Colorimetric LAMP Test Matches PCR for Rapid Mpox Detection in Clinical Validation

Monkeypox virus, now officially known as mpox, has evolved from a largely regional public health problem in Central and West Africa into a sustained global concern. Since the unprecedented multi-country outbreak of 2022, which prompted the World Health Organization to declare a public health emergency of international concern, transmission has been documented in more than 130 countries. According to the World Health Organization, 52,845 confirmed mpox cases and 215 associated deaths were reported globally during 2025 alone, affecting 98 countries, with active transmission persisting particularly in several African nations. Against this backdrop, researchers at the ICMR-National Institute of Virology in Pune, India, have developed and clinically validated a colorimetric isothermal amplification assay that promises to bring rapid, accurate mpox diagnosis to laboratories that lack the sophisticated infrastructure demanded by conventional molecular testing.

The reference method for mpox diagnosis remains real-time quantitative polymerase chain reaction, or qPCR, which offers high sensitivity and specificity. However, qPCR depends on expensive thermocycling instruments, trained personnel, and biosafety-compliant laboratory facilities, all of which limit its accessibility in decentralized laboratories, outbreak settings, and resource-limited regions. Alternative molecular approaches such as restriction fragment length polymorphism analysis and next-generation sequencing are either labor-intensive, costly, or unsuitable for rapid frontline diagnostics. The World Health Organization has repeatedly emphasized the expansion of laboratory diagnostic capacity and the deployment of rapid, reliable, and accessible assays as a core component of its global mpox preparedness and response strategy, creating an urgent need for tools that can operate outside centralized reference laboratories.

The new assay, described in a study published in New Microbes and New Infections, is built on loop-mediated isothermal amplification, commonly known as LAMP. This nucleic acid amplification technique operates under constant-temperature conditions and enables rapid DNA amplification using a set of primers that recognize multiple regions of the target genome. LAMP-based assays require substantially less equipment than qPCR, offer shorter turnaround times, and allow visual interpretation of results. In the colorimetric format used by the Indian team, amplification is read out through a pH-sensitive dye: the reaction mixture starts pink under alkaline conditions and turns yellow when amplification succeeds, a transition that can be judged by eye without any specialized instrumentation.

To design the assay, the researchers retrieved complete and partial genomic sequences of monkeypox virus and other representative orthopoxviruses, including Vaccinia, Variola, Buffalopox, and Camelpox viruses, from the NCBI Virus database. Multiple sequence alignments were analyzed to identify conserved genomic regions suitable for isothermal amplification. Candidate genes evaluated included H2R, encoding a putative viral transmembrane protein; B6R, encoding an envelope protein; F3L, encoding a double-stranded RNA-binding protein; and F8L, encoding DNA polymerase. After preliminary analytical sensitivity testing and temperature optimization, primer sets targeting the orthopoxvirus genus-specific B6R gene and the monkeypox virus species-specific F3L gene were selected for full assay development. Primers were designed with PrimerExplorer V5, optimized for GC contents of approximately 50 to 60 percent, compatible melting temperatures, and minimal secondary structure or primer-dimer formation.

A defining feature of the assay is its dual-target architecture, which incorporates an internal control targeting the human beta-actin gene to verify sample integrity and amplification suitability. Under the predefined interpretation criteria, a specimen is classified as mpox-positive only if both the genus-specific B6R and species-specific F3L reactions yield positive colorimetric results. Specimens that are B6R-positive but F3L-negative are interpreted as non-mpox orthopoxvirus-positive, while specimens negative for both targets are classified as mpox-negative. This design provides two important advantages: reliable identification of monkeypox virus infections and the ability to differentiate mpox from other circulating orthopoxviruses, a capability that is particularly valuable in regions where multiple orthopoxviruses may co-circulate.

Clinical evaluation was performed using a well-characterized panel of 130 specimens obtained retrospectively from suspected mpox cases received for routine diagnostic testing at the Maximum Containment Facility of ICMR-NIV as part of national surveillance activities. The panel comprised 50 mpox-positive and 80 mpox-negative specimens as determined by qPCR, spanning five specimen categories: nasopharyngeal and throat swabs, vesicle swabs, lesion swabs, crust specimens, and lesion fluid specimens. All specimens had previously been tested by real-time qPCR targeting the B6R and F3L genes, which served as the reference standard. Sample processing and nucleic acid extraction were carried out in biosafety level-3 and level-4 containment laboratories in accordance with national biosafety guidelines, and the study received approval from the Institutional Ethics Committee of ICMR-NIV.

The results were striking. The LAMP assay correctly identified all 50 qPCR-positive specimens as positive and all 80 qPCR-negative specimens as negative, achieving complete concordance with the reference method. Sensitivity, specificity, positive predictive value, negative predictive value, and overall percent agreement were each 100 percent, with a Cohen’s kappa of 1.00 indicating perfect agreement beyond chance. Likelihood ratio analysis yielded a positive likelihood ratio of 160.4 and a negative likelihood ratio of 0.0099, corresponding to a diagnostic odds ratio of approximately 16,261. No discordant results were observed in any specimen category, indicating consistent performance across swabs, crusts, and lesion fluids. Per-target analysis confirmed that both the F3L and B6R assays individually achieved 100 percent sensitivity and 100 percent specificity, underscoring the robustness of the primer design and the dual-target interpretation algorithm.

The assay also demonstrated consistent detection across a broad range of viral loads. Among the 50 qPCR-positive specimens, cycle threshold values ranged from 18.55 to 37.21, with a median of 26.11. The LAMP assay detected every qPCR-positive specimen across this entire range, including the highest Ct specimen evaluated, and maintained 100 percent sensitivity within each Ct category examined, spanning values below 20, between 20 and 25, between 25 and 30, and at or above 30. The authors caution that these Ct-stratified findings should not be interpreted as a formal analytical limit of detection, because quantified monkeypox virus reference material was not available for standardized serial dilution testing. A formal limit of detection assessment will require quantified reference material, replicate testing, and predefined confidence thresholds in future validation studies.

Analytical specificity testing provided further evidence of the assay’s discriminatory power. A dedicated panel of 64 specimens included samples positive for Vaccinia virus, Buffalopox virus, Herpes simplex virus, and Varicella zoster virus, each represented by 16 specimens. Herpes simplex virus and Varicella zoster virus were included because they are clinically relevant causes of vesicular or pustular lesions that overlap with mpox in the differential diagnosis. As expected, the non-orthopox DNA viruses produced no amplification in either target, while Vaccinia and Buffalopox viruses yielded the characteristic B6R-positive, F3L-negative pattern, confirming that the assay can reliably distinguish monkeypox virus from genetically related orthopoxviruses while showing no cross-reactivity with unrelated viral pathogens.

The study’s authors note that several LAMP-based assays for mpox detection have been reported previously, but those efforts focused primarily on analytical sensitivity using synthetic templates or limited clinical evaluation sets. In contrast, the present work emphasizes clinical validation using a structured evaluation panel and comprehensive diagnostic accuracy metrics, including likelihood ratios and agreement statistics, in line with current recommendations for reporting diagnostic accuracy studies. The incorporation of uracil-DNA glycosylase in the commercial master mix further guards against carryover contamination, improving reliability in routine diagnostic settings.

Nevertheless, the researchers acknowledge several limitations. The clinical evaluation was retrospective, used archived specimens from a single reference laboratory, and included a limited sample size of 50 positive and 80 negative specimens, so the performance estimates should not be overgeneralized. A formal analytical limit of detection was not determined, the specificity panel did not include all infectious and non-infectious causes of vesiculopustular lesions, and formal reproducibility testing across multiple days, operators, reagent lots, and low-positive specimens was not performed because of limited specimen volume. Future studies incorporating quantified standards, broader specificity panels, multi-site validation, reproducibility assessment, and prospective field evaluations will be needed before wider clinical implementation.

From a public health perspective, the simplicity of the colorimetric LAMP assay, combined with its minimal equipment requirements, rapid turnaround time, and visual readout, makes it a promising tool for expanding mpox diagnostic capacity beyond centralized laboratories. The diagnostic method is covered by an Indian patent application filed in October 2022 and published in April 2024, held by the Indian Council of Medical Research. While qPCR will continue to play a central role in reference and confirmatory testing, the new assay is particularly relevant for outbreak response, surveillance activities, and diagnostic decentralization in resource-limited settings, aligning with recent WHO mpox preparedness and response frameworks. As mpox transmission continues across multiple continents, accessible tools of this kind may prove decisive in closing the diagnostic gap that has long hampered containment efforts.

Subject of Research: Development and clinical validation of a colorimetric loop-mediated isothermal amplification assay for rapid detection of monkeypox virus

Article Title: Development and clinical validation of a colorimetric isothermal assay for rapid detection of monkeypox virus

Article References: Nandi, S. S., Sawant, S. A., Yadav, P., Shete-Aich, A., Majumdar, T. D., Bavkar, K. C., Mukherjee, A., & Deshpande, J. M. (2026). Development and clinical validation of a colorimetric isothermal assay for rapid detection of monkeypox virus. New Microbes and New Infections, 73, Article 101848. https://doi.org/10.1016/j.nmni.2026.101848

Image Credits: AI Generated

DOI: 10.1016/j.nmni.2026.101848

Keywords: mpox, monkeypox virus, LAMP assay, colorimetric detection, isothermal amplification, qPCR, diagnostic validation, orthopoxvirus, B6R gene, F3L gene, ICMR-NIV, point-of-care testing