Diagnostics
spike protein, which attaches the virus to human cells during infection, and therefore affects how easily the virus spreads.1
While the frequency
of genomic surveillance for COVID-19 has now decreased – with the Medicines and Healthcare Products Regulatory Agency (MHRA) now only requiring a surveillance report to be presented by companies operating in the diagnostics field every two months – ongoing monitoring is still required.
Although respiratory disease surveillance has only recently been placed in the spotlight, epidemiologists have actually been carrying out regular influenza monitoring for many years.4 Influenza A and B are endemic in humans, and the regular mutations that these pathogens undergo make them responsible for annual epidemics and seasonal shifts across the globe.5 Furthermore, the influenza virus has been the cause of recurring pandemics throughout human history, with the four most recent outbreaks emerging over the course of just a hundred years. As a result, regular surveillance now forms a key component of pandemic preparedness, as it allows scientists to detect novel influenza strains as they emerge. A global surveillance network was originally established in the 1950s by the World Health Organization,5
and databases – such as the
global initiative on sharing all influenza data (GISAID) EpiFLu database – have been created as repositories for influenza sequences reported by testing laboratories all over the world. This information is used by major pharmaceutical companies in the diagnostics and vaccine space that rely on the data from previous influenza seasons to predict which viral strains will be circulating in the next season, and to update their product offerings on an annual basis.
The ability of multiplexed respiratory assays to simultaneously detect a range of pathogens represents a transformative leap forward in infectious disease management. As we navigate a future where SARS-CoV-2 remains a persistent threat – alongside a host of seasonal illnesses – multiplexed testing panels represent a way to manage respiratory health.
Keeping diagnostics solutions up to date Diagnostic real-time PCR (qPCR) assays are normally developed to detect the areas of the viral genome that are least likely to manifest mutations. These parts of the virus – known as conserved regions – are typically stable and well preserved across all the strains of a particular pathogen, so molecular tests developed with primers and probes to detect these regions are more likely to identify all viral lineages or variants. During assay development, bioinformaticians will examine the genomic sequencing data available for various strains of a virus from an appropriate timeframe – such as the last five years – and find the regions where the fewest mutations occur. Cross-referencing these findings with the latest epidemiological literature can help them to ensure that they are basing their test on the most consistent, conserved parts of the genome. Unfortunately, mutations do sometimes occur in conserved regions of the viral genome, posing a critical challenge to diagnostics providers. These mutations may interrupt disease
detection and affect the accuracy of the test, requiring the assay provider to re-evaluate its testing protocols. They will either need to modify the current primers and probe sequences, recreate the assay with new primers and probes targeting a different conserved region – if the variant is prevalent and widespread – or update the information pack that they provide with the test to inform users that it may not detect a particular variant limited to a specific geographical area. Discovering new, effective conserved sites in the viral genome can be an extremely difficult task, as viral genomes tend to be very small in comparison to those of eukaryotes. A typical viral genome contains between 7,000 and 20,000 base pairs of DNA or RNA, while a human cell contains over 3 billion nucleotides.6 It is therefore occasionally impossible to find a novel conserved region with no mutations in a small viral genome, and so qPCR assay designers will instead be forced to rely on two conserved regions simultaneously to engineer a test that can detect a broader range of variants. Nonetheless, the best diagnostics companies will take a proactive approach to genomic surveillance, and regularly update their products to ensure that they can keep up with ongoing viral evolution, continuing to detect new strains and ever-changing disease targets.
Tackling overlapping respiratory diseases The healthcare industry’s swift actions in response to the COVID-19 pandemic spoke volumes about its ability to rapidly counter threats from emerging pathogens.7
Controlling
Figure 2: Multiplexed assays offer a complete solution to diagnose and differentiate between numerous prevalent respiratory illnesses.
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www.clinicalservicesjournal.com I December 2023
the virus required rapid innovations in research and development to produce efficient diagnostic assays, vaccines and therapeutics. In particular, the pandemic brought about a significant shift in disease testing compared to the pre- pandemic era. Testing prior to the pandemic was generally characterised by longer turnaround times, limited accessibility and a general reliance on traditional laboratory-based assays.
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