Transmission of Omicron (B.1.1.529) - SARS-CoV-2 Variant of Concern in a designated quarantine hotel for travelers: a challenge of elimination strategy of COVID-19.
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ABSTRACT:
SUBMITTER: Wong SC
PROVIDER: S-EPMC8696199 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: Not available
| S-EPMC8447387 | biostudies-literature
Project description:In November 2021, the World Health Organization designated a new SARS-CoV-2 variant of concern, Omicron (PANGO lineage B.1.1.529). We report on first two cases of breakthrough COVID-19 caused by Omicron in Japan among international travelers returning from the country with undetected infection. The spread of infection by Omicron were considered.
| S-EPMC8755371 | biostudies-literature
Project description:ImportanceSeveral jurisdictions in the United States have secured hotels to temporarily house people experiencing homelessness who require isolation or quarantine for confirmed or suspected coronavirus disease 2019 (COVID-19). To our knowledge, little is known about how these programs serve this vulnerable population outside the hospital setting.ObjectiveTo assess the safety of a hotel-based isolation and quarantine (I/Q) care system and its association with inpatient hospital capacity.Design, setting, and participantsThis retrospective cohort study of a hotel-based I/Q care system for homeless and unstably housed individuals in San Francisco, California, was conducted from March 19 to May 31, 2020. Individuals unable to safely isolate or quarantine at home with mild to moderate COVID-19, persons under investigation, or close contacts were referred from hospitals, outpatient settings, and public health surveillance to 5 I/Q hotels. Of 1009 I/Q hotel guests, 346 were transferred from a large county public hospital serving patients experiencing homelessness.ExposureA physician-supervised team of nurses and health workers provided around-the-clock support, including symptom monitoring, wellness checks, meals, harm-reduction services, and medications for opioid use disorder.Main outcomes and measuresCharacteristics of I/Q hotel guests, program retention, county hospital readmissions, and mean length of stay.ResultsOverall, the 1009 I/Q hotel guests had a median age of 44 years (interquartile range, 33-55 years), 756 (75%) were men, 454 (45%) were Latinx, and 501 (50%) were persons experiencing sheltered (n = 295) or unsheltered (n = 206) homelessness. Overall, 463 (46%) received a diagnosis of COVID-19; 303 of 907 (33%) had comorbid medical disorders, 225 of 907 (25%) had comorbid mental health disorders, and 236 of 907 (26%) had comorbid substance use disorders. A total of 776 of 955 guests (81%) completed their I/Q hotel stay; factors most strongly associated with premature discontinuation were unsheltered homelessness (adjusted odds ratio, 4.5; 95% CI, 2.3-8.6; P < .001) and quarantine status (adjusted odds ratio, 2.6; 95% CI, 1.5-4.6; P = .001). In total, 346 of 549 patients (63%) were transferred from the county hospital; of 113 ineligible referrals, 48 patients (42%) had behavioral health needs exceeding I/Q hotel capabilities. Thirteen of the 346 patients transferred from the county hospital (4%) were readmitted for worsening COVID-19. Overall, direct transfers to I/Q hotels from emergency and outpatient departments were associated with averting many hospital admissions. There was a nonsignificant decrease in the mean hospital length of stay for inpatients with confirmed or suspected COVID-19 from 5.5 to 2.7 days from March to May 2020 (P = .11).Conclusions and relevanceTo support persons experiencing homelessness during the COVID-19 pandemic, San Francisco rapidly and safely scaled a hotel-based model of I/Q that was associated with reduced strain on inpatient capacity. Strategies to improve guest retention and address behavioral health needs not met in hotel settings are intervention priorities.
| S-EPMC7926291 | biostudies-literature
Project description:ObjectivesThe aim of this study was to develop a RT-PCR assay for the specific detection of the SARS-CoV-2 Omicron Variant of Concern (VOC) as a rapid alternative to sequencing.MethodsA RT-PCR was designed in silico and then validated using characterised clinical samples containing Omicron (both BA.1 and BA.2 lineages) and the Omicron synthetic RNA genome. As negative controls, SARS-CoV-2 positive clinical samples collected in May 2020, and synthetic RNA genomes of the isolate Wuhan Hu-1 and of the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Iota (B.1.526), Epsilon (B.1.429) and Delta (B.1.617.2) SARS-CoV-2 VOC were used.ResultsExperiments performed using as templates the synthetic RNA genomes demonstrate the high specificity of the PCR-method for the SARS-CoV-2 Omicron. Despite the synthetic RNAs were used at high copy numbers, specific signal was mainly detected with the Omicron synthetic genome. Only a non-specific late signal was detected using the Alpha variant genome, but these results were considered negligible as Alpha VOC has been replaced by the Delta and it is not circulating anymore in the world. Using our method, we confirmed the presence of Omicron on clinical samples containing this variant but not of other SARS-CoV-2 lineages. The method is highly sensitive and can detect up to 1 cp of the Omicron virus per µl.ConclusionsThe method presented here, in combination with other methods in use for detection of SARS-CoV-2, can be used for an early identification of Omicron.
| S-EPMC9126828 | biostudies-literature
Project description: Not available
| EMPIAR-10947 | biostudies-other
Project description:The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody resistance of the SARS-CoV-2 variant are determined by its mutations on the spike (S) protein receptor-binding domain (RBD). However, a complete experimental evaluation of Omicron might take weeks or even months. Here, we present a comprehensive quantitative analysis of Omicron's infectivity, vaccine-breakthrough, and antibody resistance. An artificial intelligence (AI) model, which has been trained with tens of thousands of experimental data points and extensively validated by experimental data on SARS-CoV-2, reveals that Omicron may be over ten times more contagious than the original virus or about twice as infectious as the Delta variant. Based on 132 three-dimensional (3D) structures of antibody-RBD complexes, we unveil that Omicron may be twice more likely to escape current vaccines than the Delta variant. The Food and Drug Administration (FDA)-approved monoclonal antibodies (mAbs) from Eli Lilly may be seriously compromised. Omicron may also diminish the efficacy of mAbs from Celltrion and Rockefeller University. However, its impact on Regeneron mAb cocktail appears to be mild.
| S-EPMC8647651 | biostudies-literature
Project description:The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody resistance of the SARS-CoV-2 variant are determined by its mutations on the spike (S) protein receptor-binding domain (RBD). However, a complete experimental evaluation of Omicron might take weeks or even months. Here, we present a comprehensive quantitative analysis of Omicron's infectivity, vaccine breakthrough, and antibody resistance. An artificial intelligence (AI) model, which has been trained with tens of thousands of experimental data and extensively validated by experimental results on SARS-CoV-2, reveals that Omicron may be over 10 times more contagious than the original virus or about 2.8 times as infectious as the Delta variant. On the basis of 185 three-dimensional (3D) structures of antibody-RBD complexes, we unveil that Omicron may have an 88% likelihood to escape current vaccines. The U.S. Food and Drug Administration (FDA)-approved monoclonal antibodies (mAbs) from Eli Lilly may be seriously compromised. Omicron may also diminish the efficacy of mAbs from AstraZeneca, Regeneron mAb cocktail, Celltrion, and Rockefeller University. However, its impacts on GlaxoSmithKline's sotrovimab appear to be mild. Our work calls for new strategies to develop the next generation mutation-proof SARS-CoV-2 vaccines and antibodies.
| S-EPMC8751645 | biostudies-literature
Project description:On the 24 th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.
| S-EPMC8722586 | biostudies-literature
Project description:Airborne transmission of SARS-CoV-2 has been increasingly recognized in the outbreak of COVID-19, especially with the Omicron variant. We investigated an outbreak due to Omicron variant in a restaurant. Besides epidemiological and phylogenetic analyses, the secondary attack rates of customers of restaurant-related COVID-19 outbreak before (Outbreak R1) and after enhancement of indoor air dilution (Outbreak R2) were compared. On 27th December 2021, an index case stayed in restaurant R2 for 98 min. Except for 1 sitting in the same table, six other secondary cases sat in 3 corners at 3 different zones, which were served by different staff. The median exposure time was 34 min (range: 19-98 min). All 7 secondary cases were phylogenetically related to the index. Smoke test demonstrated that the airflow direction may explain the distribution of secondary cases. Compared with an earlier COVID-19 outbreak in another restaurant R1 (19th February 2021), which occurred prior to the mandatory enhancement of indoor air dilution, the secondary attack rate among customers in R2 was significantly lower than that in R1 (3.4%, 7/207 vs 28.9%, 22/76, p<0.001). Enhancement of indoor air dilution through ventilation and installation of air purifier could minimize the risk of SARS-CoV-2 transmission in the restaurants.
| S-EPMC8848576 | biostudies-literature
Project description:Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.
| S-EPMC8314830 | biostudies-literature