scholarly journals Local monitoring of SARS-CoV-2 Variants in Two Large California Counties in 2021

2021 ◽  
Author(s):  
Noah Kojima ◽  
Eugenia Khorosheva ◽  
Lauren Lopez ◽  
Mikhail Hanewich-Hollatz ◽  
J. Cesar Ignacio-Espinoza ◽  
...  
Keyword(s):  
Public Health ◽  
Los Angeles ◽  
Private Sector ◽  
Genomic Data ◽  
Quality Criteria ◽  
Threshold Value ◽  
Sequencing Data ◽  
Riverside County ◽  
Study Enrollment ◽  
Institutional Review

Abstract Introduction: Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to persist due to mutations resulting in newer, more infectious variants of concern. The initial government response to COVID-19 failed to engage the private sector. Engaging the private sector could have bolstered the national capacity to process diagnostic tests and track variants of concern for disease for public health surveillance. We aimed to leverage an ongoing private SARS-CoV-2 testing laboratory’s infrastructure to monitor SARS-CoV-2 variants in two large California counties.Methods: Study enrollment was offered to adults aged 18 years or older in Los Angeles County and Riverside County in California who recently tested positive for SARS-CoV-2 by polymerase chain reaction (PCR) with a cycle threshold value less than or equal to 30 cycles. Trained healthcare workers directly observed self-collection of oral fluid or anterior nares specimens within 5 days of study enrollment. Specimens were transported and stored at 8°C or cooler. RNA was extracted from samples. Samples underwent library preparation and were sequenced. Sequencing data were filtered by quality criteria. High-quality genomic data were analyzed to identify SARS-CoV-2 lineages. Participant and genomic data were analyzed using statistical tools and visualized with toolkits. The study was approved by Advarra Institutional Review Board (Pro00053729).Results: From May 27, 2021 to September 9, 2021, 503 participants were enrolled and underwent specimen collection. Of those enrolled, there were 238 (47.3%) females, 329 (63.6%) vaccinated, and 221 (43.9%) of Hispanic or Spanish origin. Of the cohort, 496 (98.6%) had symptoms at the time of collection. Among the 503 participants, 443 (88.1%) nasal specimens and 353 (70.2%) oral specimens yielded sequencing results. Over our study period, the prevalence of the Alpha variant of SARS-CoV-2 decreased (initially 23.1% [95% confidence interval (95% CI): 0% to 0.49%] to 0% [95% CI: 0.0% to 0.0%]) as the prevalence of the Delta variant of SARS-CoV-2 increased (initially 33.3% [95% CI: 0.0% to 100.0%] to 100.0% [95% CI: 100.0% to 100.0%]). A strain that carried mutations of both Delta and Mu was identified.Conclusion: We found that outpatient SARS-CoV-2 variant surveillance could be conducted in private laboratory in a timely and accurate manner. The prevalence of different variants changed over time. A higher proportion of nasal specimens yielded results when compared to oral specimens. Timely outpatient SARS-CoV-2 variant surveillance could be used for public health efforts to identify changes in SARS-CoV-2 strain epidemiology in local areas. Government agencies should engage private laboratories in the surveillance of diseases that threaten the public’s health to supplement national disease reporting networks.

scholarly journals Investigating the first wave of the COVID-19 pandemic in Ukraine using epidemiological and genomic sequencing data

2021 ◽  
Author(s):  
Yuriy Gankin ◽  
Vladimir Koniukhovskii ◽  
Alina Nemira ◽  
Gerardo Chowell ◽  
Thomas A. Weppelmann ◽  
...  
Keyword(s):  
Public Health ◽  
Genomic Data ◽  
World Health ◽  
Viral Population ◽  
Genomic Sequencing ◽  
Sequencing Data ◽  
Population Number ◽  
The Public ◽  
Health Measures ◽  
The Impact

AbstractThe novel coronavirus SARS-CoV-2 emerged in China in December 2019 and has rapidly spread around the globe. The World Health Organization declared COVID-19 a pandemic in March 2020 just three months after the introduction of the virus. Individual nations have implemented and enforced with varying degrees of success a variety of social distancing interventions to slow the virus spread. Investigating the role of non-pharmaceutical interventions on COVID-19 transmission in different settings is an important research. While most transmission modeling studies have focused on the dynamics in China, neighboring Asian counties, Western Europe, and North America, there is a scarcity of studies for Eastern Europe. This study starts to fill this gap by analyzing the characteristics of the first epidemic wave in Ukraine using mathematical and statistical models together with epidemiological and genomic sequencing data. Using an agent-based model, the trajectory of the first wave in terms of cases and deaths and explore the impact of quarantine strategies via simulation studies have been characterized. The implemented stochastic model for epidemic counts suggests, that even a small delay of weeks could have increased the number of cases by up to 50%, with the potential to overwhelm hospital systems. The genomic data analysis suggests that there have been multiple introductions of SARS-CoV-2 into Ukraine during the early stages of the epidemic with eight distinct transmission clusters identified. The basic reproduction number for the epidemic has been estimated independently both from case counts data and from genomic data. The findings support the hypothesis that, the public health measures did not have a decreasing effect on the existing viral population number at the time of implementation, since strains were detected after the quarantine date. However, the public health measures did help to prevent the appearance of new (and potentially more virulent) SARS-CoV-2 variants in Ukraine.

scholarly journals High-precision and cost-efficient sequencing for real-time COVID-19 surveillance

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sung Yong Park ◽  
Gina Faraci ◽  
Pamela M. Ward ◽  
Jane F. Emerson ◽  
Ha Youn Lee
Keyword(s):  
Los Angeles ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
High Precision ◽  
High Throughput Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Public Health Response ◽  
Cost Efficient

AbstractCOVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achieved high precision, simple workflow, and low cost. We developed a high-precision, cost-efficient SARS-CoV-2 whole genome sequencing platform for COVID-19 genomic surveillance, CorvGenSurv (Coronavirus Genomic Surveillance). CorvGenSurv directly amplified viral RNA from COVID-19 patients’ Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens and sequenced the SARS-CoV-2 whole genome in three segments by long-read, high-throughput sequencing. Sequencing of the whole genome in three segments significantly reduced sequencing data waste, thereby preventing dropouts in genome coverage. We validated the precision of our pipeline by both control genomic RNA sequencing and Sanger sequencing. We produced near full-length whole genome sequences from individuals who were COVID-19 test positive during April to June 2020 in Los Angeles County, California, USA. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. With its readily adaptable design, CorvGenSurv grants wide access to genomic surveillance, permitting immediate public health response to sudden threats.

scholarly journals A Comparison of Methylprednisolone and Dexamethasone in Intensive Care Patients With COVID-19

2021 ◽  
pp. 088506662199405
Author(s):  
Justine J. Ko ◽  
Clay Wu ◽  
Neha Mehta ◽  
Noah Wald-Dickler ◽  
Wei Yang ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Intensive Care ◽  
Los Angeles ◽  
Usual Care ◽  
Low Income ◽  
Corticosteroid Treatment ◽  
Intensive Care Patients ◽  
Institutional Review ◽  
Mortality Effect ◽  
All Cause Mortality

Objectives: This study retrospectively compares the effectiveness of methylprednisolone to dexamethasone in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or COVID-19) requiring intensive care. Design: This is an institutional review board approved cohort study in patients with COVID-19 requiring intensive care unit (ICU) admission. Patients admitted and requiring oxygen supplementation were treated with no steroids, methylprednisolone, or dexamethasone. Setting: This study takes place in the ICU’s at a large, tertiary, public teaching hospital serving a primarily low-income community in urban Los Angeles. Patients: All eligible patients admitted to the ICU for COVID-19 respiratory failure from March 1 to July 31, 2020 were included in this study. Interventions: A total of 262 patients were grouped as receiving usual care (n = 75), methylprednisolone dosed at least at 1mg/kg/day for ≥ 3 days (n = 104), or dexamethasone dosed at least at 6 mg for ≥7 days (n = 83). Measurements and Main Results: All-cause mortality within 50 days of initial corticosteroid treatment as compared to usual care was calculated. The mortality effect was then stratified based on levels of respiratory support received by the patient. In this cohort of 262 patients with severe COVID-19, all-cause mortalities in the usual care, methylprednisolone, and dexamethasone groups were 41.3%, 16.4% and 26.5% at 50 days ( P < 0.01) respectively. In patients requiring mechanical ventilation, mortality was 42% lower in the methylprednisolone group than in the dexamethasone group (hazard ratio 0.48, 95% CI: 0.235-0.956, P = 0.0385). Conclusions: In COVID-19 patients requiring mechanical ventilation, sufficiently dosed methylprednisolone can lead to a further decreased mortality as compared to dexamethasone.

Impact of conspiracy beliefs on Covid-19 fear and health protective behavior: a case of university students

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Muhammad Asif Naveed ◽  
Amara Malik ◽  
Khalid Mahmood
Keyword(s):  
Public Health ◽  
Health Education ◽  
University Students ◽  
Private Sector ◽  
Protective Behavior ◽  
Cross Sectional Survey ◽  
Content Type ◽  
Conspiracy Beliefs ◽  
The Impact ◽  
Health Education And Promotion

PurposeThis study investigated the impact of conspiracy beliefs on fear of Covid-19 and health protective behavior of university students in Pakistan.Design/methodology/approachA cross-sectional survey using an online questionnaire was conducted at three universities in Punjab (e.g. two public sectors and one private sector) with permission from concerned authorities for data collection. A total of 374 responses were received that were analyzed by applying both descriptive and inferential statistics.FindingsThe results indicated the prevalence of conspiracy beliefs and fear of Covid-19 among university students of two public sector universities and one private sector university. Furthermore, the conspiracy beliefs of university students predicted their fear of Covid-19. However, conspiracy beliefs did not predict the health protective behavior of university students.Research limitations/implicationsThese results had serious implications for public health in Pakistan demonstrating the critical need for health education and promotion as individual preparedness along with system preparedness is essential to combat Covid-19 pandemic and infodemic. These results are useful for policymakers, healthcare professionals, university administration and library staff for making evidence-based decisions toward health education and promotion related to the Covid-19 pandemic.Originality/valueIt is hoped that the present study would make an invaluable contribution to existing research on promotional health in general and the role of conspiracy beliefs in putting public health at risk in particular as limited studies have been published so far.

P–530 The use of wide thresholds for detecting intermediate chromosomal CNV up to 80% doesn’t improve PGT-A ability to discriminate true mosaic from uniformly aneuploid embryos

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
L Girardi ◽  
M Serdaroğulları ◽  
C Patassini ◽  
S Caroselli ◽  
M Costa ◽  
...  
Keyword(s):  
Inner Cell Mass ◽  
False Negative ◽  
Cell Mass ◽  
Categorical Variables ◽  
P Value ◽  
Sequencing Data ◽  
Preimplantation Genetic Testing ◽  
Exact Test ◽  
Institutional Review ◽  
Wide Range

Abstract Study question What is the effect of varying diagnostic thresholds on the accuracy of Next Generation Sequencing (NGS)-based preimplantation genetic testing for aneuploidies (PGT-A)? Summary answer When single trophectoderm biopsies are tested, the employment of 80% upper threshold increases mosaic calls and false negative aneuploidy results compared to more stringent thresholds. What is known already Trophectoderm (TE) biopsy coupled with NGS-based PGT-A technologies are able to accurately predict Inner Cell Mass’ (ICM) constitution when uniform whole chromosome aneuploidies are considered. However, minor technical and biological inconsistencies in NGS procedures and biopsy specimens can result in subtle variability in analytical results. In this context, the stringency of thresholds employed for diagnostic calls can lead to incorrect classification of uniformly aneuploid embryos into the mosaic category, ultimately affecting PGT-A accuracy. In this study, we evaluated the diagnostic predictivity of different aneuploidy classification criteria by employing blinded analysis of chromosome copy number values (CNV) in multifocal blastocyst biopsies. Study design, size, duration The accuracy of different aneuploidy diagnostic cut-offs was assessed comparing chromosomal CNV in intra-blastocysts multifocal biopsies. Enrolled embryos were donated for research between June and September 2020. The Institutional Review Board at the Near East University approved the study (project: YDU/20l9/70–849). Embryos diagnosed with uniform chromosomal alterations (single or multiple) in their clinical TE biopsy (n = 27) were disaggregated into 5 portions: the ICM and 4 TE biopsies. Overall, 135 specimens were collected and analysed. Participants/materials, setting, methods Twenty-seven donated blastocysts were warmed and disaggregated in TE biopsies and ICM (n = 135 biopsies). PGT-A analysis was performed using Ion ReproSeq PGS kit and Ion S5 sequencer (ThermoFisher). Sequencing data were blindly analysed with Ion-Reporter software. Intra-blastocyst comparison of raw NGS data was performed employing different thresholds commonly used for aneuploidy classification. CNV for each chromosome were reported as aneuploid according to 70% or 80% thresholds. Categorical variables were compared using Fisher’s exact test. Main results and the role of chance In this study, a total of 50 aneuploid patterns in 27 disaggregated embryos were explored. Single TE biopsy results were considered as true positive when they displayed the same alteration detected in the ICM at levels above the 70% or 80% thresholds. Alternatively, alterations detected in the euploid or mosaic range were considered as false negative aneuploidy results. When the 70% threshold was applied, aneuploidy findings were confirmed in 94.5% of TE biopsies analyzed (n = 189/200; 95%CI=90.37–37.22), while 5.5% showed a mosaic profile (50–70%) but uniformly abnormal ICM. Positive (PPV) and negative predictive value (NPV) per chromosome were 100.0% (n = 189/189; 95%CI=98.07–100.00) and 99.5% (n = 2192/2203; 95%CI=99.11–99.75) respectively. When the upper cut-off was experimentally placed at 80% of abnormal cells, a significant decrease (p-value=0.0097) in the percentage of confirmed aneuploid calls was observed (86.5%; n = 173/200; 95%CI=80.97–90.91), resulting in mosaicism overcalling, especially in the high range (50–80%). Less stringent thresholds led to extremely high PPV (100.0%; n = 173/173; 95%CI=97.89–100.00), while NPV decreased to 98.8% (n = 2192/2219; 95%CI=98.30–99.23). Furthermore, no additional true mosaic patterns were identified with the use of wide range thresholds for aneuploidy classification. Limitations, reasons for caution This approach involved the analysis of aneuploidy CNV thresholds at the embryo level and lacked from genotyping-based confirmation analysis. Moreover, aneuploid embryos with known meiotic partial deletion/duplication were not included. Wider implications of the findings: The use of wide thresholds for detecting intermediate chromosomal CNV up to 80% doesn’t improve PGT-A ability to discriminate true mosaic from uniformly aneuploid embryos, lowering overall diagnostic accuracy. Hence, a proportion of the embryos diagnosed as mosaic using wide calling thresholds may actually be uniformly aneuploid and inadvertently transferred. Trial registration number N/A

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