Infectious disease research

What is an infectious disease?

Infectious diseases are illnesses caused by pathogenic organisms like bacteria, viruses, fungi, or parasites. They are spread through external exposure to contaminated food, water, person-to-person contact, or other means. When these contagious organisms spread throughout a population at uncontrolled rates, they can have global implications, as seen most recently with the SARS-CoV-2 pandemic and the mpox health emergency. Other infectious diseases, including but not limited to tuberculosis, HIV, Ebola, Zika, Polio, and malaria, have also had significant impacts on human health globally.

Infectious disease research

Infectious disease research is essential because it provides important information about the origin and evolution as well as the transmission routes of disease-causing organisms. Further, infectious disease researchers can conduct population surveillance studies to monitor the prevalence of pathogenic organisms in communities. One recent example of this includes wastewater-based epidemiology (WBE) research that has been conducted to monitor SARS-CoV-2 levels and emerging variants.

There are numerous methods for studying infectious diseases, many of which utilize the genetic material of the disease-causing organism or monitor the immune response of infected individuals.

Examples of infectious disease research methods include:

• Real-time qPCR (RT-qPCR)
• Digital PCR (dPCR)
• Antibody-based monitoring
• Next generation sequencing (NGS)

Choosing a method for infectious disease research can depend on multiple factors including sample type, sample quantity and quality, research objectives, and budget. Researchers often use a combination of these methods while investigating an infectious disease.

How antibodies can be used to identify infectious diseases

Antibody-based methods, such as immunological assays (e.g., enzyme-linked immunosorbent assays [ELISA] or immunochromatographic lateral flow assays) can be specific, fast, and simple to use [1]. Unlike RT-qPCR, dPCR, and NGS these methods are not high throughput and have relatively low sensitivity levels. Developing an immunological assay for virus, bacteria, fungi, etc. requires the identification of specific antibodies that bind with high affinity to the target. Phage display and/or yeast display are coupled with large numbers of DNA sequences to identify and develop very specific antibodies to the target of interest.

If your research goal is to identify new antibodies that bind specific targets of infectious agents, IDT provides high-quality genes, gene fragments, and fragment libraries that can be used in the antibody discovery process. These same reagents can then be used to modify mammalian cells for production of the antibody for use in the specific testing device.

RT-qPCR and dPCR

RT-qPCR approaches allow clinicians and researchers to obtain results rapidly using relatively simple and streamlined protocols. This approach is often used for pathogen detection, and when coupled with high-quality controls that are correctly validated, RT-qPCR assays can be quantitative. IDT gene fragments are one reagent that can be used to establish the relative fluorescent signal that correlates with the copy number of targets. This approach does not provide full genomic information though, and RT-qPCR assays need thorough optimization before they can be established as a diagnostic by the FDA [2].

Digital PCR allows researchers to directly quantify the number of DNA molecules in a sample, and therefore provides an absolute value. This method also has lower limits of detection than RT-qPCR and is more precise than RT-qPCR. This features make dPCR better at identifying rare mutations [3]. This approach has also been shown to have a better tolerance to inhibitors than qPCR [2]. Unlike RT-qPCR however, dPCR is less scalable and may not be suitable for large projects with a large number of samples.

Both of these approaches can be used for genotyping studies -i.e., identifying genetic variations in a sample. However, genotyping using dPCR or RT-qPCR is less complete and less high throughput than NGS since the probes must be designed to known mutation sites and alleles.

Next generation sequencing (NGS)

NGS is a high-throughput approach [4]. It can be useful when studying the evolution of a disease-causing organism as this method provides genome sequence information. It is commonly used for studies identifying variants (genotyping) in many samples. NGS can be either targeted or untargeted. Specific types of untargeted NGS include shotgun metagenomic sequencing which results in information about all the DNA in a sample, or targeted sequencing, which results in sequencing of a selected target region or genome(s).

Two of the main methods of targeted sequencing are amplicon sequencing in which primers are used to amplify specific targets of interest resulting in sequences uniquely from the organism or gene of the primers were designed for; and hybridization capture sequencing in which probes are used to enrich the genetic regions of interest.

NGS can be less cost-effective than RT-qPCR or antibody-based methods. Additionally, the complex library construction and following bioinformatic analyses can also make this approach less straightforward. However, this brings the benefit of being able to assess multiple targets or positions from a single assay.

Viral Surveillance─Identifying novel variants

A number of infectious diseases are caused by viruses -e.g., COVID-19, influenza, and mpox. Large-scale viral surveillance efforts are aimed at monitoring the spread of viral diseases both geographically and temporally to allow researchers to identify new outbreaks of diseases [5]. This type of surveillance has been integral in the development of public health guidelines throughout the SARS-CoV-2 pandemic because it has allowed researchers to identify novel variants and track their spread [6].

Consistent identification of new viral variants can be difficult because as viruses or other pathogens evolve their genetic material changes, which can make the genetic tools initially designed to target or even treat that organism less effective. Read more about viral surveillance here.

Technologies for infectious disease research

Explore IDT's products for infectious disease research

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References

1. Peruski AH, Peruski LF, Jr. Immunological methods for detection and identification of infectious disease and biological warfare agents. Clin Diagn Lab Immunol. 2003;10(4):506-513.
2. Pavsic J, Zel J, Milavec M. Assessment of the real-time PCR and different digital PCR platforms for DNA quantification. Anal Bioanal Chem. 2016;408(1):107-121.
3. Tong Y, Shen S, Jiang H, et al. Application of Digital PCR in Detecting Human Diseases Associated Gene Mutation. Cell Physiol Biochem. 2017;43(4):1718-1730.
4. Pfeifer SP. From next-generation resequencing reads to a high-quality variant data set. Heredity (Edinb). 2017;118(2):111-124.
5. Carroll D, Morzaria S, Briand S, et al. Preventing the next pandemic: the power of a global viral surveillance network. BMJ. 2021;372:n485.
6. Ibrahim NK. Epidemiologic surveillance for controlling Covid-19 pandemic: types, challenges and implications. J Infect Public Health. 2020;13(11):1630-1638.