HIV-1 viral diversity and its implications for viral load testing: review of current platforms

The 2008 Recommendations for care of the International AIDS Society reaffirmed the importance of both accurate and sensitive viral load assessment, and by necessity, access to viral load assays. HIV-1 viral load testing is considered essential when initiating antiretroviral therapy (ART), when monitoring ART response, and when considering switching ART regimens. The demand for accurate, reproducible, and cost-effective viral load assays is therefore a global issue. Although the North American and Western European experience has historically been with HIV-1 group M subtype B virus, this paradigm is changing rapidly as migrants and refugees from developing countries with non-B subtype infections often now present for care in the developed world, and travelers to developing countries acquire non-B subtype infection abroad and present for care at home. Awareness of any clinical or laboratory differences between the common HIV-1 group M subtype B and the newer HIV-1 strains being seen in practice is therefore increasingly important. This review of current HIV-1 viral load testing is focused on the potential value of a standardized genotype assignment for HIV-1 viral subtypes, regular monitoring of the performance of available commercial HIV viral load assays on emerging non-B HIV subtypes, circulating recombinant forms (CRFs) and unique recombinant forms (URFs), and a discussion of the implications for resource-limited settings.     

HIV-1 p24和gp41融合基因表达载体的构建及融合蛋白的表达纯化

目的用基因重组技术将HIV-1p24基因以及gp41基因具有抗原线性中和表位的部分重组连接，构建重组质粒，并在大肠埃希菌中高效表达融合蛋白。方法设计带有酶切位点的引物，分别PCR扩增p24和gp41两个基因，将它们分别连接到pMD18-T载体中，测序验证后，挑选出含有目的基因的正确克隆。将p24片段酶切后连接到gp41基因所在的pMD18T载体中，再将连接后的两个基因酶切，重新连接到pET21a表达载体中。将表达载体转染大肠埃希菌诱导表达，经Western-blot验证表达正确。结果融合蛋白p24-gp41在大肠埃希菌中高效表达。结论融合蛋白p24-gp41可以在pET21a表达载体中高效表达。     

First Report of Distinct Bamboo mosaic virus (BaMV) Isolates Infecting Bambusa funghomii in Vietnam and the Identification of a Highly Variable Region in the BaMV Genome

New isolates of the Bamboo mosaic virus (BaMV) were identified in Bambusa funghomii bamboo in Vietnam. Sequence analyses revealed that the Vietnam isolates are distinct from all known BaMV strains, sharing the highest sequence identities (about 77%) with the Yoshi isolates reported in California, USA. Unique satellite RNAs were also found to be associated with the BaMV Vietnam isolates. A possible recombination event was detected in the genome of BaMV-VN2. A highly variable region was identified in the ORF1 gene, in between the methyl transferase domain and helicase domain. These results revealed the presence of unique BaMV isolates in an additional bamboo species in one more country, Vietnam, and provided evidence in support of the possible involvement of environmental or host factors in the diversification and evolution of BaMV.     

Identification of risk factors associated with national transmission and late presentation of HIV-1, Denmark, 2009 to 2017

BackgroundDespite availability of pre-exposure prophylaxis (PrEP), the incidence of HIV-1 in Europe remained stable the past decade. Reduction of new HIV-1 infections requires more knowledge about the profiles of high-risk transmitters and late presenters (LP).AimWe aimed to investigate risk factors associated with HIV-1 transmission clusters and late presentation with HIV-1 in Denmark.MethodsBlood samples and epidemiological information were collected from newly diagnosed HIV-1 patients between 2009 and 2017. We genotyped pol genes and performed phylogenetic analyses to identify clusters. Risk factors for clustering and LP were investigated with partial proportional odds and logistic regression. Covariates included transmission mode, HIV-1 subtype, age, origin and cluster activity.ResultsWe included 1,040 individuals in the analysis, 59.6% identified with subtype B and 48.4% in a cluster. Risk factors for clustering included Danish origin (odds ratio (OR): 2.95; 95% confidence interval (CI): 2.21–3.96), non-LP (OR: 1.44; 95% CI: 1.12–1.86), and men who have sex with men (MSM). Increasing age and non-B subtype infection decreased risk (OR: 0.69; 95% CI: 0.50–0.94). Risk for late presentation was lower for active clusters (OR: 0.60; 95% CI: 0.44–0.82) and Danish origin (OR: 0.43; 95% CI: 0.27–0.67). Non-Danish MSM had a lower risk than non-Danish heterosexuals (OR: 0.34; 95% CI: 0.21–0.55).ConclusionHIV-1 transmission in Denmark is driven by early diagnosed, young, subtype B infected MSM. These may benefit most from PrEP. Non-Danish heterosexual HIV-1 patients could benefit from improved communication to achieve earlier diagnosis and treatment.     

Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius,Republic of Korea

Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.