Novel HCV Genotype 4d Infectious Systems and Assessment of Direct-Acting Antivirals and Antibody Neutralization.

Hepatitis C virus (HCV) genotype 4 is highly prevalent in the Middle East and parts of Africa. Subtype 4d has recently spread among high-risk groups in Europe. However, 4d infectious culture systems are not available, hampering studies of drugs, as well as neutralizing antibodies relevant for HCV vaccine development. We determined the consensus 4d sequence from a chronic hepatitis C patient by next-generation sequencing, generated a full-length clone thereof (pDH13), and demonstrated that pDH13 RNA-transcripts were viable in the human-liver chimeric mouse model, but not in Huh7.5 cells. However, a JFH1-based DH13 Core-NS5A 4d clone encoding A1671S, T1785V, and D2411G was viable in Huh7.5 cells, with efficient growth after inclusion of 10 additional substitutions [4d(C5A)-13m]. The efficacies of NS3/4A protease- and NS5A- inhibitors against genotypes 4a and 4d were similar, except for ledipasvir, which is less potent against 4d. Compared to 4a, the 4d(C5A)-13m virus was more sensitive to neutralizing monoclonal antibodies AR3A and AR5A, as well as 4a and 4d patient plasma antibodies. In conclusion, we developed the first genotype 4d infectious culture system enabling DAA efficacy testing and antibody neutralization assessment critical to optimization of DAA treatments in the clinic and for vaccine design to combat the HCV epidemic.

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.

Long-range sequencing information is required for haplotype phasing, de novo assembly, and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirements. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enables a low-cost, high-accuracy, and high-throughput short-read second-generation sequencer to generate over 100 kb of long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcoded linked-reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate megabase-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.

Arsenic and other trace elements in groundwater and human urine in Ha Nam province, the Northern Vietnam: contamination characteristics and risk assessment.

The contamination characteristics of arsenic and other trace elements in groundwater and the potential risks of arsenic from the groundwater were investigated. Elevated contamination of arsenic, barium and manganese was observed in tube-well water of two villages (Chuyen Ngoai and Chau Giang) in Ha Nam province in the Northern Vietnam. Concentrations of As in the groundwater ranged from 12.8 to 884 µg/L with mean values in Chuyen Ngoai and Chau Giang were 614.7 and 160.1 µg/L, respectively. About 83 % of these samples contained As concentrations exceeding WHO drinking water guideline of 10 µg/L. The mean values of Mn and Ba in groundwater from Chuyen Ngoai and Chau Giang were 300 and 657 µg/L and 650 and 468 µg/L, respectively. The mean value of Ba concentration in groundwater in both Chuyen Ngoai and Chau Giang was about 22 % of the samples exceeded the WHO guideline (700 µg/L). Arsenic concentrations in human urine of residents from Chuyen Ngoai and Chau Giang were the range from 8.6 to 458 µg/L. The mean values of Mn and Ba in human urine of local people from Chuyen Ngoai were 46.9 and 62.8 µg/L, respectively, while those in people from Chau Giang were 25.9 and 45.9 µg/L, respectively. The average daily dose from ingesting arsenic for consuming both untreated and treated groundwater is from 0.02 to 11.5 and 0.003 to 1.6 µg/kg day, respectively. Approximately, 57 % of the families using treated groundwater and 64 % of the families using untreated groundwater could be affected by elevated arsenic exposure.