphene are highly sensitive to the adjacent pentacene layers. In particular, the plasmon wavelength declines systematically but nonlinearly with increasing pentacene thickness. Further analysis and density functional theory (DFT) calculations indicate that the observed peculiar thickness dependence is mainly due to the tunneling-type electron transfer from pentacene to graphene. Our work unveils a new method for tailoring graphene plasmons and deepens our understanding of the intriguing nano-optical phenomena due to interlayer couplings in novel vdW heterostructures.

[Influence of antiretroviral prophylaxis on growth of HIV-exposed uninfected infants]

Objective: To evaluate the influence of antiretroviral prophylaxis on the growth and development of HIV-exposed uninfected infants in Guangzhou. Methods: Data were from the national information system for prevention of mother-to-child transmission of HIV infection, syphilis and hepatitis B. After excluding death and perinatal HIV infection cases, 564 HIV-exposed uninfected infants were included. The infants were divided into three groups, nevirapine (NVP) group, zidovudine (AZT) group and untreated group. The influences of antiretroviral prophylaxis on the body weight and height of the HIV-exposed uninfected infants were analyzed by using generalized estimating equations. Results: The HIV-exposed uninfected infants at 1-month old had lower Z scores of body weight-for-age and body height-for-age than the World Health Organization's reference standard. The prevalence of wasting in AZT group (17.5%) was higher than that in NVP group (6.2%) for 1-month old infants. Taking NVP or AZT was a protective factor for Z score of body length-for-age (P<0.05). Intrauterine exposure to triple antiviral drugs was a risk factor for the Z scores of body weight-for-age and body length-for-age (P<0.05). Conclusion: The physical growth and development of HIV-exposed uninfected infants at 1-month old was not well, and HIV-exposed uninfected infants who taking AZT had a higher incidence of wasting. Attention should be paid to these infants.

A novel one-step quantitative reverse transcription PCR assay for selective amplification of hepatitis B virus pregenomic RNA from a mixture of HBV DNA and RNA in serum

Current antiviral therapies against hepatitis B virus (HBV) infections, such as treatment with nucleos(t)ide analogs (NAs) and interferon alpha, can significantly lower HBV DNA titers, eventually to undetectable levels. However, it is still difficult to completely eliminate the stable template of HBV, the covalently closed circular DNA (cccDNA), and this contributes to viral rebound when treatment is discontinued. HBV pregenomic RNA (pgRNA), which was recently found to be present in the enveloped mature HBV viral particle in blood, is tentatively regarded, with still accumulating clinical evidence, as a novel bona fide virological marker reflecting the amount and status of cccDNA when serum HBV DNA becomes undetectable. HBV pgRNA and DNA share almost identical sequences, and it is therefore difficult to differentiate pgRNA from viral DNA using normal PCR methods. To exclude interference from viral DNA, methods for measuring pgRNA usually require a selective DNA degradation step, which is complicated and time-consuming and also compromises the accuracy of detection. In this study, we developed a simplified quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay with improved accuracy achieved by probing the polyA tail of pgRNA. Using clinical serum samples, we observed that not all patients share the same 3' sequence, suggesting slight differences between HBV strains in the way they end transcription. We then designed and evaluated a universal primer and probe set for distinguishing HBV pgRNA from HBV DNA. Our results demonstrated that a one-step qRT-PCR assay could selectively amplify HBV pgRNA from a mixture of HBV RNA and DNA, which is valuable for clinical applications.

[Association between both maternal pre-pregnancy body mass index/gestational weight gain and overweight/obesity children at preschool stage]

Objective: To investigate the association of both maternal pre-pregnancy body mass index (BMI) and gestational weight gain (GWG) with childhood overweight and adiposity in preschool children. Methods: A total of 4 303 preschool children aged 3-5 years were enrolled in our study during June and November 2016 in Guangzhou. Children defined as overweight and obesity were according to the criteria of WHO while weight status during maternal pre-pregnancy was using the China Adult Reference. Gestational weight gain was defined according to the Institute of Medicine guidelines. Results: After adjusting the possible confounding factors, results from the logistic regression analysis showed that both maternal pre-pregnancy overweight and obesity would increase the risk for both childhood overweight and obesity (OR=1.820, 95%CI: 1.368-2.422). The analysis of covariance results also showed that both maternal overweight and obesity before pregnancy and excessive maternal weight gain during pregnancy increased the BMI Z-score in children. Maternal GWG over the recommended level were associated with both the childhood overweight and obesity (OR=1.296, 95%CI: 1.007-1.667). Joint associations of pre-pregnancy BMI and inappropriate GWG were also noticed in the study. Stratified analysis was conducted in three groups according to the pre-pregnancy BMI of the mothers. Result showed that there was no statistical difference in the risks of either overweight or obesity in children (P>0.05). However, when compared to mothers with adequate pre-pregnancy higher BMI and adequate GWG, under the combination of high pre-pregnancy BMI and excessive GWG, their adverse effects on childhood overweight and obesity were much higher (OR=1.574, 95%CI: 1.029-2.409). Conclusions: Both high pre-pregnancy BMI and inappropriate GWG were associated with greater BMI of their offspring. Pregnant women should follow the appropriate weight gain program and help their children to prevent from becoming obese.

Dual therapy with lopinavir/ritonavir plus lamivudine could be a viable alternative for antiretroviral-therapy-naive adults with HIV-1 infection regardless of HIV viral load or subgenotype in resource-limited settings: A randomised, open-label and non-inferiority study from China

Backgrounds

This randomised controlled, open-label, non-inferiority trial was conducted in antiretroviral-naïve HIV-1-infected patients to assess the efficacy and safety of 48-week dual therapy of LPV/r plus 3TC (DT group) compared with Chinese first-line triple-therapy regimen (TT group).

Methods

198 were randomised to DT (n = 100) or TT (n = 98).

Results

Ninety-two DT patients (92%) and 88 TT patients (89.8%) achieved HIV-1 RNA <50 copies/ml at week 48 (P = 0.629). Moreover, the safety profile was similar between two groups, and no secondary HIV resistance was observed.

Conclusion

The results suggest that dual therapy of LPV/r plus 3TC is non-inferior to the first-line triple-therapy regimen in China.

Arsenic Trioxide Impacts Viral Latency and Delays Viral Rebound after Termination of ART in Chronically SIV-Infected Macaques

The latent viral reservoir is the source of viral rebound after interruption of antiretroviral therapy (ART) and is the major obstacle in eradicating the latent human immunodeficiency virus-1 (HIV-1). In this study, arsenic class of mineral, arsenic trioxide, clinically approved for treating acute promyelocytic leukemia, is demonstrated to reactivate latent provirus in CD4+ T cells from HIV-1 patients and Simian immunodeficiency virus (SIV)-infected macaques, without significant systemic T cell activation and inflammatory responses. In a proof-of-concept study using chronically SIVmac239-infected macaques, arsenic trioxide combined with ART delays viral rebound after ART termination, reduces the integrated SIV DNA copies in CD4+ T cells, and restores CD4+ T cells counts in vivo. Most importantly, half of arsenic trioxide-treated macaques show no detectable viral rebound in the plasma for at least 80 days after ART discontinuation. Mechanistically, the study reveals that CD4 receptors and CCR5 co-receptors of CD4+ T cells are significantly downregulated by arsenic trioxide treatment, which reduces susceptibility to infection after provirus reactivation. Furthermore, an increase in SIV-specific immune responses after arsenic trioxide treatment may contribute to suppression of viral rebound. This work suggests that arsenic trioxide in combination with ART is a novel regimen in down-sizing or even eradicating latent HIV-1 reservoir.

Characterization of Four Nearly Full-Length Genomic Sequences of HIV-1 Subtype G Identified in Guangdong Province, China

Four cases infected by HIV-1 subtype G strain were identified in Guangdong, China. The nearly full-length genome was amplified and sequenced for phylogenetic analysis. The four sequences clustered together with subtype G references in the tree (bootstrap value ≥98%). To determine whether HIV-1 subtype G has been spreading in China, all subtype G sequences identified in China were downloaded from HIV Database for further phylogenetic analysis. In the phylogenetic tree of pol gene (nucleotides 2283-3245 by using HXB2 as a calibrator), four clusters with bootstrap value >70% comprised nine sequences from China were identified, suggesting that subtype G might have been spreading in local areas in China. The detailed sequence data in this study will provide more information on HIV epidemic in China. The result also highlighted that more surveillance on subtype G prevalence in China is necessary.

FOXA1 promotes proliferation, migration and invasion by transcriptional activating KRT7 in human gastric cancer cells

Gastric cancer (GC) is the fourth leading cause of gynecological malignancies worldwide. 5-fluorouracil (5-FU)-mediated chemotherapy is the adjuvant treatment for patients with GC following surgical resection. Many studies have indicated the cancer-type specific roles of forkhead box protein A1 (FOXA1) and keratin 7 (KRT7) in human malignancies. However, the potential mechanism underlying the involvement of FOXA1 and KRT7 in the pathogenesis and chemoresistance of GC are still not entirely clear. In our study, gain- and loss-of-function experiments proved that FOXA1 promoted cell proliferation, migration and invasion in AGS and SGC-7901 cells. Consequently, KRT7 was identified to be transcriptional activated by FOXA1 using Dual luciferase reporter assay. Our results also indicated that FOXA1 exerted its functions in enhancing viability and invasion of AGS and SGC-7901 cells through activating KRT7. Finally, interference of FOXA1 or KRT7 increased the chemosensitivity of AGS and SGC-7901 cells to 5-fluorouracil (5-Fu) treatment by suppressing cell proliferation. In conclusion, these data indicate that FOXA1 promoted proliferation, migration, invasion, and decreased chemosensitivity of GC cells to 5-Fu treatment through transcriptional activator KRT7. The present study provides a novel therapeutic strategy for the enhancement of efficacy in GC treatment and provides important insights into the molecular mechanism underlying 5-FU-mediated chemoresistance.

Al2O3-YAG:Ce composite ceramics for high-brightness lighting

LD chips, combined with phosphor converters, are considered as optimum candidates for high brightness lighting. In this work, Al₂O₃-YAG:Ce composite ceramics were prepared as the phosphor converters. The sintering temperature and the sintering additives were optimized to obtain the highest quantum efficiency. The effect of the molar ratio of Al₂O₃ to YAG:Ce on the performance of the ceramics that were excited by the LD chips was studied. The results show that the light extraction efficiency from the ceramic surfaces increases with the increasing molar ratio of Al₂O₃ to YAG:Ce. Moreover, the improved thermal conductivity caused the ceramics with higher molar ratio of Al₂O₃ to YAG:Ce show alleviative luminescence saturation and improved reliability.

Sex, Residence and Fish Intake Predict Vitamin D Status in Chinese Centenarians

OBJECTIVES

This study aims to investigate the prevalence of vitamin D deficiency in Chinese centenarians and to identify the factors associated with vitamin D deficiency.

DESIGN

Cross-sectional population-based study.

SETTING

Hainan province in the south of China.

PARTICIPANTS

943 subjects aged 100 years old and older.

METHODS

Details on sociodemographics and lifestyle characteristics were collected using a structured questionnaire. Anthropometrics and blood samples were obtained. Vitamin D deficiency was defined as serum 25-hydroxyvitamin D concentration < 20ng/mL (50nmol/L).

RESULTS

The overall prevalence of vitamin D deficiency among these 943 centenarians was 39.9% (376 subjects) and the mean serum vitamin D concentrations were 22.7±9.5 (ng/mL). Female centenarians had higher prevalence of vitamin D deficiency than male (44.0% vs. 21.7%, P <0.001). Multivariate logistic regression analyses showed that being female, urban residency, lower body mass index, higher serum parathyroid hormone levels, no fish consumption, and less sun exposure time were all significant and independent determinants of vitamin D deficiency. No significant associations of vitamin D deficiency with ethnic, education, geographic location, tea drinking, alcohol use, or smoking were found in this study.

CONCLUSION

Vitamin D deficiency was common in Chinese centenarians, especially in women. Given that vitamin D deficiency is linked to numerous adverse health outcomes, dietary, outdoor activities and other intervention measures are needed to correct vitamin D deficiency in this population.

Characterization of small genomic regions of the hepatitis B virus should be performed with more caution

BACKGROUND

Hepatitis B virus is a hepatotropic DNA virus that reproduces via an RNA intermediate. It can lead to an increased risk of serious liver diseases such as hepatocellular carcinoma and is a serious threat to public health. Currently, the HBV are designated based on greater than 8% nucleotide variation along the whole genome. The recombination of HBV is very common, a large majority of which are recombinants between 2 genotypes. The current work aims to characterize a suspected recombinant involving 3 genotypes.

METHODS

Fifty-seven HBV full-genome sequences were obtained from 57 patients co-infected with HBV and HIV-1 by amplification coupled with sequencing. JpHMM and RDP4 were used to perform recombination analysis respectively. The recombination results of a suspected 3-genotypic recombinant were further confirmed by both maximum likelihood phylogenetic tree and Mrbayes tree.

RESULTS

JpHMM recombination analysis clearly indicated one 3-genotypic HBV recombinant composing of B/C/D. The genotype assignments are supported by significant posterior probabilities. The subsequent phylogenetic analysis of sub-regions derived from inferred breakpoints led to a disagreement on the assignment of D segment. Investigating the conflict, further exploration by RDP4 and phylogenies revealed that the jpHMM-derived 3-genotypic recombinant is actually a B/C genotypic recombinant with C fragment spanning 1899 to 2295 (jpHMM) or 1821 to 2199 (RDP4).

CONCLUSIONS

The whole analysis indicated that (i) determination of small genomic regions should be performed with more caution, (ii) combinations of various recombination detection approaches conduce to obtain impartial results, and (iii) a unified system of nomenclature of HBV genotypes is necessary.