Browsing by Author "Wang, Shuyi"
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Item Restricted Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.(PLoS Pathog, 2012) Li, Hui; Stoddard, Mark B; Wang, Shuyi; Blair, Lily M; Giorgi, Elena E; Parrish, Erica H; Learn, Gerald H; Hraber, Peter; Goepfert, Paul A; Saag, Michael S; Denny, Thomas N; Haynes, Barton F; Hahn, Beatrice H; Ribeiro, Ruy M; Perelson, Alan S; Korber, Bette T; Bhattacharya, Tanmoy; Shaw, George MA precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures.Item Open Access Microbial Impacts of Selected Pharmaceutically Active Compounds Found in Domestic Wastewater Treatment Plants(2009) Wang, ShuyiLarge amounts of human pharmaceutical products are consumed worldwide. Many drugs and their metabolites, referred to as pharmaceutically active compounds (PhACs), are not fully metabolized prior to household discharge resulting in their common occurrence in wastewater treatment plants (WWTPs). In most instances, WWTPs present the first treatment opportunity for removing PhACs and preventing significant environmental exposure. Because most municipal WWTPs rely on the microbial component of the activated sludge process, there is a need to estimate the influence of PhACs in wastewater influent on the activated sludge microbial communities and the treatment performance of WWTPs. The objective of this dissertation was to determine the impact of selected PhACs (i.e., ketoprofen, naproxen, clofibric acid, carbamazepine and gemfibrozil) on activated sludge microorganisms and key individual microbial species in domestic wastewater treatment. Analyses were performed in batch reactors initially and then in laboratory-scale sequencing batch reactors (SBR) which mimic WWTP operations. Ammonia oxidizing bacteria (AOB) were selected as indicator organisms because of their importance in wastewater treatment and demonstrated sensitiveness to toxic compounds.
The batch experiments results suggested that microbial growth inhibition was correlated to organic loadings. In the presence of 0.2% (v/v) ethanol, significant inhibition, ranging from 34 to 43%, was observed for all PhACs other than clofibric acid.
Nitrification inhibition studies using Nitrosomonas europaea, a model AOB strain showed that ketoprofen, naproxen, carbamazepine and gemfibrozil inhibited nitrite production. The corresponding maximum nitrification inhibition rates were 25, 29, 22 and 26%, respectively. Inhibition was shown to increase with PhAC concentration for concentrations greater than 0.1 µM. Results from membrane integrity tests suggest that the inhibition may be due to the disturbance of the cell membrane by PhACs and such inhibition was shown to be irreversible.
Even though PhACs were shown to inhibit the nitrification rate in pure culture studies, the performance of SBRs exposed to individual PhACs was not adversely affected neither in terms of COD nor ammonia removal. Microbial fingerprinting for both total bacteria and AOB confirmed that no significant shifts occurred when microbial communities were exposed to PhACs. However, some PhACs introduced in binary mixture were found to both inhibit the nitrification of N. europaea as well as the performance of SBRs. The mixture composed of 0.5 μM ketoprofen and 0.5 μM naproxen showed significant inhibition (25%) on the nitrite production of N. europaea although neither 0.5 μM ketoprofen nor 0.5 μM naproxen had significant effect when presented alone. Similarly, both COD and ammonia removal were significantly impacted by binary mixtures of PhACs. These results suggest that mixture effects can play an important role in an overall treatment's nitrification potential and this phenomenon should be further investigated.
Item Open Access New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure.(Journal of virology, 2021-03-03) Li, Hui; Wang, Shuyi; Lee, Fang-Hua; Roark, Ryan S; Murphy, Alex I; Smith, Jessica; Zhao, Chengyan; Rando, Juliette; Chohan, Neha; Ding, Yu; Kim, Eunlim; Lindemuth, Emily; Bar, Katharine J; Pandrea, Ivona; Apetrei, Cristian; Keele, Brandon F; Lifson, Jeffrey D; Lewis, Mark G; Denny, Thomas N; Haynes, Barton F; Hahn, Beatrice H; Shaw, George MPreviously, we showed that substitution of HIV-1 Env residue 375-Ser by bulky aromatic residues enhances binding to rhesus CD4 and enables primary HIV-1 Envs to support efficient replication as simian-human immunodeficiency virus (SHIV) chimeras in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing SHIVs containing ten primary Envs corresponding to HIV-1 subtypes A, B, C, AE and AG. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4+ T cells, but only one replicated efficiently in primary rhesus cells. This was a subtype AE SHIV that naturally contained His at Env375. Replacement of wildtype Env375 residues by Trp, Tyr, Phe or His in the other nine SHIVs led to efficient replication in rhesus CD4+ T cells in vitro and in vivo Nine SHIVs containing optimized Env375 alleles were grown large-scale in primary rhesus CD4+ T cells to serve as challenge stocks in preclinical prevention trials. These virus stocks were genetically homogeneous, native-like in Env antigenicity and tier-2 neutralization sensitivity, and transmissible by rectal, vaginal, penile, oral or intravenous routes. To facilitate future SHIV constructions, we engineered a simplified second-generation design scheme and validated it in RMs. Overall, our findings demonstrate that SHIVs bearing primary Envs with bulky aromatic substitutions at Env375 consistently replicate in RMs, recapitulating many features of HIV-1 infection in humans. Such SHIVs are efficiently transmitted by mucosal routes common to HIV-1 infection and can be used to test vaccine efficacy in preclinical monkey trials.ImportanceSHIV infection of Indian rhesus macaques is an important animal model for studying HIV-1 transmission, prevention, immunopathogenesis and cure. Such research is timely, given recent progress with active and passive immunization and novel approaches to HIV-1 cure. Given the multifaceted roles of HIV-1 Env in cell tropism and virus entry, and as a target for neutralizing and non-neutralizing antibodies, Envs selected for SHIV construction are of paramount importance. Until recently, it has been impossible to strategically design SHIVs bearing clinically relevant Envs that replicate consistently in monkeys. This changed with the discovery that bulky aromatic substitutions at residue Env375 confer enhanced affinity to rhesus CD4. Here, we show that 10 new SHIVs bearing primary HIV-1 Envs with residue 375 substitutions replicated efficiently in RMs and could be transmitted efficiently across rectal, vaginal, penile and oral mucosa. These findings suggest an expanded role for SHIVs as a model of HIV-1 infection.Item Open Access Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth.(Science (New York, N.Y.), 2020-11-19) Roark, Ryan S; Li, Hui; Williams, Wilton B; Chug, Hema; Mason, Rosemarie D; Gorman, Jason; Wang, Shuyi; Lee, Fang-Hua; Rando, Juliette; Bonsignori, Mattia; Hwang, Kwan-Ki; Saunders, Kevin O; Wiehe, Kevin; Moody, M Anthony; Hraber, Peter T; Wagh, Kshitij; Giorgi, Elena E; Russell, Ronnie M; Bibollet-Ruche, Frederic; Liu, Weimin; Connell, Jesse; Smith, Andrew G; DeVoto, Julia; Murphy, Alexander I; Smith, Jessica; Ding, Wenge; Zhao, Chengyan; Chohan, Neha; Okumura, Maho; Rosario, Christina; Ding, Yu; Lindemuth, Emily; Bauer, Anya M; Bar, Katharine J; Ambrozak, David; Chao, Cara W; Chuang, Gwo-Yu; Geng, Hui; Lin, Bob C; Louder, Mark K; Nguyen, Richard; Zhang, Baoshan; Lewis, Mark G; Raymond, Donald D; Doria-Rose, Nicole A; Schramm, Chaim A; Douek, Daniel C; Roederer, Mario; Kepler, Thomas B; Kelsoe, Garnett; Mascola, John R; Kwong, Peter D; Korber, Bette T; Harrison, Stephen C; Haynes, Barton F; Hahn, Beatrice H; Shaw, George MNeutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution strikingly similar to those in humans. This included conserved immunogenetic, structural and chemical solutions to epitope recognition and precise Env-am ino acid substitutions, insertions and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2-apex mode of recognition like that of human bNAbs PGT145/PCT64-35S. Another rhesus antibody bound the CD4-binding site by CD4 mimicry mirroring human bNAbs 8ANC131/CH235/VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.Item Restricted Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.(PLoS One, 2010-08-20) Fischer, Will; Ganusov, Vitaly V; Giorgi, Elena E; Hraber, Peter T; Keele, Brandon F; Leitner, Thomas; Han, Cliff S; Gleasner, Cheryl D; Green, Lance; Lo, Chien-Chi; Nag, Ambarish; Wallstrom, Timothy C; Wang, Shuyi; McMichael, Andrew J; Haynes, Barton F; Hahn, Beatrice H; Perelson, Alan S; Borrow, Persephone; Shaw, George M; Bhattacharya, Tanmoy; Korber, Bette TWe used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely infected subjects, and modeled viral evolution during the critical first weeks of infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because of limited sampling; now, we have greatly increased our confidence in this observation through modeling the observed earliest sample diversity based on vastly more extensive sampling. Conventional sequencing of HIV-1 from acute/early infection has shown different patterns of escape at different epitopes; we investigated the earliest escapes in exquisite detail. Over 3-6 weeks, ultradeep sequencing revealed that the virus explored an extraordinary array of potential escape routes in the process of evading the earliest CD8 T-lymphocyte responses--using 454 sequencing, we identified over 50 variant forms of each targeted epitope during early immune escape, while only 2-7 variants were detected in the same samples via conventional sequencing. In contrast to the diversity seen within epitopes, non-epitope regions, including the Envelope V3 region, which was sequenced as a control in each subject, displayed very low levels of variation. In early infection, in the regions sequenced, the consensus forms did not have a fitness advantage large enough to trigger reversion to consensus amino acids in the absence of immune pressure. In one subject, a genetic bottleneck was observed, with extensive diversity at the second time point narrowing to two dominant escape forms by the third time point, all within two months of infection. Traces of immune escape were observed in the earliest samples, suggesting that immune pressure is present and effective earlier than previously reported; quantifying the loss rate of the founder virus suggests a direct role for CD8 T-lymphocyte responses in viral containment after peak viremia. Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape.