Lab Matters Spring 2023 | Page 19

I still consider the LRN a jewel in CDC ’ s crown , but it ’ s an old jewel , and it has not adapted to the world we live in now . It simply needs to be reset for today and the future . ”
Jill Taylor , PhD health world — and how those specimens are shared with the public health world ,” Hughes says . The commercial laboratories may not be keeping specimens and are not necessarily giving the samples to the public health laboratories or CDC to learn more about the disease outbreak through sample culturing or sequencing .
“ There is a risk to relying solely on commercial labs for public health-related testing ,” Hughes says .
Another LRN bottleneck during the mpox outbreak was the CDC ’ s LRN Results Messenger ( RM ) system , which required laboratory staff to manually type in a lot of patient demographic data and a case history in order to report a mpox test result .
“ It ’ s fine when you have one sample , but when you ’ ve got hundreds of samples … It was taking our team , for 10 to 20 samples , between an hour and an hour and a half to just put in the results and the data for each sample ,” Hauser says .
Her team worked with CDC , which eventually allowed the laboratory to bulkupload a spreadsheet of all the results , she says . Later , the CDC data team helped the laboratory switch over to electronic messaging and skip the RM portion .
“ But for a really long time we were doing both ,” Hauser says . “ So , I think it ’ s worth spending the time and the resources to be able to get electronic reporting for these and be able to collect all the information that they would get from RM .”
The reason CDC asks for so much information is valid , Taylor says , allowing the agency to develop case reports , learn more about the disease and put out recommendations . “ But in reality ,” she says , “ it ’ s more efficient to get the patient tested , and then when you get a positive result , the epidemiologists follow up with that individual and get the information for a case report .”
Also , she points out , when testing was switched to the commercial laboratories , those facilities were not required to provide as much data with the results .
Use of Whole Genome Sequencing
Los Angeles County began whole genome sequencing ( WGS ) in July 2022 to learn more about the mpox clade , but when the commercial entities took over , it also had trouble getting samples , Green says .
“ The same thing happened with COVID-19 — we were the only place in town to get the COVID-19 test and then it went off to the commercial laboratories ,” Green says . “ And now , because our role has changed … we don ’ t have anything to sequence . So now , we have to get the samples back from these laboratories .”
She compares it to a merry-go-round : “ It seems kind of inefficient , that ’ s all .”
As Los Angeles County considered doing WGS on the mpox virus , Green ’ s staff heard about a laboratory at the Yale University School of Public Health that had developed a sequencing assay but had no samples to test it on . So , Los Angeles County reached out , and the two teams formed a partnership : Yale provided the laboratory with the test — and reagent initially — to evaluate their method with the county ’ s samples . It worked .
Sequencing in-house meant the laboratory could provide data about the virus to their epidemiologists faster , Green says . The laboratory learned several things from WGS . The team continued to confirm that the strain in the outbreak was the West African clade , not the deadlier Congo Basin clade . Furthermore , the laboratory detected genome deletions that could affect the accuracy of diagnostic tests .
“ What we realized was that the parts of the genome that were missing potentially were areas that certain diagnostic tests were using as targets , meaning that if you had a patient that had a strain that had this deletion , it may not be detected ,” she says .
Through WGS , the laboratory also identified mutations in samples that could make those patients resistant to tecovirimat , or TPOXX , which is approved to treat smallpox and is being used to treat mpox under an investigational new drug protocol . Green ’ s laboratory shared their data with CDC , the National Center for Biotechnology Information and with databases such as GISAID .
The Future of the LRN
While experts agree the LRN needs to be updated , modernization will likely require a different perspective — perhaps a reframing . Mangal believes the LRN needs elevation at the CDC , that more divisions need to consider it as the go-to laboratory response arm .
Taylor agrees : “ It ’ s a preexisting network with highly trained people , with funding that goes up and down ( which is a problem ), and instead it needs to be the frontline of the response .
“ I still consider the LRN a jewel in CDC ’ s crown ,” Taylor continues , “ but it ’ s an old jewel , and it has not adapted to the world we live in now . It simply needs to be reset for today and the future .” g
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