A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

Mass spectrometry in animal health laboratories: recent history, current applications, and future directions

Mass spectrometry (MS) has long been considered a cornerstone technique in analytical chemistry. However, the use of MS in animal health laboratories (AHLs) has been limited, however, largely because of the expense involved in purchasing and maintaining these systems. Nevertheless, since ~2020, the use of MS techniques has increased significantly in AHLs. As expected, developments in new instrumentation have shown significant benefits in veterinary analytical toxicology as well as bacteriology. Creative researchers continue to push the boundaries of MS analysis, and MS now promises to impact disciplines other than toxicology and bacteriology. I include a short discussion of MS instrumentation, more detailed discussions of the MS techniques introduced since ~2020, and a variety of new techniques that promise to bring the benefits of MS to disciplines such as virology and pathology.

A micro-disc-based multiplex method for monitoring emerging SARS-CoV-2 variants using the molecular diagnostic tool Intelli-OVI

BACKGROUND

Highly transmissible viruses including SARS-CoV-2 frequently accumulate novel mutations that are detected via high-throughput sequencing. However, there is a need to develop an alternative rapid and non-expensive approach. Here we developed a novel multiplex DNA detection method Intelli-OVI for analysing existing and novel mutations of SARS-CoV-2.

METHODS

We have developed Intelli-OVI that includes the micro-disc-based method IntelliPlex and computational algorithms of objective variant identification (OVI). More than 250 SARS-CoV-2 positive samples including wastewater ones were analysed to verify the efficiency of the method.

RESULTS

IntelliPlex uses micro-discs printed with a unique pictorial pattern as a labelling conjugate for DNA probes, and OVI allows simultaneous identification of several variants using multidimensional data obtained by the IntelliPlex method. Importantly, de novo mutations can be identified by decreased signals, which indicates that there is an emergence of de novo variant virus as well as prompts the need to design additional primers and probes. We have upgraded probe panel according to the emergence of new variants and demonstrated that Intelli-OVI efficiently identified more than 20 different SARS-CoV-2 variants by using 35 different probes simultaneously.

CONCLUSIONS

Intelli-OVI can be upgraded to keep up with rapidly evolving viruses as we showed in this study using SARS-CoV-2 as an example and may be suitable for other viruses but would need to be validated.

Testing for SARS-CoV-2: lessons learned and current use cases

SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.

Isotope-encoded tetrahedral DNA for multiple SARS-CoV-2 variant diagnosis

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an unprecedented demand for accurate and cost-effective diagnostic assays to discriminate between different variants. Whilst many bioassays have been successfully demonstrated for SARS-CoV-2 detection, diagnosis of its variants remains challenging and mainly relies on time-consuming and costly sequencing techniques. Herein, we proposed a triplevalent tetrahedral DNA nanostructure (tTDN) with three overhang isotope probes capable of multiplex simultaneous analysis. HV69/70 del (alpha-specific), K417N (beta-specific) and T478K (delta-specific) and omicron with common mutations above of the SARS-CoV-2 S gene were detected selectively with the aid of the TDN scaffold and MNAzyme system, and a sensitive strategy enabling the screening of four kinds of variants of concern (VOC) was achieved.

Rapid Detection of SARS-CoV-2 Variants of Concern by Genomic Surveillance Techniques

This chapter describes the application of genomic, transcriptomic, proteomic, and metabolomic methods in the study of SARS-CoV-2 variants of concern. We also describe the important role of machine learning tools to identify the most significant biomarker signatures and discuss the latest point-of-care devices that can be used to translate these findings to the physician's office or to bedside care. The main emphasis is placed on increasing our diagnostic capacity and predictability of disease outcomes to guide the most appropriate treatment strategies.

Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay

The emergence of the SARS-CoV-2 Omicron variant in 2021 is associated with a global surge of cases in late 2021 and early 2022. Identifying the introduction of novel SARS-CoV-2 variants to a population is imperative to inform decisions by clinicians and public health officials. Here, we describe a quantitative reverse transcription PCR-based assay (RT-qPCR) targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 viral genomes. This assay accurately and precisely detect the presence of these Omicron variants in patient samples in less than four hours. Using this assay, we tested 270 clinical samples and detected the introduction of Omicron BA.1/BA1.1 and BA.2 in the Santa Barbara County (SBC) population in December 2021 and February 2022, respectively. Identifying Omicron variants using this RT-qPCR assay showed complete concordance with whole viral genome sequencing; both assays indicated that Omicron was the dominant variant in SB County. Our data substantiate that RT-qPCR-based virus detection assays offer a fast and inexpensive alternative to NGS for virus variant-specific detection approach, which allows streamlining the detection of Omicron variants in patient samples.