Multiplex Fragment Analysis for Flexible Detection of All SARS-CoV-2 Variants of Concern.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge, and effective tracking requires rapid return of results. Surveillance of variants is typically performed by whole genome sequencing (WGS), which can be financially prohibitive and requires specialized equipment and bioinformatic expertise. Genotyping approaches are rapid methods for monitoring SARS-CoV-2 variants but require continuous adaptation. Fragment analysis may represent an approach for improved SARS-CoV-2 variant detection. METHODS: A multiplex fragment analysis approach (CoVarScan) was validated using PCR targeting variants by size and fluorescent color. Eight SARS-CoV-2 mutational hot spots in variants of concern (VOCs) were targeted. Three primer pairs (recurrently deleted region [RDR] 1, RDR2, and RDR3-4) flank RDRs in the S-gene. Three allele-specific primers target recurrent spike receptor binding domain mutants. Lastly, 2 primer pairs target recurrent deletions or insertions in ORF1A and ORF8. Fragments were resolved and analyzed by capillary electrophoresis (ABI 3730XL), and mutational signatures were compared to WGS results. RESULTS: We validated CoVarScan using 3544 clinical respiratory specimens. The assay exhibited 96% sensitivity and 99% specificity compared to WGS. The limit of detection for the core targets (RDR1, RDR2, and ORF1A) was 5 copies/reaction. Variants were identified in 95% of samples with cycle threshold (CT) <30 and 75% of samples with a CT 34 to 35. Assay design was frozen April 2021, but all subsequent VOCs have been detected including Delta (n = 2820), Mu, (n = 6), Lambda (n = 6), and Omicron (n = 309). Genotyping results are available in as little as 4 h. CONCLUSIONS: Multiplex fragment analysis is adaptable and rapid and has similar accuracy to WGS to classify SARS-CoV-2 variants.

Clinical and Infection Prevention Applications of Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping: an Infectious Diseases Society of America/American Society for Microbiology Consensus Review Document.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with more than 2 million genomes sequenced at the time of writing. The rise of more transmissible variants of concern that impact vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, and clinical reporting for laboratories, as well as emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretells a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.

Clinical and Infection Prevention Applications of Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping: An Infectious Diseases Society of America/American Society for Microbiology Consensus Review Document.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with >2 million genomes sequenced at this writing. The rise of more transmissible variants of concern that affect vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, clinical reporting for laboratories, and emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretell a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.

Envisioning Future Urinary Tract Infection Diagnostics.

Urinary tract infections (UTIs) are among the most common bacterial infections in the United States and are a major driver of antibiotic use, both appropriate and inappropriate, across healthcare settings. Novel UTI diagnostics are a strategy that might enable better UTI treatment. Members of the Antibacterial Resistance Leadership Group Laboratory Center and the Infectious Diseases Society of America Diagnostics Committee convened to envision ideal future UTI diagnostics, with a view towards improving delivery of healthcare, patient outcomes and experiences, and antibiotic use, addressing which types of UTI diagnostics are needed and how companies might approach development of novel UTI diagnostics.

To Test, Perchance to Diagnose: Practical Strategies for Severe Acute Respiratory Syndrome Coronavirus 2 Testing.

Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in symptomatic and asymptomatic patients is an important component of the multifaceted approach of managing the coronavirus disease 2019 pandemic. Determining how to best define testing strategies for different populations and incorporating these into broader infection prevention programs can be complex. Many circumstances are not addressed by federal, local, or professional guidelines. This commentary describes various scenarios in which testing of symptomatic or asymptomatic individuals for SARS-CoV-2 virus (antigen or ribonucleic acid) can be of potential benefit. Consideration to pretest probability, risks of testing (impact of false-positive or false-negative results), testing strategy, as well as action based on test results are explored. Testing, regardless of setting, must be incorporated into overarching infection control plans, which include use of personal protective equipment (eg, masks), physically distancing, and isolation when exposure is suspected.

Expanding COVID-19 Vaccine Availability: Role for Combined Orthogonal Serology Testing (COST).

BACKGROUND: The persisting Coronavirus disease 2019 (COVID-19) pandemic and limited vaccine supply has led to a shift in global health priorities to expand vaccine coverage. Relying on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular testing alone cannot reveal the infection proportion, which could play a critical role in vaccination prioritization. We evaluated the utility of a combination orthogonal serological testing (COST) algorithm alongside RT-PCR to quantify prevalence with the aim of identifying candidate patient clusters to receive single and/or delayed vaccination. METHODS: We utilized 108,505 patients with suspected COVID-19 in a retrospective analysis of SARS-CoV-2 RT-PCR vs. IgG-nucleocapsid (IgGNC) antibody testing coverage in routine practice for the estimation of prevalence. Prospectively, an independent cohort of 21,388 subjects was simultaneously tested by SARS-CoV-2 RT-PCR and IgGNC to determine the prevalence. We used 614 prospective study subjects to assess the utility of COST (IgGNC, IgM-spike (IgMSP), and IgG-spike (IgGSP)) in establishing the infection proportion to identify a single-dose vaccination cohort. RESULTS: Retrospectively, we observed a 6.3% (6871/108,505) positivity for SARS-CoV-2 RT-PCR, and only 2.3% (2533/108,505) of cases had paired IgGNC serology performed. Prospectively, IgGNC serology identified twice the number of COVID-positive cases in relation to RT-PCR alone. COST further increased the number of detected positive cases: IgGNC+ or IgMSP+ (18.0%); IgGNC+ or IgGSP+ (23.5%); IgMSP+ or IgGSP+ (23.8%); and IgGNC+ or IgMSP+ or IgGSP+ (141/584 = 24.1%). CONCLUSION: COST may be an effective tool for the evaluation of infection proportion and thus could define a cohort for a single dose and/or delayed vaccination.

Laboratory-developed test regulation and the immunocompromised patient: uncertainty ahead.

PURPOSE OF THE REVIEW: Laboratory-developed tests (LDTs) are essential for the clinical care of immunocompromised individuals. These patients often require specialized testing not available from commercial manufacturers and are therefore dependent on the laboratory to create, validate, and perform these assays. Recent paradigm-shifting legislation could alter the way that LDTs are operationalized and regulated. RECENT FINDINGS: On March 5th, 2020 the Verifying Accurate and Leading-Edge In-Vitro Clinical Tests Development Act (VALID) was introduced in the US Congress. This statute would overhaul existing regulatory framework by unifying the oversight of LDTs and commercial in-vitro diagnostic tests (IVDs) through the FDA. If enacted, LDTs would be subject to regulatory requirements like those found in commercial submissions for market review. Stakeholders continue to discuss the details and scope of the proposed legislation in the setting of the Severe Acute Respiratory Syndrome Coronavirus 2 pandemic, where LDTs are integral to the national COVID-19 response. SUMMARY: Congressional lawmakers have introduced legislation to alter the regulatory framework governing LDTs. Moving forward, a balance must be struck to ensure the availability of safe and accurate testing without delays or overregulation that could be harmful to patients. The downstream implications of how VALID and other legislation will impact laboratories, clinicians, and patients warrant close examination.

The role of electronic health record and "add-on" clinical decision support systems to enhance antimicrobial stewardship programs.

Increasingly, demands are placed on healthcare systems to meet antimicrobial stewardship standards and reporting requirements. This trend, combined with reduced financial and personnel resources, has created a need to adopt information technology (IT) to help ease these burdens and facilitate action. The incorporation of IT into an antimicrobial stewardship program can help improve stewardship intervention efficiencies and facilitate the tracking and reporting of key metrics, including outcomes. This paper provides a review of the stewardship-related functionality within these IT systems, describes how these platforms can be used to improve antimicrobial use, and identifies how they can support current and potential future antimicrobial stewardship regulatory and accreditation standards. Finally, recommendations to help close the gaps in existing systems are provided and suggestions for future areas of development within these programs are delineated.

Antimicrobial prophylaxis may not be the answer: Surgical site infections among patients receiving care per recommended guidelines.

BACKGROUND: It is believed that compliance with all 3 components of perioperative antimicrobial prophylaxis, ie, timing, choice, and duration, yields greater reduction in surgical site infections (SSI). METHODS: An observational study was performed among patients in the surgical care improvement project at a tertiary public academic hospital in the United States. The rates of SSI among patients who received appropriate antimicrobial agent(s) per current guidelines were compared with patients who did not. Medical record review was performed to compare the clinical characteristics of patients with SSI (cases) and an equal number of patients without SSI (matched controls). RESULTS: From January 2008 to June 2009, 762 patients underwent 763 eligible surgical procedures. Forty-seven (6.2%) developed SSI. The rate of SSI in patients who received appropriate antimicrobial prophylaxis per guidelines was not different from those who did not (42/611, 6.9% vs 5/152, 3.3%, respectively; P value = .13). Patients with SSI were more likely to have an elevated body mass index (median and interquartile range in cases: 28.7 [27.0-34.9] vs 25.0 [22.4-30.4] in controls; P value = .02) and more likely to have diabetes (36% vs 9%, respectively; odds ratio, 5.71; 95% confidence interval: 1.43-22.8; P value = .02). CONCLUSION: Compliance with timing, choice, and duration of antimicrobial prophylaxis as a whole did not lead to lower SSI. Elevated body mass index and diabetes were associated with a higher rate of SSI.