Dataset Information

Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes.

ABSTRACT: Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of C_T values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non-SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R² = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.

SUBMITTER: Shrestha L

PROVIDER: S-EPMC9290336 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes.

Shrestha Lasata L Lin Michelle J MJ Xie Hong H Mills Margaret G MG Mohamed Bakhash Shah A SA Gaur Vinod P VP Livingston Robert J RJ Castor Jared J Bruce Emily A EA Botten Jason W JW Huang Meei-Li ML Jerome Keith R KR Greninger Alexander L AL Roychoudhury Pavitra P

The Journal of molecular diagnostics : JMD 20220718 9

Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection ...[more]

PMID: 35863699

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Project description:Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.

Project description:BackgroundAvailable data suggest that the obstetric population is particularly vulnerable to severe respiratory syndrome coronavirus 2 infection, with a variable clinical course leading to severe respiratory failure. However, established early warning scores designed to identify patients at risk of clinical deterioration were never validated in the obstetric population.ObjectiveThis retrospective cohort study sought to evaluate the initial clinical characteristics of pregnant patients diagnosed with severe acute respiratory syndrome coronavirus 2 infection and to develop a pregnancy-specific early warning score to identify patients at risk for clinical deterioration and requiring advanced respiratory support.Study designThis was a single center, retrospective cohort study of pregnant patients diagnosed with severe acute respiratory syndrome coronavirus 2 infection between April 2020 and December 2020. A total of 50 patients with severe acute respiratory syndrome coronavirus 2 infection between April 2020 and November 2020 were used to create the prediction model. Initial clinical characteristics identified at the time of diagnosis were compared between patients who required advanced respiratory support and those who were asymptomatic or had mild symptoms for those diagnosed during the period of April 2020 to November 2020. Risk factors associated with a requirement for advanced respiratory support were used to create the Obstetric Warning Score system. The Obstetric Warning Score system was then validated using 30 patients diagnosed with severe acute respiratory syndrome coronavirus 2 infection in December 2020. A receiver operating characteristic curve was generated to evaluate the test characteristics of the Obstetric Warning Score system compared with other scoring systems including the Early Warning Score, the National Early Warning Score 2, and the Maternal Early Warning Criteria.ResultsWomen who required advanced respiratory support were more likely to present with dyspnea (100% vs 33.3%; P<.001), have a higher heart rate (113.4 beats per minute vs 93 beats per minute; P<.001), respiratory rate (23.5 breaths per minute vs 17.7 breaths per minute; P<.001), temperature (99.1°F vs 98.3°F; P=.004), and C-reactive protein level (7.4 mg/dL vs 2.4 mg/dL; P<.001). Furthermore, 88.2% of patients requiring advanced respiratory support showed chest x-ray findings consistent with pneumonia, compared with 20.0% of the patients not requiring advanced respiratory support (P<.001). All patients requiring advanced respiratory support presented with at least 1 coronavirus disease 2019 symptom, whereas only 51.5% of patients not requiring advanced respiratory support were symptomatic (P<.001). The Obstetrical Warning Score model allocated 1 point each for a hazard ratio of >100 beats per minute, temperature of >99.0°F, C-reactive protein level of >2.0 mg/dL, respiratory rate between 20 and 24 breaths per minute, complaints of dyspnea, and a positive chest x-ray. A respiratory rate of >24 breaths per minute was assigned 2 points. The area under the curve for the Obstetric Warning Score system was 0.97 compared with 0.72 for the Early Warning Score system, 0.92 for the National Early Warning Score 2 system, and 0.85 for the Maternal Early Warning Criteria system. An Obstetric Warning Score of ≥3 was predictive of a requirement for advanced respiratory support with a sensitivity of 100%, specificity 64%, and a positive predictive value of 36%.ConclusionThe Obstetric Warning Score system presents a validated method for providers to identify pregnant patients who are at risk for respiratory failure and a requirement for advanced respiratory support.

Dataset Information

Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes.

Publications

Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes.

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