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The SARS-CoV-2 transmission dynamics in low- and middle-income countries remain poorly understood. This study aimed to estimate the SARS-CoV-2 antibodies seroprevalence in Jakarta, Indonesia, and to increase knowledge of SARS-CoV-2 transmission in urban settings. A population-based serosurvey among individuals aged one year or older was conducted in Jakarta. Employing a multistage sampling design, samples were stratified by district, slum, and non-slum residency, sex, and age group. Blood samples were tested for IgG against three different SARS-CoV-2 antigens. Seroprevalence was estimated after applying sample weights and adjusting for cluster characteristics. In March 2021, this study collected 4,919 respondents. The weighted estimate of seroprevalence was 44.5% (95% CI = 42.5-46.5). Seroprevalence was highest among adults aged 30-49 years, with higher seroprevalence in women and the overweight/obese group. Respondents residing in slum areas were 1.3-fold more likely to be seropositive than non-slum residents. It was estimated that4,717,000 of Jakarta's 10.6 million residents had prior SARS-CoV-2 infection. This suggests that approximately 10 infections were undiagnosed/underreported for every reported case. About one year after the first COVID-19 case was confirmed, close to half of Jakarta's residents have been infected by SARS-CoV-2.

Background: The dynamics of SARS CoV-2 transmission among urban centers in low- and middle-income countries (LMICs) remains poorly understood. We aimed to estimate the seroprevalence of SARS CoV-2 antibodies in Jakarta, Indonesia – the country in Southeast Asia with the highest number of reported cases and deaths, to increase knowledge of SARS CoV-2 transmission in large urban settings in Southeast Asia. Methods: We conducted a population-based serosurvey among individuals aged one year or older across Jakarta’s six districts. A stratified multi-stage sampling design was employed. Samples were stratified by district, slum and non-slum residency, sex, and age-group. Participants were interviewed to collect information on socio-demographic characteristics, weight and height measurements, and a history of COVID-19 diagnosis and/or recent contact. Blood samples were collected and tested for IgG against three different SARS-CoV-2 antigens using the Human IgG Tetracore® FlexImmArray™ SARS-CoV-2 Human IgG test. Seroprevalence was estimated after applying sample weights and adjusting for cluster characteristics. Findings: During March 2021, 4,919 individuals were enrolled in the study. The weighted estimate of seroprevalence was 44·5% (95% CI 42·5-46·5). Seroprevalence was highest among adults 30-49 years old, with higher seroprevalence detected in women and among those with a body mass index that was overweight or obese. Respondents residing in slum areas were 1·3-fold more likely to be seropositive than non-slum residents. We estimated that 4,717,000 of Jakarta’s 10·6 million residents had prior SARS CoV-2 infection. These findings suggest that for every reported confirmed case, approximately 10 infections were undiagnosed or underreported. Interpretation: Approximately one year after the first cases of COVID-19 were confirmed, close to half of Jakarta’s residents have been infected by SARS CoV-2. Urban centers in LMICs remain the places in the world most vulnerable to SARS CoV-2 transmission, as well as its adverse health and social consequences. Funding: Provincial Government of Jakarta, CDC, Eijkman Institute for Molecular Biology-National Research and Innovation Agency Declaration of Interest: All authors declare no conflict of interest. Ethical Approval: The study protocol was approved by the Ethics Committee of University of Atmajaya (No 1245A/III/LPPM.PM.10.05/11/2020).

Advances in high-throughput proteomic approaches have provided substantial momentum to novel disease-biomarker discovery research and have augmented the quality of clinical studies. Applications based on multiplexed microsphere suspension array technology are making strong in-roads into the clinical diagnostic/prognostic practice. Conventional proteomic approaches are designed to discover a broad set of proteins that are associated with a specific medical condition. In comparison, multiplex microsphere immunoassays use quantitative measurements of selected set(s) of specific/particular molecular markers such as cytokines, chemokines, pathway signaling or disease-specific markers for detection, metabolic disorders, cancer, and infectious agents causing human, plant and animal diseases. This article provides a foundation to the multiplexed microsphere suspension array technology, with an emphasis on the improvements in the technology, data analysis approaches, and applications to translational and clinical research with implications for personalized and precision medicine.

Single-domain antibodies (sdAb), recombinantly produced variable heavy domains derived from the unconventional heavy chain antibodies found in camelids, provide stable, well-expressed binding elements with excellent affinity that can be tailored for specific applications through protein engineering. Complex matrices, such as plasma and serum, can dramatically reduce assay sensitivity. Thus, to achieve highly sensitive detection in complex matrices a highly efficient assay is essential. We produced sdAb as genetically linked dimers, and trimers, each including SpyTag at their C-terminus. The constructs were immobilized onto dyed magnetic microspheres to which SpyCatcher had been coupled and characterized in terms of their performance as capture reagents in sandwich assays. Initial tests on the ability of oriented monomer, dimer, and trimer captures to improve detection versus unoriented constructs in an assay for staphylococcal enterotoxin B spiked into buffer showed the oriented dimer format provided the best sensitivity while offering robust protein production. Thus, this format was utilized to improve a sdAb-based assay for the detection of dengue virus (DENV) nonstructural protein 1 (NS1) in serum. Detection of NS1 from each of the four DENV serotypes spiked into 50% normal human serum was increased by at least a factor of 5 when using the oriented dimer capture. We then demonstrated the potential of using the oriented dimer capture to improve detection of NS1 in clinical samples. This general method should enhance the utility of sdAb incorporated into any diagnostic assay, including those for high consequence pathogens.

Arthropod-borne viruses (Arboviruses) constitute a serious threat to global health by causing significant mortality and morbidity. Recent years have seen the emergence of arboviruses due to climatic changes, the adaptation of mosquitoes, and other arthropods to a newer geographic area, urbanization, and increased global travel and trade. Currently, most serosurveillance programs focus on single pathogen testing that may miss the prevalent pathogen or misdiagnose due to the presence of cross-reacting antibodies from closely related arboviruses. In the wake of the 2015–2016 Zika virus outbreaks, we developed a multiplex suspension array for the detection of IgG antibodies and avidity to multiple analytes of arboviruses on the Luminex platform to overcome these limitations. We used optically coded magnetic microspheres to immobilize antigens from 10 different arboviruses, namely, Zika (ZIKV), Dengue all four serotypes (DENV 1–4), West Nile (WNV), Japanese Encephalitis (JEV), Yellow Fever (YFV), Tick-Borne Encephalitis (TBEV), and Chikungunya (CHIKV. This 18-plex assay also includes five different internal controls that assure the assay and reagent performance. Initial characterization of the platform was performed using experimentally infected primate samples collected longitudinally before and after infection with ZIKV. In this paper, we describe the results of the evaluation of this multiplex platform using over 400 well-characterized healthy and diseased state human serum and plasma samples from various commercial and collaborating resources. We conclude that this assay provides a relevant tool for efficient monitoring of population based arboviral antibodies in endemic areas and also for detection of outbreaks.

This paper describes the spatial and temporal distribution of cases, demographic characteristics of patients, and clinical manifestations of Zika virus (ZIKV) during the 2016 outbreak in Grenada. The first reported case was recorded in St. Andrew Parish in April, and the last reported case was seen in November, with peak transmission occurring in the last week of June, based on test results. Data were collected from a total of 514 patients, of whom 207 (40%) tested positive for ZIKV. No evidence was found that testing positive for ZIKV infection was related to age, gender, or pregnancy status. Clinical presentation with rash (OR = 2.4, 95% CI = 1.5 to 3.7) or with lymphadenopathy (OR = 1.7, 95% CI = 1.0 to 2.9) were the only reported symptoms consistent with testing positive for ZIKV infection. During the Zika outbreak, the infection rate was 20 clinical cases per 10,000 in the population compared to 41 cases per 10,000 during the chikungunya outbreak in Grenada in 2014 and 17 cases per 10,000 during the dengue outbreak in 2001-2002. Even though the country has employed vector control programs, with no apparent decrease in infection rates, it appears that new abatement approaches are needed to minimize morbidity in future arbovirus outbreaks.

In this work we investigate the interplay between flow and boundary condition effects on the orientation field of a thermotropic nematic liquid crystal under flow and confinement in a microfluidic device. Two types of experiments were performed using synchrotron small-angle X-ray-scattering (SAXS). In the first, a nematic liquid crystal flows through a square-channel cross section at varying flow rates, while the nematic director orientation projected onto the velocity/velocity gradient plane is measured using a 2D detector. At moderate-to-high flow rates, the nematic director is predominantly aligned in the flow direction, but with a small tilt angle of ∼±11° in the velocity gradient direction. The director tilt angle is constant throughout most of the channel width but switches sign when crossing the center of the channel, in agreement with the Ericksen–Leslie–Parodi (ELP) theory. At low flow rates, boundary conditions begin to dominate, and a flow profile resembling the escaped radial director configuration is observed, where the director is seen to vary more smoothly from the edges (with homeotropic alignment) to the center of the channel. In the second experiment, hydrodynamic focusing is employed to confine the nematic phase into a sheet of liquid sandwiched between two layers of Triton X-100 aqueous solutions. The average nematic director orientation shifts to some extent from the flow direction toward the liquid boundaries, although it remains unclear if one tilt angle is dominant through most of the nematic sheet (with abrupt jumps near the boundaries) or if the tilt angle varies smoothly between two extreme values (∼90 and 0°). The technique presented here could be applied to perform high-throughput measurements for assessing the influence of different surfactants on the orientation of nematic phases and may lead to further improvements in areas such as boundary lubrication and clarifying the nature of defect structures in LC displays.

The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A means to achieve this goal is to create synthetic polymers of defined sequence where all relevant folding information is incorporated into a single polymer strand. We present here the aqueous self-assembly of peptoid polymers (N-substituted glycines) into ultrathin, two-dimensional highly ordered nanosheets, where all folding information is encoded into a single chain. The sequence designs enforce a two-fold amphiphilic periodicity. Two sequences were considered: one with charged residues alternately positive and negative (alternating patterning), and one with charges segregated in positive and negative halves of the molecule (block patterning). Sheets form between pH 5 and 10 with the optimal conditions being pH 6 for the alternating sequence and pH 8 for the block sequence. Once assembled, the nanosheets remain stable between pH 6 and 10 with observed degradation beginning to occur below pH 6. The alternating charge nanosheets remain stable up to concentrations of 20% acetonitrile, whereas the block pattern displayed greater robustness remaining stable up to 30% acetonitrile. These observations are consistent with expectations based on considerations of the molecules' electrostatic interactions. This study represents an important step in the construction of abiotic materials founded on biological informatic and folding principles. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 586–595, 2011.

Arboviruses cause a serious public health problem in tropical and subtropical countries and are emerging as a threat in western hemisphere also. Rapid and accurate detection of these infections can help in improving patient care and disease control. The cross-reactivity of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to ZIKV with dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV) and some other related flaviviruses poses a significant challenge for an accurate detection of ZIKV infection in serological assay such as IgM capture ELISA. To overcome these challenges we developed a multiplex serological assay that will simultaneously detect antibody response to ZIKV, other related flaviviruses and Chikungunya virus (CHIKV). Various recombinant arboviral antigens were coupled to optically encoded microspheres from Luminex Corporation. This fluorescent microsphere immunoassay was used to differentiate between recent, past, and/or co-infections that may occur in endemic regions. We also developed an easy detection algorithm for quick multiplex data analysis to differentiate ZIKV IgM response from other arboviruses. This rapid assay can be performed from sample to answer in less than 2 hours. This assay was validated with more than 200 samples procured from commercial sources; ZIKV, DENV, CHIKV, and WNV positive samples for sensitivity; EBV, CMV, flu positive samples, and normal samples for specificity. We obtained good concordance with the results provided by the vendor. Results indicated that serological response to ZIKV NS1 antigen is more specific than ZIKV envelope antigen. A significant IgM antibodies to ZIKV envelope antigen was detected in samples that were positive for other flaviviruses.

Microfluidics-based separation of biomolecules has numerous applications, including fundamental characterization of biomolecules, sequencing of genomes for biological functions, biometric fingerprinting, and identification of pathogens and genetic diseases. One of the main drawbacks, however, for making microfluidic based separations more commercially viable is the non-specific adsorption of biomolecules at the channel walls during separations. Herein, we compare five commonly employed surface coatings, and evaluate their performance in terms of successful silanization of channel surface walls, long term stability, and antifouling performance, using BSA or IgG as model proteins. We compare adsorption of fluorescently-tagged proteins on glass slides with those confined within channels, showing similar behavior with static measurements, but differences when incorporating electrokinetic flow. Based on these data, we find that MPEG is an effective surface coating for applications where long term stability is critical. However, for separation experiments, where the channel is used shortly after coating, a silanized zwitterionic sultone has superior anti-fouling characteristics.

A fundamental study of peptide transport behavior provides information about length dependent transport and sequence structure relationships. In these highly accurate investigations of peptide electrokinetic properties and peptide conformations using a Micro-Electro-Mechanical Systems (MEMS)-fabricated capillary zone electrophoresis (CZE) platform, we demonstrate accurate and repeatable separations of polyglutamate peptides of two different lengths (10 and 20 amino acids). We investigate this separation phenomenon as a function of electrolyte concentration and ionic composition, counter-ion radius, ionic strength and pH. We report a length-dependent counter-ion species selectivity and enhanced separation at pH much higher than the pKa of the peptides that can aid in understanding the relationship between the function of biological peptides and their microenvironments. The ability of our platform to optimize separation resolution between very similar peptides is promising for distinguishing molecular characteristics of peptides and can contribute to resolving current challenges in peptidomics.

Human immunoglobulin (IgM) antibody capture enzyme linked immunosorbent assay (MAC-ELISA) is recommended by US Centers for Disease Control (CDC) to detect the Zika Virus (ZIKV) infection in samples collected after few days of the onset of disease. However, the cross-reactivity of IgM and immunoglobulin G (IgG) antibodies to ZIKV with dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV) and some other related flaviviruses poses a significant challenge for an accurate detection of ZIKV infection in a singleplex serological assay. To overcome these challenges we developed a novel multiplex serological assay that will simultaneously detect antibody response to ZIKV, other related flaviviruses and Chikungunya virus (CHIKV). Various recombinant arboviral antigens were coupled to optically-coded microspheres from Luminex Corporation. This fluorescent labeled microsphere assay was used to differentiate between recent, past arbovirus infections, or co-infections that may occur in endemic regions. We used plasma samples from non-human primates (NHPs) prior to and after ZIKV infection for longitudinal assessment of IgM and IgG antibody responses for evaluation of this method. 37 blood samples from 5 different animals challenged with either African strain or Asian lineage strain of ZIKV were analyzed for antibody responses to multiple antigens included in this test. We developed a detection algorithm for automation of IgM result analysis to differentiate ZIKV IgM response from other arboviruses. Thus this multiplex arbovirus assay has great promise for testing human samples for detecting ZIKV infection.

Single-stranded nucleic acid molecules can interact under certain conditions with other nucleic acids in the regions of base complementarily to form double-stranded hybrid molecules. From measurement of kinetics of the hybridisation and the extent of hybrid formation, information on nucleotide sequence heterogeneity of nucleic acid fractions, sequence properties of purified classes of molecules or the degree of homology between different samples of nucleic acids can be obtained. A specific deoxyribonucleic acid or ribonucleic acid sequence with an identifiable marker can be used as a nucleic acid probe. This paper reviews the use of nucleic acid probes for classifying the microorganisms and their detection in clinical or environmental samples.

Two-dimensional nanomaterials play a critical role in biology (e.g., lipid bilayers) and electronics (e.g., graphene), but are difficult to directly synthesize with a high level of precision. Biomimetic peptoid nanosheet bilayers are a versatile synthetic platform for constructing multifunctional, precisely ordered two-dimensional nanostructures. Here we show that nanosheet formation occurs through an unusual monolayer intermediate at the air-water interface. Lateral compression of a self-assembled peptoid monolayer beyond a critical collapse pressure results in the irreversible production of nanosheets. An unusual thermodynamic cycle is employed on a preparative scale, where mechanical energy is used to buckle an intermediate monolayer into a more stable nanosheet. Detailed physical studies of the monolayer-compression mechanism revealed a simple preparative technique to produce nanosheets in 95% overall yield, by cyclical monolayer compressions in a rotating closed vial. Compression of monolayers into stable, free-floating products may be a general and preparative approach to access two-dimensional nanomaterials.View Large Image | View Hi-Res Image | Download PowerPoint Slide