Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation.

Genome-wide analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains is essential to better understand infectivity and virulence and to track coronavirus disease 2019 (COVID-19) cases and outbreaks. We performed whole-genome sequencing of 27 SARS-CoV-2 strains isolated between January 2020 and April 2020. A total of 54 mutations in different genomic regions was found. The D614G mutation, first detected in March 2020, was identified in 18 strains and was more likely associated with a lower cycle threshold (<25) in real-time reverse-transcription polymerase chain reaction diagnostic tests than the original D614 (prevalence ratio = 2.75; 95% confidence interval, 1.19-6.38). The integration of sequencing and epidemiological data suggests that SARS-CoV-2 transmission in both quarantine areas and in the community in Vietnam occur at the beginning of the epidemic although the country implemented strict quarantine quite early, with strict contact tracing, and testing. These findings provide insights into the nature of the epidemic, as well as shape strategies for COVID-19 prevention and control in Vietnam.

Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam.

In January 2020, we identified two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients in a familial cluster with one person coming from Wuhan, China. The complete genome sequences of two SARS-CoV-2 strains isolated from these patients were identical and 99.98% similar to strains isolated in Wuhan. This is genetically suggestive of human-to-human transmission of SARS-CoV-2 and indicates Wuhan as the most plausible origin of the early outbreak in Vietnam. The younger patient had a mild upper respiratory illness and a brief viral shedding, whereas the elderly with multi-morbidity had pneumonia, prolonged viral shedding, and residual lung damage. The evidence of nonsynonymous substitutions in the ORF1ab region of the viral sequence warrants further studies.

Molecular recognition and packing frustration in a helical protein.

Biomolecular recognition entails attractive forces for the functional native states and discrimination against potential nonnative interactions that favor alternate stable configurations. The challenge posed by the competition of nonnative stabilization against native-centric forces is conceptualized as frustration. Experiment indicates that frustration is often minimal in evolved biological systems although nonnative possibilities are intuitively abundant. Much of the physical basis of minimal frustration in protein folding thus remains to be elucidated. Here we make progress by studying the colicin immunity protein Im9. To assess the energetic favorability of nonnative versus native interactions, we compute free energies of association of various combinations of the four helices in Im9 (referred to as H1, H2, H3, and H4) by extensive explicit-water molecular dynamics simulations (total simulated time > 300 µs), focusing primarily on the pairs with the largest native contact surfaces, H1-H2 and H1-H4. Frustration is detected in H1-H2 packing in that a nonnative packing orientation is significantly stabilized relative to native, whereas such a prominent nonnative effect is not observed for H1-H4 packing. However, in contrast to the favored nonnative H1-H2 packing in isolation, the native H1-H2 packing orientation is stabilized by H3 and loop residues surrounding H4. Taken together, these results showcase the contextual nature of molecular recognition, and suggest further that nonnative effects in H1-H2 packing may be largely avoided by the experimentally inferred Im9 folding transition state with native packing most developed at the H1-H4 rather than the H1-H2 interface.

Applications of engineered biochar in remediation of heavy metal(loid)s pollution from wastewater: Current perspectives toward sustainable development goals.

Environmental pollution of heavy metal(loid)s (HMs) caused adverse impacts, has become one of the emerging concerns and challenges worldwide. Metal(loid)s can pose significant threats to living organisms even when present in trace levels within environmental matrices. Extended exposure to these substances can lead to adverse health consequences in humans. Removing HM-contaminated water and moving toward sustainable development goals (SDGs) is critical. In this mission, biochar has recently gained attention in the environmental sector as a green and alternative material for wastewater removal. This work provides a comprehensive analysis of the remediation of typical HMs by biochars, associated with an understanding of remediation mechanisms, and gives practical solutions for ecologically sustainable. Applying engineered biochar in various fields, especially with nanoscale biochar-aided wastewater treatment approaches, can eliminate hazardous metal(loid) contaminants, highlighting an environmentally friendly and low-cost method. Surface modification of engineered biochar with nanomaterials is a potential strategy that positively influences its sorption capacity to remove contaminants. The research findings highlighted the biochars' ability to adsorb HM ions based on increased specific surface area (SSA), heightened porosity, and forming inner-sphere complexes with oxygen-rich groups. Utilizing biochar modification emerged as a viable approach for addressing lead (Pb), cadmium (Cd), arsenic (As), mercury (Hg), and chromium (Cr) pollution in aqueous environments. Most biochars investigated demonstrated a removal efficiency >90 % (Cd, As, Hg) and can reach an impressive 99 % (Pb and Cr). Furthermore, biochar and advanced engineered applications are also considered alternative solutions based on the circular economy.

Design of a protein-targeted DNA aptamer using atomistic simulation.

The concentrations of specific macromolecular species can be quantified using diagnostic tools that rely on molecular recognition by nucleic acid aptamers. One such approach involves the formation of osmium tetroxide 2,2'-bipyridine protein adducts, followed by electrochemical detection of analytes that bind specifically to electrode-tethered aptamers. In conjunction with a 27-mer DNA aptamer that binds specifically to exosite II on human alpha thrombin, this technique permits, in theory, a highly sensitive diagnostic tool for the quantification of serum thrombin levels. However, thrombin's aptamer binding site is lined by two tryptophan residues and the conjugation of bulky osmium groups to these residues weakens aptamer binding by an estimated 4 to 12 kcal/mol, undermining detection sensitivity. Therefore, we have rationally modified this DNA aptamer to strengthen its thrombin binding in the presence of conjugated osmium. Specifically, aptamers carrying long hydrophobic thymine derivatives in place of guanine 21 have binding affinities for osmium-conjugated thrombin that are enhanced by 10 to 15 kcal/mol, suggesting that these modified aptamers may be effective in a highly sensitive electrochemical sensor for the quantification of low concentrations of thrombin. Our approach of using molecular simulation to subtly re-engineer a DNA aptamer may be generally applicable for the optimization of other macromolecular binding interfaces.Communicated by Ramaswamy H. Sarma.

Computational approaches to the rational design of nanoemulsions, polymeric micelles, and dendrimers for drug delivery.

Nanoparticles are promising drug delivery systems whose selection and optimization can be gainfully conducted by theoretical methods. This review is targeted to experimentalists who are interested in enhancing their time and cost efficiency through the incorporation of theoretical approaches. This review thus begins with a brief overview of theoretical approaches available to the development of contemporary drug delivery systems. Approaches include solubility parameters, Flory-Huggins theory, analytical predictions of partition coefficients, and molecular simulations. These methods are then compared as they relate to the optimization of drug-material pairs using important performance-related parameters including the size of the delivery particles, their surface properties, and the compatibility of the materials with the drug to be sequestered. Next, this review explores contemporary efforts to optimize a selection of existing nanoparticle platforms, including nanoemulsions, linear and star-shaped block co-polymer micelles, and dendrimers. The review concludes with an outlook on the challenges remaining in the successful application of these theoretical methods to the development of new drug formulations. FROM THE CLINICAL EDITOR: This paper is a comprehensive review of the many approaches available to assist the optimization of nanoparticle drug delivery vehicles, including a detailed discussion of methodological applicability, a survey of contemporary efforts to optimize a selection of frequently used nanoparticle subtypes.

Two Liberibacter Proteins Combine to Suppress Critical Innate Immune Defenses in Citrus.

We adopted a systems-based approach to determine the role of two Candidatus Liberibacter asiaticus (CLas) proteins, LasP 235 and Effector 3, in Huanglongbing (HLB) pathogenesis. While a published work suggests the involvement of these CLas proteins HLB pathogenesis, the exact structure-based mechanism of their action has not been elucidated. We conducted the following experiments to determine the structure-based mechanisms of action. First, we immunoprecipitated the interacting citrus protein partners of LasP 235 and Effector 3 from the healthy and CLas-infected Hamlin extracts and identified them by Liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Second, we performed a split green fluorescent protein (GFP) assay in tobacco to validate that the interactions observed in vitro are also retained in planta. The notable in planta citrus targets of LasP 235 and Effector 3 include citrus innate immune proteins. Third, in vitro and in planta studies were performed to show that LasP 235 and Effector 3 interact with and inhibit the functions of multiple citrus proteins belonging to the innate immune pathways. These inhibitory interactions led to a high level of reactive oxygen species, blocking of bactericidal lipid transfer protein (LTP), and induction of premature programed cell death (PCD), all of which are beneficial to CLas lifecycle and HLB pathogenesis. Finally, we performed molecular dynamics simulations to visualize the interactions of LasP 235 and Effector 3, respectively, with LTP and Kunitz protease inhibitor. This led to the design of an LTP mimic, which sequestered and blocked LasP 235 and rescued the bactericidal activity of LTP thereby proving that LasP 235 , indeed, participates in HLB pathogenesis.

Seroprevalence of SARS-CoV-2 Neutralizing Antibodies among Blood Donors in Ho Chi Minh City, Vietnam, August-November 2020.

Relatively little is known about the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG antibodies and COVID-19-related behaviors in the general population in Vietnam, where the first case of COVID-19 was detected on January 22, 2020. We surveyed a group of 885 blood donors at community blood donation sessions in Ho Chi Minh City from August 27 to November 7, 2020. Blood was collected to test for SARS-CoV-2 IgG antibodies using the plaque reduction neutralization test. We adjusted the seroprevalence by weight for ages 18 to 59 years old obtained from the 2019 population census. The weighted seroprevalence estimate for SARS-CoV-2 neutralizing IgG antibodies was 0.20% (95% CI, 0.05-0.81). Reports of usually or always using a mask in public places were observed at high levels of 28.6% and 67.5%, respectively. The percentages of usually or always washing hands with soap or disinfecting with hand sanitizer after touching items in public places were 48.0% and 37.6%, respectively. Although our findings suggest undocumented exposure to the virus, the seroprevalence of SARS-CoV-2 IgG antibodies among blood donors was low in this city.

Combination drug delivery strategy for the treatment of multidrug resistant ovarian cancer.

The onset of multidrug resistance (MDR) in ovarian cancer is one of the main causes of treatment failure and low survival rates. Inadequate drug exposure and treatment-free periods due to intermittent chemotherapy select for cancer cells overexpressing drug efflux transporters, resulting in resistant disease. The present study examines the sustained administration of the chemotherapeutic agent docetaxel (DTX) alone and in combination with cepharanthine (CEP), a potent drug efflux transporter inhibitor. DTX and CEP were delivered via the intraperitoneal route in a sustained manner using an injectable polymer-lipid formulation. In vitro, the combination strategy resulted in significantly (p < 0.05) more apoptosis, greater intracellular accumulation of DTX, and lower DTX efflux in ovarian cancer cells showing the MDR phenotype. In vivo, sustained treatment with DTX and CEP showed significantly greater (p < 0.05) tumor inhibition (91 ± 4%) in a murine model of multidrug resistant ovarian cancer compared to sustained DTX treatment (76 ± 6%) and was more than twice as efficacious as intermittent DTX treatment. Overall findings from these studies highlight the impact of sustained delivery of monotherapy and combination therapy in the management of refractory ovarian cancer displaying the MDR phenotype.

Rational design of antimicrobial peptides targeting Gram-negative bacteria.

Membrane-targeting host antimicrobial peptides (AMPs) can kill or inhibit the growth of Gram-negative bacteria. However, the evolution of resistance among microbes poses a substantial barrier to the long-term utility of the host AMPs. Combining experiment and molecular dynamics simulations, we show that terminal carboxyl capping enhances both membrane insertion and antibacterial activity of an AMP called P1. Furthermore, we show that a bacterial strain with evolved resistance to this peptide becomes susceptible to P1 variants with either backbone capping or lysine-to-arginine substitutions. Our results suggest that cocktails of closely related AMPs may be useful in overcoming evolved resistance.

Maternal and neonatal outcomes related to Zika virus in pregnant women in Southern Vietnam: An epidemiological and virological prospective analysis.

BACKGROUND: In 2016-2017, 68 women in Southern Vietnam had RT-PCR confirmed Zika virus (ZIKV) infection during pregnancy. We report here the outcomes of the pregnancies and the virological analyses related to this outbreak. METHODS: We collected clinical and epidemiological information from the women who were enrolled in the study. Medical records related to the pregnancy in 2016-2017 were retrieved for those who were not able to be enrolled in the study. Children born to women with ZIKV infection during pregnancy were also enrolled. Serum samples were evaluated for presence of ZIKV antibodies. Phylogenetic analyses were performed on Zika virus genomes sequenced from the 2016-2017 serum samples. FINDINGS: Of the 68 pregnancies, 58 were livebirths and 10 were medically terminated. Four of the medical records from cases of fetal demise were able to be retrieved, of which one was consistent with congenital ZIKV infection. Of the 58 women with a livebirth, 21 participated in the follow-up investigation. All but two women had serologic evidence of ZIKV infection. Of the 21 children included in the study (mean age: 30.3 months), 3 had microcephaly at birth. No other clinical abnormalities were reported and no differences in neurodevelopment were observed compared to a control group. Phylogenetic analysis revealed a clade within the ZIKV Asian lineage and branch at the root of samples from the 2013-2014 French Polynesian outbreak. The prM S139N mutation was not observed. INTERPRETATION: We have been able to demonstrate a clade within the ZIKV Asian lineage implicated in adverse pregnancy outcomes in Southern Vietnam. FUNDING: INCEPTION project (PIA/ANR-16-CONV-0005) and a grant received from BNP Paribas Simplidon.

Enhancement of docetaxel solubility via conjugation of formulation-compatible moieties.

Computer-based theoretical calculations were employed to direct the design of docetaxel conjugates with enhanced solubility in the internal phase of a nano-emulsion formulation. The theoretically-identified optimal docetaxel conjugates were synthesized by direct attachment of lauroyl moieties through an ester linkage to docetaxel. In comparison to docetaxel, the conjugates exhibited significantly improved solubility in oil, as predicted by our theoretical calculations. This contributed to high drug entrapment efficiencies (up to 97%) and a high drug loading capacity (5.7% w/w) for the docetaxel conjugates. The mono-substitution of an acyl group at C-2' of docetaxel resulted in a conjugate with 37- to 46-fold lower cytotoxicity than that of the parent drug in two human cancer cell lines. Importantly, the activity exerted by the mono-substituted docetaxel on the cancer cells was due in part to the cytotoxicity of the parent drug that was released via hydrolysis of the ester bond between the lauroyl moiety and the drug under biologically relevant conditions. In contrast, di- and tri-substitution of acyl groups at C-2', C-7 and/or C-10 of docetaxel resulted in non-hydrolysable conjugates that were found to be inactive. Overall, our results show that computer-based theoretical calculation is a promising strategy for guiding the enhancement of material-drug compatibility in formulation development. Also, these studies confirm that chemical modification of docetaxel for enhancement of material-drug compatibility should be limited to mono-substitution at C-2' and result in a prodrug that is hydrolysable at a moderate rate under biologically relevant conditions.

Zika preparedness and response in Viet Nam.

The findings and conclusions in this article are those of the authors and do not necessarily represent the official positions of the United States Centers for Disease Control and Prevention.

Glycaemic control in children with neonatal diabetes and type 1 diabetes in Vietnam.

Childhood diabetes care may be suboptimal in resource-poor countries. A cross-sectional study of youths with diabetes aged ≤19 years attending the three major paediatric centres in Vietnam was performed. Diabetes management was documented by questionnaire. Glycated haemoglobin (HbA1c) was measured with a fingerprick blood sample. Multiple linear regression analysis was used to examine factors associated with glycaemic control. In total, 105 patients participated, comprising 93 with type 1 diabetes and 12 with neonatal diabetes. The median age was 11.5 years [interquartile range (IQR) 6.4-14.5 years] and the median duration of diabetes was 2.6 years (IQR 1.5-6.1 years). Patients with type 1 diabetes performed few blood glucose tests per month (median 8, IQR 4-30). Mean HbA1c was higher in patients with type 1 diabetes compared with neonatal diabetes (9.9% vs. 7.5%; P = 0.01). In type 1 diabetes using multivariate analysis, higher HbA1c was associated with older age (ß = 0.3, 95% CI 0.2-0.4; P < 0.001), lower frequency of blood glucose monitoring (ß = -0.06, 95% CI -0.10 to 0.12; P = 0.01) and use of pre-mixed insulin (ß = -1.7, 95% CI -3.4 to 0.0; P = 0.05). In conclusion, international glycaemic control targets for childhood diabetes (HbA1c <7.5%) are not being achieved in Vietnam, and intensive diabetes management is rare. There is an urgent need to address barriers to achieving optimal control in this population.

Predicting the solubility of the anti-cancer agent docetaxel in small molecule excipients using computational methods.

PURPOSE: To develop an in silico model that provides an accurate prediction of the relative solubility of the lipophilic anticancer agent docetaxel in various excipients. MATERIALS AND METHODS: The in silico solubility of docetaxel in the excipients was estimated by means of the solubility (delta) and Flory-Huggins interaction (chi (FH)) parameters. The delta values of docetaxel and excipients were calculated using semi-empirical methods and molecular dynamics (MD) simulations. Cerius(2) software and COMPASS force-field were employed for the MD simulations. The chi (FH) values for the binary mixtures of docetaxel and excipient were also estimated by MD simulations. RESULTS: The values obtained from the MD simulations for the solubility of docetaxel in the various excipients were in good agreement with the experimentally determined values. The simulated values for solubility of docetaxel in tributyrin, tricaproin and vitamin E were within 2 to 6% of the experimental values. MD simulations predicted docetaxel to be insoluble in beta-caryophyllene and this result correlated well with experimental studies. CONCLUSIONS: The MD model proved to be a reliable tool for selecting suitable excipients for the solubilization of docetaxel.