Study compares monkeypox PCR testing protocols and efficiency at two U.S. reference labs

In a recent study posted to the medRxiv* preprint server, researchers examined sample collection practices, epidemiological characteristics, and cycle threshold (Ct) values for polymerase chain reaction (PCR) tests used in two reference laboratories in the United States (U.S.) to detect monkeypox virus (MPXV).

Study: Clinical Performance and Trends During the First Two Months of Monkeypox Virus PCR Testing at Two United States Reference Labs. Image Credit: Salov Evgeniy / Shutterstock

Background

The recent outbreak of monkeypox in non-endemic countries such as the U.S. has resulted in increased MPXV PCR diagnostic testing. Monkeypox is caused by a virus in the Orthopoxvirus genus, similar to the smallpox-causing Variola virus. With the almost complete eradication of smallpox, most countries discontinued the smallpox vaccination, leaving gaps in immunity.

The substantial decrease in the spread of orthopoxviruses had also resulted in clinicians being unfamiliar with orthopoxvirus infections and fewer diagnostic testing facilities. Before the 2022 outbreak, MPXV testing was carried out only in U.S. Food and Drug Administration (FDA) approved laboratories or by the Centers for Disease Control and Prevention (CDC). Between June and July 2022, laboratory-developed and FDA-authorized testing of monkeypox expanded to clinical laboratories.

While clinical and reference laboratories can process substantially higher numbers of cases than public health facilities, and report qualitative test results to the CDC and state health departments, data such as Ct values and test performances are not regularly reported. Monitoring these data can help identify emerging variants and improve testing practices.

About the study

The present study investigated MPXV PCR testing data from two reference laboratories in the U.S — the University of Washington Virology Lab (UW) in Seattle, Washington, and ARUP Laboratories (ARUP) in Salt Lake City, Utah. The examined data included information for more than 10,000 specimens collected between July and August 2022.

Descriptive epidemiological factors such as age and sex distribution in MPXV PCR testing were compared across the two laboratories. Additionally, the researchers examined the average Ct values in both laboratories to compare the viral loads detected in the PCR tests. Finally, the test result concordance was compared using the percentage of patients who submitted multiple swabs.

Results

The results reported an increase in testing among males aged 18 to 40, considered to be at greater risk of monkeypox. The authors observed that positivity rates decreased with the increase in the number of submitted specimens. They also detected a more significant number of positive test results among males than among females, which is consistent with other study results reporting a higher incidence of monkeypox infections among men who have sex with men.

The Ct values between the two reference laboratories were comparable, with ARUP laboratory tests detecting a slightly higher viral load. The collection and extraction methods, however, differed significantly. The Chemagic nucleic acid extractor used by ARUP has higher analytical sensitivity than the viral inactivation and lysis protocol used in UW. The authors believe that the difference in specimen processing and extraction procedures could account for the variation in viral loads from the two laboratories.

Collecting multiple swabs from the same individual resulted in an overall test concordance of more than 95%. A very low percentage (less than 1.5%) needed three or more tests for a positive result, and their Ct values were significantly high, indicating a low viral load. Dry swabs suspended in phosphate-buffered saline revealed higher viral loads than swabs in viral transport media (VTM), which the authors attribute to the dilution of the viral load in VTM.

According to the authors, while discordant positive results could be due to low viral loads, cross-contamination cannot be ruled out as a reason. The CDC recently released an advisory about the risk of false positives and urged laboratories to test two specimens for results with Ct values greater than 34.

Conclusions

Overall, the study showed that monitoring MPXV PCR testing factors other than qualitative test results across clinical and reference laboratories is extremely useful in understanding the differences in and improving the processes of diagnostic tests.

The authors report that while multiple swabs from one individual do improve the overall test concordance, a considerable portion of PCR testing facilities and resources are used for one individual, which is inefficient in terms of resources and time. Therefore, they instead propose a method of combining multiple swabs from one individual in VTM to improve diagnostic performance while reducing overall costs.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information

Written by

Dr. Chinta Sidharthan

Chinta Sidharthan is a writer based in Bangalore, India. Her academic background is in evolutionary biology and genetics, and she has extensive experience in scientific research, teaching, science writing, and herpetology. Chinta holds a Ph.D. in evolutionary biology from the Indian Institute of Science and is passionate about science education, writing, animals, wildlife, and conservation. For her doctoral research, she explored the origins and diversification of blindsnakes in India, as a part of which she did extensive fieldwork in the jungles of southern India. She has received the Canadian Governor General’s bronze medal and Bangalore University gold medal for academic excellence and published her research in high-impact journals.