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1.
AJOG Glob Rep ; 3(2): 100192, 2023 May.
Article in English | MEDLINE | ID: covidwho-2297021

ABSTRACT

BACKGROUND: Immune changes that occur during pregnancy may place pregnant women at an increased risk for severe disease following viral infections like SARS-CoV-2. Whether these immunologic changes modify the immune response to SARS-CoV-2 infection during pregnancy is not well understood. OBJECTIVE: This study aimed to compare the humoral immune response to SARS-CoV-2 infection in pregnant and nonpregnant women. The immune response following vaccination for SARS-CoV-2 was also explored. STUDY DESIGN: In this cohort study, 24 serum samples from 20 patients infected with SARS-CoV-2 during pregnancy were matched by number of days after a positive test with 46 samples from 40 nonpregnant women of reproductive age. Samples from 9 patients who were vaccinated during pregnancy were also examined. Immunoglobulin G and immunoglobulin M levels were measured. Trends in the log antibody levels over time and mean antibody levels were assessed using generalized estimating equations. RESULTS: The median number of days from first positive test to sampling was 6.5 in the pregnant group (range, 3-97) and 6.0 among nonpregnant participants (range, 2-97). No significant differences in demographic or sampling characteristics were noted between the groups. No differences in immunoglobulin G or immunoglobulin M levels over time or mean antibody levels were noted among pregnant and nonpregnant participants following SARS-CoV-2 infection for any of the SARS-CoV-2 antigen targets examined (spike, spike receptor-binding domain, spike N-terminal domain, and nucleocapsid). Participants who were vaccinated during pregnancy had higher immunoglobulin G levels than pregnant patients who tested positive for all SARS-CoV-2 targets except nucleocapsid antibodies (all P<.001) and had lower immunoglobulin M spike (P<.05) and receptor-binding domain (P<.01) antibody levels. CONCLUSION: This study suggests that the humoral response following SARS-CoV-2 infection does not seem to differ between pregnant women and their nonpregnant counterparts. These findings should reassure patients and healthcare providers that pregnant patients seem to mount a nondifferential immune response to SARS-CoV-2.

2.
AJOG global reports ; 2023.
Article in English | EuropePMC | ID: covidwho-2264259

ABSTRACT

Background Immune changes that occur during pregnancy may place pregnant women at an increased risk for severe disease following viral infections like SARS-CoV-2. Whether these immunological changes modify immune response to SARS-CoV-2 infection during pregnancy is not well understood. Objective The objective of the present study is to compare humoral immune response to SARS-CoV-2 infection in pregnant and non-pregnant women. Immune response following vaccination for SARS-CoV-2 was also explored. Study Design In the present cohort study, 24 serum samples from 20 patients infected with SARS-CoV-2 during pregnancy were matched on number of days post positive test to 46 samples from 40 non-pregnant women of reproductive age. Samples from nine patients vaccinated during pregnancy were also examined. Immunoglobulin G (IgG) and immunoglobulin M (IgM) antibody levels were measured. Trends in log antibody levels over time and mean antibody levels were assessed using generalized estimating equations. Results Median number of days from first positive test to sampling was 6.5 in the pregnant group (range 3-97) and 6.0 among non-pregnant participants (range 2-97). No significant differences in demographic or sampling characteristics were noted between groups. No differences in IgG or IgM levels over time or mean antibody levels were noted in pregnant and non-pregnant participants following SARS-CoV-2 infection for any of the SARS-CoV-2 antigens targets examined [Spike, Spike Receptor Binding Domain (RBD), Spike N-Terminal Domain (NTD), and Nucleocapsid]. Participants vaccinated during pregnancy had higher IgG levels than pregnant positive patients for all SARS-CoV-2 targets except Nucleocapsid (all p < 0.001), as well as lower IgM Spike (p < 0.05) and RBD (p < 0.01) antibody levels. Conclusions The present study suggests that humoral response following SARS-CoV-2 infection does not appear to differ in pregnant women compared to their non-pregnant counterparts. These findings should reassure patients and healthcare providers that pregnant patients appear to mount a non-differential immune response to SARS-CoV-2.

3.
Transl Behav Med ; 13(7): 432-441, 2023 Jul 01.
Article in English | MEDLINE | ID: covidwho-2279455

ABSTRACT

Racial and ethnic disparities in COVID-19 incidence are pronounced in underserved U.S./Mexico border communities. Working and living environments in these communities can lead to increased risk of COVID-19 infection and transmission, and this increased risk is exacerbated by lack of access to testing. As part of designing a community and culturally tailored COVID-19 testing program, we surveyed community members in the San Ysidro border region. The purpose of our study was to characterize knowledge, attitudes, and beliefs of prenatal patients, prenatal caregivers, and pediatric caregivers at a Federally Qualified Health Center (FHQC) in the San Ysidro region regarding perceived risk of COVID-19 infection and access to testing. A cross-sectional survey was used to collect information on experiences accessing COVID-19 testing and perceived risk of COVID-19 infection within San Ysidro between December 29, 2020 and April 2, 2021. A total of 179 surveys were analyzed. Most participants identified as female (85%) and as Mexican/Mexican American (75%). Over half (56%) were between the age of 25 and 34 years old. Perceived Risk: 37% reported moderate to high risk of COVID-19 infection, whereas 50% reported their risk low to none. Testing Experience: Approximately 68% reported previously being tested for COVID-19. Among those tested, 97% reported having very easy or easy access to testing. Reasons for not testing included limited appointment availability, cost, not feeling sick, and concern about risk of infection while at a testing facility. This study is an important first step to understand the COVID-19 risk perceptions and testing access among patients and community members living near the U.S./Mexico border in San Ysidro, California.


COVID-19 testing strategies that fail to incorporate culturally competent methods to reach traditionally underserved communities can lead to persistent transmission and increased infection rates. During the early stages of the COVID-19 pandemic, we surveyed 179 people living in a community with high burden of COVID-19 infection about their perception of infection risk and their experiences accessing testing. Capturing and understanding these community perceptions on COVID-19 risk are vital when developing a testing program that is accessible and appropriate for the target population. In our study, we found half of survey respondents thought their risk of COVID-19 infection as low to none and over half of respondents stated they had already been tested for COVID-19. These findings provide insight to the beliefs of individuals who live and seek health care in communities with high rates of COVID-19 infection and will help guide the design and implementation of culturally tailored testing strategies.


Subject(s)
COVID-19 Testing , COVID-19 , Health Knowledge, Attitudes, Practice , Health Services Accessibility , Adult , Child , Female , Humans , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/ethnology , COVID-19/psychology , COVID-19 Testing/statistics & numerical data , Cross-Sectional Studies , Mexican Americans/psychology , Mexican Americans/statistics & numerical data , California/epidemiology , Risk , Health Knowledge, Attitudes, Practice/ethnology , Caregivers/statistics & numerical data , Health Services Accessibility/statistics & numerical data , Pregnancy , Surveys and Questionnaires/statistics & numerical data
4.
BMC Public Health ; 23(1): 409, 2023 02 28.
Article in English | MEDLINE | ID: covidwho-2277360

ABSTRACT

BACKGROUND: Community Advisory Boards (CABs) have been frequently used to engage diverse partners to inform research projects. Yet, evaluating the quality of engagement has not been routine. We describe a multi-method ethnographic approach documenting and assessing partner engagement in two "virtual" CABs, for which we conducted all meetings remotely. METHODS: Two research projects for increasing equitable COVID-19 testing, vaccination, and clinical trial participation for underserved communities involved remote CAB meetings. Thirty-three partners representing 17 community groups participated in 15 sessions across the two CABs facilitated by a social change organization. We developed ethnographic documentation forms to assess multiple aspects of CAB member engagement (e.g., time spent speaking, modality used, types of interactions). Documenters were trained to observe CAB sub-groups via virtual sessions. Debriefing with the documentation team after CAB meetings supported quality assurance and process refinement. CAB members completed a brief validated survey after each meeting to assess the quality and frequency of engagement. Content and rapid thematic analysis were used to analyze documentation data. Quantitative data were summarized as frequencies and means. Qualitative and quantitative findings were triangulated. RESULTS: A total of 4,540 interactions were identified across 15 meetings. The most frequent interaction was providing information (44%), followed by responding (37-38%). The quality and frequency of stakeholder engagement were rated favorably (average 4.7 of 5). Most CAB members (96%) reported good/excellent engagement. Specific comments included appreciation for the diversity of perspectives represented by the CAB members and suggestions for improved live interpretation. Debriefing sessions led to several methodological refinements for the documentation process and forms. CONCLUSION: We highlight key strategies for documenting and assessing community engagement. Our methods allowed for rich ethnographic data collection that refined our work with community partners. We recommend ongoing trainings, including debriefing sessions and routinely reviewed assessment of data to strengthen meaningful community engagement.


Subject(s)
COVID-19 , Humans , COVID-19 Testing , Anthropology, Cultural , Data Collection , Documentation
5.
Lancet Reg Health Am ; 19: 100449, 2023 Mar.
Article in English | MEDLINE | ID: covidwho-2240692

ABSTRACT

Background: Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods: The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021. Findings: In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%-98%); 67% were associated with a positive wastewater sample (95% CI: 57%-77%), and 40% were associated with a positive surface sample (95% CI: 29%-52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation: Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding: County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.

6.
Front Health Serv ; 22022.
Article in English | MEDLINE | ID: covidwho-2080305

ABSTRACT

Background: Meaningful community engagement is instrumental to effective implementation and sustainment of equitable public health interventions. Significant resources are necessary to ensure that community engagement takes place in culturally sensitive, trusted ways that optimize positive public health outcomes. However, the types and costs of resources best suited to enable meaningful community engagement in implementation research are not well-documented. This study's objectives are (1) to describe a pragmatic method for systematically tracking and documenting resources utilized for community engagement activities, (2) report resources across phases of implementation research, and (3) provide recommendations for planning and budgeting for community engagement in health equity implementation research. Methods: Community engagement partners completed a tracking log of their person-hours for community engagement activities across three phases of community engagement (startup, early, maintenance) in two implementation research projects to promote equity in COVID-19 testing and vaccination for underserved communities. Both projects completed a six-session Theory of Change (i.e., a facilitated group discussion about current and desired conditions that culminated with a set of priorities for strategic change making) over 4 months with respective Community Advisory Boards (CAB) that included community organizers, promotores, federally qualified health center providers and administrators, and public health researchers. The reported person-hours that facilitated community member engagement were documented and summarized within and across project phases. Results: For both projects, the startup phase required the highest number of person-hours (M = 60), followed by the maintenance (M = 53) and early phase (M = 47). Within the startup phase, a total of 5 community engagement activities occurred with identifying and inviting CAB members incurring the greatest number of person-hours (M = 19). Within the early phase, a total of 11 community engagement activities occurred with coordinating and leading live interpretation (Spanish) during CAB sessions incurring the greatest number of person-hours (M = 10). The maintenance phase included 11 community engagement activities with time dedicated to written translation of CAB materials into Spanish incurring the greatest number of person-hours (M = 10). Conclusions: Study findings indicate that the most significant investment of resources is required in the startup period. Needed resources decreased, albeit with a greater diversity of activities, in later phases of community engagement with Spanish language translation requiring most in the later stage of the study. This study contributes to the community engagement and implementation science literature by providing a pragmatic tracking and measurement approach and recommendations for planning for and assessing costs to facilitate meaningful community engagement in public health implementation research.

7.
mSystems ; 7(4): e0010922, 2022 Aug 30.
Article in English | MEDLINE | ID: covidwho-1891744

ABSTRACT

A promising approach to help students safely return to in person learning is through the application of sentinel cards for accurate high resolution environmental monitoring of SARS-CoV-2 traces indoors. Because SARS-CoV-2 RNA can persist for up to a week on several indoor surface materials, there is a need for increased temporal resolution to determine whether consecutive surface positives arise from new infection events or continue to report past events. Cleaning sentinel cards after sampling would provide the needed resolution but might interfere with assay performance. We tested the effect of three cleaning solutions (BZK wipes, Wet Wipes, RNase Away) at three different viral loads: "high" (4 × 104 GE/mL), "medium" (1 × 104 GE/mL), and "low" (2.5 × 103 GE/mL). RNase Away, chosen as a positive control, was the most effective cleaning solution on all three viral loads. Wet Wipes were found to be more effective than BZK wipes in the medium viral load condition. The low viral load condition was easily reset with all three cleaning solutions. These findings will enable temporal SARS-CoV-2 monitoring in indoor environments where transmission risk of the virus is high and the need to avoid individual-level sampling for privacy or compliance reasons exists. IMPORTANCE Because SARS-CoV-2, the virus that causes COVID-19, persists on surfaces, testing swabs taken from surfaces is useful as a monitoring tool. This approach is especially valuable in school settings, where there are cost and privacy concerns that are eliminated by taking a single sample from a classroom. However, the virus persists for days to weeks on surface samples, so it is impossible to tell whether positive detection events on consecutive days are a persistent signal or new infectious cases and therefore whether the positive individuals have been successfully removed from the classroom. We compare several methods for cleaning "sentinel cards" to show that this approach can be used to identify new SARS-CoV-2 signals day to day. The results are important for determining how to monitor classrooms and other indoor environments for SARS-CoV-2 virus.

8.
mSystems ; 7(4): e0010322, 2022 Aug 30.
Article in English | MEDLINE | ID: covidwho-1891743

ABSTRACT

Surface sampling for SARS-CoV-2 RNA detection has shown considerable promise to detect exposure of built environments to infected individuals shedding virus who would not otherwise be detected. Here, we compare two popular sampling media (VTM and SDS) and two popular workflows (Thermo and PerkinElmer) for implementation of a surface sampling program suitable for environmental monitoring in public schools. We find that the SDS/Thermo pipeline shows superior sensitivity and specificity, but that the VTM/PerkinElmer pipeline is still sufficient to support surface surveillance in any indoor setting with stable cohorts of occupants (e.g., schools, prisons, group homes, etc.) and may be used to leverage existing investments in infrastructure. IMPORTANCE The ongoing COVID-19 pandemic has claimed the lives of over 5 million people worldwide. Due to high density occupancy of indoor spaces for prolonged periods of time, schools are often of concern for transmission, leading to widespread school closings to combat pandemic spread when cases rise. Since pediatric clinical testing is expensive and difficult from a consent perspective, we have deployed surface sampling in SASEA (Safer at School Early Alert), which allows for detection of SARS-CoV-2 from surfaces within a classroom. In this previous work, we developed a high-throughput method which requires robotic automation and specific reagents that are often not available for public health laboratories such as the San Diego County Public Health Laboratory (SDPHL). Therefore, we benchmarked our method (Thermo pipeline) against SDPHL's (PerkinElmer) more widely used method for the detection and prediction of SARS-CoV-2 exposure. While our method shows superior sensitivity (false-negative rate of 9% versus 27% for SDPHL), the SDPHL pipeline is sufficient to support surface surveillance in indoor settings. These findings are important since they show that existing investments in infrastructure can be leveraged to slow the spread of SARS-CoV-2 not in just the classroom but also in prisons, nursing homes, and other high-risk, indoor settings.

9.
mSystems ; 7(3): e0141121, 2022 Jun 28.
Article in English | MEDLINE | ID: covidwho-1846330

ABSTRACT

Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions and to test whether our past observations linking SARS-CoV-2 abundance to Rothia sp. in hospitals also hold in a residential setting, we performed a detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences (to assess the bacterial community at each location), and to the Cq value of the contemporaneous clinical test. Our results showed that the highest SARS-CoV-2 load in this setting is on touched surfaces, such as light switches and faucets, but a detectable signal was present in many untouched surfaces (e.g., floors) that may be more relevant in settings, such as schools where mask-wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g., touching a light switch) or indirectly (e.g., by droplets or aerosols settling). We found the highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g., in schools, where students did not touch the light switches and also wore masks such that they had no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

10.
Sci Rep ; 12(1): 5077, 2022 03 24.
Article in English | MEDLINE | ID: covidwho-1815587

ABSTRACT

Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, with great sequencing comes great computation, and while cloud computing platforms bring high-performance computing directly into the hands of all who seek it, optimal design and configuration of a cloud compute cluster requires significant system administration expertise. We developed ViReflow, a user-friendly viral consensus sequence reconstruction pipeline enabling rapid analysis of viral sequence datasets leveraging Amazon Web Services (AWS) cloud compute resources and the Reflow system. ViReflow was developed specifically in response to the COVID-19 pandemic, but it is general to any viral pathogen. Importantly, when utilized with sufficient compute resources, ViReflow can trim, map, call variants, and call consensus sequences from amplicon sequence data from 1000 SARS-CoV-2 samples at 1000X depth in < 10 min, with no user intervention. ViReflow's simplicity, flexibility, and scalability make it an ideal tool for viral molecular epidemiological efforts.


Subject(s)
COVID-19 , Software , COVID-19/epidemiology , Genome, Viral/genetics , Humans , Pandemics , SARS-CoV-2/genetics
11.
Front Bioeng Biotechnol ; 10: 877603, 2022.
Article in English | MEDLINE | ID: covidwho-1785315

ABSTRACT

The global pandemic caused by the SARS-CoV-2 virus has underscored the need for rapid, simple, scalable, and high-throughput multiplex diagnostics in non-laboratory settings. Here we demonstrate a multiplex reverse-transcription loop-mediated isothermal amplification (RT-LAMP) coupled with a gold nanoparticle-based lateral flow immunoassay (LFIA) capable of detecting up to three unique viral gene targets in 15 min. RT-LAMP primers associated with three separate gene targets from the SARS-CoV-2 virus (Orf1ab, Envelope, and Nucleocapsid) were added to a one-pot mix. A colorimetric change from red to yellow occurs in the presence of a positive sample. Positive samples are run through a LFIA to achieve specificity on a multiplex three-test line paper assay. Positive results are indicated by a characteristic crimson line. The device is almost fully automated and is deployable in any community setting with a power source.

12.
Health Serv Res ; 57 Suppl 1: 149-157, 2022 06.
Article in English | MEDLINE | ID: covidwho-1731058

ABSTRACT

OBJECTIVES: To describe the use of a Theory of Change to meaningfully engage community members from or support underserved communities in two National Institutes of Health-funded implementation science projects aimed at promoting equitable access to COVID-19 testing and vaccination for underserved communities. STUDY SETTING: Both projects focused on Latino, Black, and immigrant and refugee communities in South/Central San Diego and/or individuals accessing care at a federally qualified health center near the US/Mexico border during December 2020-April 2021. STUDY DESIGN: By using a participatory action research design, Community Advisory Boards (CABs) were established for each project with 11 and 22 members. CAB members included community organizers, promotores de salud (community health workers), clinic providers and administrators, and public health researchers. The CABs were guided through a seven-session Theory of Change process, focused on identifying necessary conditions that must exist to eliminate COVID-19 disparities along with specified actions to create those conditions and a blueprint for assessing the impact of those actions. DATA COLLECTION: Each session lasted 2 h hosted virtually and was augmented by interactive web-based activities. There was a live interpreter who facilitated the participation of Spanish-speaking CAB members. A Theory of Change for each project was completed in approximately 4 months. PRINCIPAL FINDINGS: Nine necessary conditions were identified related to (1) accessible and available services; (2) culturally and linguistically competent programming; (3) investment in trusted community and faith leaders; (4) social safety nets to provide ancillary services. Corresponding actions to create these conditions and measures to indicate success in creating these conditions were operationalized by the CAB. CONCLUSIONS: While resource-intensive, a CAB-led Theory of Change process yielded a rich opportunity to engage diverse groups that typically are not invited to inform these processes.


Subject(s)
COVID-19 , Vaccines , COVID-19/prevention & control , COVID-19 Testing , Community Health Workers , Hispanic or Latino , Humans
13.
mSystems ; 6(6): e0113621, 2021 Dec 21.
Article in English | MEDLINE | ID: covidwho-1494994

ABSTRACT

Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with coronavirus disease 2019 (COVID-19) and inform appropriate infection mitigation responses. Research groups have reported detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2-positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative PCR (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over 7 days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle [Cq]) can be correlated with surface viral load using only one linear regression model per material category. The same experiment was performed with untreated viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods. IMPORTANCE Environmental monitoring is an important tool for public health surveillance, particularly in settings with low rates of diagnostic testing. Time between sampling public environments, such as hospitals or schools, and notifying stakeholders of the results should be minimal, allowing decisions to be made toward containing outbreaks of coronavirus disease 2019 (COVID-19). The Safer At School Early Alert program (SASEA) (https://saseasystem.org/), a large-scale environmental monitoring effort in elementary school and child care settings, has processed >13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT-qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles.

15.
Data Brief ; 38: 107278, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1351628

ABSTRACT

We present supplementary data for the published article, "Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer" [1]. The assay described is designed to be performed at home or in a clinic without expensive instrumentation or professional training. SARS-CoV-2 is detected by an aptamer-based assay that targets the Nucleocapsid (N) or Spike (S) antigens. Binding of the N or S protein to their respective aptamer results in the competitive release of a complementary antisense-invertase enzyme complex. The released enzyme then catalyzes the conversion of sucrose to glucose that is measured by an off-the-shelf glucometer. The data presented here describe the optimization of the assay parameters and their contribution to developing this aptamer-based assay to detect SARS-CoV-2. The assay performance was checked in a standard buffer, contrived samples, and patient samples validated with well-established scientific methods. The resulting dataset can be used to further develop glucometer-based assays for diagnosing other communicable and non-communicable diseases.

16.
Cell ; 184(19): 4939-4952.e15, 2021 09 16.
Article in English | MEDLINE | ID: covidwho-1330684

ABSTRACT

The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.


Subject(s)
COVID-19/epidemiology , Epidemics , SARS-CoV-2/physiology , COVID-19/transmission , Databases as Topic , Disease Outbreaks , Humans , Louisiana/epidemiology , Phylogeny , Risk Factors , SARS-CoV-2/classification , Texas , Travel , United States/epidemiology
17.
Infect Control Hosp Epidemiol ; 43(5): 657-660, 2022 05.
Article in English | MEDLINE | ID: covidwho-1253833

ABSTRACT

Transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is possible among symptom-free individuals. Patients are avoiding medically necessary healthcare visits for fear of becoming infected in the healthcare setting. We screened 489 symptom-free healthcare workers for SARS-CoV-2 and found no positive results, strongly suggesting that the prevalence of SARS-CoV-2 was <1%.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Delivery of Health Care , Health Personnel , Humans , Mass Screening
18.
Cell ; 184(10): 2587-2594.e7, 2021 05 13.
Article in English | MEDLINE | ID: covidwho-1157175

ABSTRACT

The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%-50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.


Subject(s)
COVID-19 , Models, Biological , SARS-CoV-2 , COVID-19/genetics , COVID-19/mortality , COVID-19/transmission , Female , Humans , Male , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , United States/epidemiology
19.
Biosens Bioelectron ; 180: 113111, 2021 May 15.
Article in English | MEDLINE | ID: covidwho-1108095

ABSTRACT

Significant barriers to the diagnosis of latent and acute SARS-CoV-2 infection continue to hamper population-based screening efforts required to contain the COVID-19 pandemic in the absence of widely available antiviral therapeutics or vaccines. We report an aptamer-based SARS-CoV-2 salivary antigen assay employing only low-cost reagents ($3.20/test) and an off-the-shelf glucometer. The test was engineered around a glucometer as it is quantitative, easy to use, and the most prevalent piece of diagnostic equipment globally, making the test highly scalable with an infrastructure that is already in place. Furthermore, many glucometers connect to smartphones, providing an opportunity to integrate with contact tracing apps, medical providers, and electronic health records. In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads - as benchmarked by RT-qPCR - within 1 h, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). We propose that this approach provides an inexpensive, rapid, and accurate diagnostic for distributed screening of SARS-CoV-2 infection at scale.


Subject(s)
Antigens, Viral/analysis , Biosensing Techniques/methods , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Point-of-Care Testing , SARS-CoV-2/immunology , Saliva/virology , Adult , COVID-19 Testing , Coronavirus Nucleocapsid Proteins/analysis , Female , Humans , Male , Phosphoproteins/analysis , SARS-CoV-2/isolation & purification , SELEX Aptamer Technique , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/analysis
20.
mSystems ; 5(6)2020 Oct 29.
Article in English | MEDLINE | ID: covidwho-894830

ABSTRACT

Due to the COVID-19 pandemic and potential public health implications, we are publishing this peer-reviewed manuscript in its accepted form. The final, copyedited version of the paper will be available at a later date. Although SARS-CoV-2 is primarily transmitted by respiratory droplets and aerosols, transmission by fomites remains plausible. During Halloween, a major event for children in numerous countries, SARS-CoV-2 transmission risk via candy fomites worries many parents. To address this concern, we enrolled 10 recently diagnosed asymptomatic or mildly/moderately symptomatic COVID-19 patients to handle typical Halloween candy (pieces individually wrapped) under three conditions: normal handling with unwashed hands, deliberate coughing and extensive touching, and normal handling following handwashing. We then used a factorial design to subject the candies to two post-handling treatments: no washing (untreated) and household dishwashing detergent. We measured SARS-CoV-2 load by RT-qPCR and LAMP. From the candies not washed post-handling, we detected SARS-CoV-2 on 60% of candies that were deliberately coughed on, 60% of candies normally handled with unwashed hands, but only 10% of candies handled after hand washing. We found that treating candy with dishwashing detergent reduced SARS-CoV-2 load by 62.1% in comparison to untreated candy. Taken together, these results suggest that although the risk of transmission of SARS-CoV-2 by fomites is low even from known COVID-19 patients, viral RNA load can be reduced to near zero by the combination of handwashing by the infected patient and ≥1 minute detergent treatment after collection. We also found that the inexpensive and fast LAMP protocol was more than 80% concordant with RT-qPCR.IMPORTANCE The COVID-19 pandemic is leading to important tradeoffs between risk of SARS-CoV-2 transmission and mental health due to deprivation from normal activities, with these impacts being especially profound in children. Due to the ongoing pandemic, Halloween activities will be curtailed as a result of the concern that candy from strangers might act as fomites. Here we demonstrate that these risks can be mitigated by ensuring that prior to handling candy, the candy giver washes their hands, and by washing collected candy with household dishwashing detergent. Even in the most extreme case, with candy deliberately coughed on by known COVID-19 patients, viral load was reduced dramatically after washing with household detergent. We conclude that with reasonable precautions, even if followed only by either the candy giver or the candy recipient, the risk of viral transmission by this route is very low.

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