COVID-19 results in exponential growth for MDx in 2020

The Indian MDx market saw an additional ₹7000 crore sales on account of RT-PCR testing.

As the world rushes to become vaccinated against the COVID-19, the strategy turns from infection mitigation to achieving herd immunity. The pandemic and the multiple lockdowns that followed have had a huge effect on the world’s markets, butchering some industries while allowing others to boom. The medical device field has been no exception, but different sub-segments have been affected differently.

Last year saw the onset of the virus in the Western world and the lockdowns and shutdowns that followed. This meant that the field of elective surgeries saw its sales numbers tank, as everyone was staying home and surgeries were postponed. Some companies saw as much as double-digit declines in their sales segments.

These same decisions, however, led to growth in the testing market. As COVID-19 tore across the world, correctly identifying who had the virus was of paramount importance to enforce quarantines and stay-at-home orders. Polymerase chain reaction (PCR), antigen, and antibody tests skyrocketed from their original workflows to having to produce hundreds of millions, if not billions, of tests very quickly. But this explosive growth will not continue forever.

While IVD companies may still report modest growth numbers in future, as more and more of the world becomes immunized, the demand for tests will decrease until they are no longer needed.

This may lead to an unfortunate situation for the molecular diagnostics market. As the need for COVID-19 testing collapses to a fraction of its current demand, molecular diagnostics companies will be holding and maintaining facilities that can create immense supply. This mismatch between demand and supply will either lead to a collapse in prices of molecular diagnostic tests, as suppliers struggle to break even on their facilities maintenance costs, or a mass selloff or repurposing of these facilities.

Either way, the companies in the molecular diagnostics space will have to plan their next steps very carefully. They have made a lot of money in the boom of the COVID-19 pandemic, but they must be careful not to be saddled with large illiquid material assets for a market that is a fraction of its previous price.

Since the COVID-19 outbreak, India has been at the forefront of formulating COVID-19 testing protocols. With an average daily testing of more than 1.7 million in the month of August, India has tested 500 million samples across the country till date.

India has achieved the milestone of the last one hundred million tests in only 55 days. On July 21, 2021, India had tested 450 million COVID-19 samples, which reached the 500 million mark on August 18, 2021. This has been enabled by rapidly increasing testing infrastructure and capacity across the country. ICMR has been enhancing COVID-19 testing capability across the country by expanding and diversifying testing capacity by leveraging technology and facilitating innovation in affordable diagnostic kits. The testing strategy has been carefully calibrated to increase access and availability of testing.

The concerted efforts toward augmenting and diversifying testing prepared the infrastructure, which made it possible to deliver on India’s increased testing requirements in the wake of the second wave of COVID-19. COVID-19 testing capability across the country has been enhanced by leveraging technology and facilitating innovation in affordable diagnostic kits. Easy-at-home self-diagnostic kits have been developed and approved.

A specific testing platform is available, addressing general testing (RT-PCR), high-throughput testing (COBAS), testing at remotest places and PHCs (TrueNAT, CBNAAT), in containment areas (rapid antigen testing) and for large number of migrant population (pooled sample testing). The total number of diagnostic laboratories has reached 2876, of which dedicated government laboratories are 1322 and private laboratories’ number stands at 1554.

This has given a huge impetus to the molecular diagnostics market. While as yet data is not available on how large the market became, estimates indicate that the escalation in demand from extraction machines, extraction kits, amplification test equipment, and RT-PCR kits is ₹7000 crore in 2020, translating into a total Indian molecular diagnostic of ₹7264 crore.

And since now capacities have been created, and huge investments made, apart from the continuity in COVID-19 tests 2021 onwards, molecular diagnostics is expected to start a new chapter, where tests for dengue, malaria, chikungunya, etc., will be conducted on the molecular diagnostic techniques.

Next-generation techniques have begun to make their way into the clinic in a range of diagnostic applications, including prenatal screening for genetic disease, transplant typing, and risk assessment and treatment selection in oncology. While traditional molecular diagnostic techniques, such as PCR (polymerase chain reaction) and ISH (in-situ hybridization) will remain relevant for years to come, many emerging applications require the rich information NGS can offer. New associations between the broad/deep genetic information NGS can provide and disease prognosis or treatment are being reported with increasing frequency. The next huge impetus is expected from these tests, albeit costs of NGS continue to plummet.

The global MDx market, including new tests for COVID-19, exceeded USD 13 billion in 2020, according to Kalorama Information. That is about USD 5 billion larger than 2019, and reflects the large volume of sales for COVID-19 molecular tests in the US and worldwide.

COVID-19 testing is slated to continue into 2021 if present disease trends continue. While it is possible COVID-19 tests will be panelized, that is added to existing tests in combination with flu and other respiratory conditions, and while it is also true that the market may not support the kind of emergency crisis sales of 2020, the influence of COVID-19 on molecular diagnostics should last a few years. It already has boosted the respiratory and healthcare infection molecular testing markets and has generally increased public awareness of PCR testing.

The news is not all positive from a revenue perspective. Molecular testing on COVID is paired with declines in more traditional molecular tests as patients avoided doctors, and continue to reduce in-person doctor visits during lockdown. Down-but-not-out segments include cancer, histology, and inherited diseases, which are expected to continue to grow, perhaps surge, later in the year. Prior to COVID-19, liquid biopsy was one of the stars of this segment. Favorable regulatory policies and promising studies will enhance companion testing. New LDT tests in inherited disease testing in particular, using IVD supplies, which includes non-invasive prenatal testing (NIPT), is driven by the demand in China. Even though the demand is for laboratory test services and not for IVD products, the demand for instruments, kits, and consumables that are approved by regulatory agencies is driving the segment. However, the market opportunities may be challenging to access by foreign IVD companies due to the regulations promoting domestic companies.

The molecular diagnostics field, up until recently, has been dominated by large firms, such as market leader, Roche, followed by Cepheid/Danaher, bioMérieux, Qiagen, Hologic, BD, Siemens, and Luminex. While many of these companies are focused on competitive strategies (e.g., sophisticated automation for molecular testing, test menu expansion) to maintain their position, emerging competitors are also entering the market by developing next-generation technologies. The global COVID-19 pandemic has accelerated these and other new approaches for molecular diagnostics to enter the market, through substantially reduced regulatory hurdles, with many novel technologies coming out of research laboratories.

Many of the vendors making COVID-19 tests also make tests for other infectious diseases, such as HIV and zika. Those focused on the novel coronavirus may disappear when the crisis is over, but others may remain. There is no shortage of new competitors entering this market, and even if a solution emerges for COVID-19, it is logical to expect that many of these new vendors will continue to develop lab test products for other conditions and some will be on standby with production knowledge and facilities for the next pandemic.

While necessity is the mother of invention, anomalies have formed the basis for most disruptive discoveries that seed innovations in the sciences. They provide the impetus for paradigm change within a field and reflect differences between observed and theoretically expected data. The coronavirus pandemic was such an anomaly that spawned innovation in the molecular diagnostic testing market and initiated a paradigm change in public health policies, regulatory hurdles, and consumer views of point-of-care (POC) testing. Prior close calls with other viruses, including SARS, MERS, and Ebola, should have prepared the world for the coronavirus pandemic. Yet, many nations, including the United States, found themselves largely unprepared.

Countries responded to the unprecedented challenge of the coronavirus pandemic differently, but in each case, innovation was at the core of the response. After the authorization of the CDC test via emergency use authorization (EUA) from the US FDA on February 4, 2020, lab-developed tests from Clinical Laboratory Improvement Amendments (CLIA)-certified labs were authorized soon thereafter. Multiple commercial diagnostic companies rapidly validated and received EUA for SARS-CoV-2 diagnostic assays on existing platforms, which enabled private testing to rapidly outstrip public health department testing.

Nucleic acid detection technology. Nucleic acid detection is an important diagnostic tool for clinical diagnosis, segregation, rehabilitation, and discharge of patients, and was also the gold standard for the detection of 2019-nCoV infection in the early stage of the epidemic. Current nucleic acid detection methods include RT-PCR, isothermal amplification, and high-throughput sequencing. At present, specimens tested by commercial nucleic acid kits mainly comprise throat swabs, oropharyngeal swabs, nasopharyngeal swabs, sputum, and alveolar lavage fluid.

RT-PCR technology. At present, RT-PCR nucleic acid detection serves an irreplaceable role in the diagnosis of 2019-nCoV and is the most important molecular diagnostic method in the early stage of the epidemic. However, there are limitations due to tedious, time-consuming operation, required biosafety laboratories ranked Class II or above, centralized inspection and shortage of personnel, and qualified biosafety sites in the epidemic area. Furthermore, there are shortcomings in responding to the rapidly increasing demand for the diagnosis of patients with suspected 2019-nCoV pneumonia and asymptomatic infections.

High-throughput sequencing technology. Gene sequencing is the most accurate and reliable technology for the detection of viruses and other pathogenic emergency infectious diseases. Additionally, it is the only method to dynamically track genome variation in pathogens.

LAMP technology. Developed in 2000, LAMP is a fast and highly specific technology for gene amplification under constant temperature conditions. RT loop-mediated isothermal amplification (RT-LAMP) combines RT with LAMP, can be used directly for RNA detection, and has previously been used in the identification of various respiratory RNA viruses, including SARS-CoV and MERS-CoV. Based on this, by adding a fluorescence quenching probe (QProbe), fluorescence RT-LAMP technology can be used for the detection of MERS-CoV. In order to make the detection of LAMP amplification products more accurate, the combination of nucleic acid detection and immunogold labeling technology has resulted in an improved RT-LAMP-combined nucleic acid strip detection technology (RT-LAMP-NAD), which has been used for the detection of Ebola virus.

Although LAMP technology has the advantages of simplicity, sensitivity, specificity, speed and is inexpensive and has low hardware requirements, the development of a kit using this technology is more complicated than an RT-PCR kit and involves multiple pairs of primers. Therefore, the development and clinical application of LAMP in 2019-nCoV pneumonia epidemic is slower than RT-PCR.

Recombinase-aided amplification technology. RAA technology utilizes recombinases, single-stranded binding proteins, and DNA polymerases to perform nucleic acid amplification under isothermal (37˚C) conditions. RAA technology is relatively new in the current nucleic acid detection technology field. The advantage of rapidity, sensitivity, and specificity of RAA technology may aid in the detection, screening, and isolation for suspected 2019-nCoV infections.

Nucleic acid mass spectrometry. Nucleic acid mass spectrometry is a novel type of soft ionized biological mass spectrometry technology that has been developed recently based on matrix assisted laser desorption ionization-time of flight technology and is very simple and efficient. This procedure integrates the high throughput of chip technology, and the high sensitivity of mass spectrometry technology, without the requirement for complex biological information analysis and is mainly used for the detection of known mutations. A single reaction of nucleic acid mass spectrometry can perform 20–50 PCR amplifications simultaneously and can detect dozens of pathogens at once. Nucleic acid mass spectrometry is a very useful tool for differential diagnosis of respiratory infections.

Nucleic acid mass spectrometry has high-throughput analysis, is simple to operate, and is inexpensive; nucleic acids are difficult to ionize, are unstable, and easily generate fragments. This makes it difficult to parse spectrum data. It is necessary to continuously improve the resolution of the detector to promote its use.

Protein detection technology. It is mainly divided into pathogen antigen detection and host antibody detection. Commonly used methodologies include colloidal gold, immunofluorescence chromatography, chemiluminescence, and ELISA.

Point-of-care testing. The current technology platform used by the majority of point-of-care testing (POCT) integrates nucleic acid extraction, amplification, and detection on a microfluidic chip that reduces detection complexity. POCT has the advantages of rapid results, unrestricted test sites, and low professional skill requirements for operators. Therefore, the research and development of POCT nucleic acid detection technology is likely to be the general direction of future development of testing. Operators only need to add samples, such as swabs or blood, into the slot on sample in, result out requirement, which will significantly simplify the detection process. POCT automatically completes nucleic acid amplification, signal collection, and result analysis in a short time. However, POCT requires improvement due to lack of authoritative control experiments and lack of uniform national standards for manufactured products.

In the future, molecular diagnostic research of 2019-nCoV infections will speed up sample preparation, increase detection throughput and accuracy, improve detection automation level, and develop novel technologies with low requirements and low costs for equipment and testing personnel. Due to antibody preparation requiring additional time, faster breakthroughs are expected in pathogen nucleic acid detection technology.

CRISPR – The future of molecular diagnostics?
CRISPR-based systems are well known for their use in gene editing and gene therapy applications due to their ability to cleave or cut nucleic acids. More recently, researchers have begun using the bacteria-derived technology to develop the next generation of rapid, accurate, and inexpensive molecular diagnostic technologies that can detect everything from antibacterial resistance and viral outbreaks to cancer-causing mutations in circulating tumor cells.

In terms of molecular diagnostics, CRISPR-based systems are ideal to detect the nucleic acid sequences of different pathogenic strains with single base specificity. For example, Cas9 and Cas12 proteins target DNA, while Cas13 targets RNA. This is a major advantage over the generated primers used to amplify target sequences in PCR, which are prone to off-target effects and non-specific amplification.

To create diagnostic applications, researchers have linked target sequence binding with readout, such as color changes, in the case of paper-based lateral flow assays, or fluorescence. In terms of fluorescence, researchers took advantage of the fact that once the Cas12 and Cas13 enzymes cleave their target sequence; they continue to cleave neighboring nucleic acids indiscriminately. Thus, by including nucleic acid reporters that fluoresce when cleaved in the sample, researchers can link cleavage of the target sequence to a fluorescent signal.

Both of these platforms are versatile and can be adapted to a variety of pathogens in response to novel outbreaks. Researchers recently used Detectr and Sherlock to develop a test for SARS-CoV-2, the latter of which could produce results in an hour.

Bacterial. The Flash-NGS platform, which combines Cas9 and NGS technologies, can target thousands of bacterial sequences linked to antibacterial drug resistance. In clinical settings, Flash-NGS has been used to detect MRSA (Methicillin-resistant Staphylococcus aureus and VRE (vancomycin-resistant E. faecium) infections.

Likewise, researchers have used Cas12a to develop a highly sensitive test for mycobacterium tuberculosis (Mtb). The test, called CRISPR-MTB, had better sensitivity (79%) than Mtb culture (33%), while maintaining a specificity of 98 percent. In addition to better sensitivity, which reduces the chance of false-negatives, because CRISPR-MTB does not require culture, patients could receive reliable results sooner.

Cancer and genetics. Identifying genetic mutations, such as single nucleotide polymorphisms (SNP), currently requires benchtop instruments or genome sequencing, but the specificity of CRISPR-based diagnostics has the potential to change that. For example, during the zika virus epidemic, researchers quickly developed a Sherlock-based test to detect an SNP associated with fetal microcephaly in patients with zika virus. Moreover, producing results in only 15 minutes, the CRISPR-chip platform has been used to detect the deletion of two exons associated with Duchenne muscular dystrophy.

The highly specific and sensitive nature of CRISPR-based tests would be especially useful for the detection of cell-free DNA and circulating tumor cells, which are present in very small amounts in serum, requiring a highly sensitive test.

Toward CLIA certification. Though PCR-based diagnostics are currently the gold standard, since their introduction in 2017, CRISPR-based diagnostics have quickly evolved with several advantages, namely speed, simplicity, and lower costs. They are ideal for POC settings, where rapid results can accelerate access to treatments and help prevent the spread of infections.

Though CRISPR-based diagnostics offer accessible readouts, and do not require complex laboratory facilities with benchtop thermocyclers, many of the other limitations of PCR-based diagnostics, such as reliable access to PPE, sample reagents, and nucleic acid extraction kits still also apply to CRISPR-based tests. These challenges must be overcome to produce a one-step diagnostic test that meets the Clinical Laboratory Improvement Amendments requirements. Even so, there is no doubt that portable CRISPR-based tests will soon revolutionize the field of clinical diagnostics.

In the future, novel epidemics or pandemics may be inevitable. It is crucial that pandemic-prevention agencies perform further research on pathogen differential diagnosis technology to improve testing times, provide definitive diagnoses, and diagnose diseases differentially with similar clinical manifestations. There are various types of pneumonia-related pathogens, including 2019-nCoV, SARS-CoV, influenza virus, parainfluenza virus, adenovirus, respiratory syncytial virus, rhinovirus, mycoplasma, and chlamydia. Considering RT-PCR results are time-consuming and laborious, there is an urgent need for medium-throughput detection technology for the differential diagnosis of 2019-nCoV and non-2019-nCoV conditions. In the future, it is necessary to focus on the development of high-throughput and low-cost differential diagnostic technologies. Furthermore, the development of detection technologies and supporting reagents that can simultaneously rapidly detect dozens of pathogens will be beneficial.