Background Regarding Enteroviruses
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Upon cellular entry, translation occurs following ribosome binding onto a type I internal ribosome entry site (IRES) located within the 5′[Untranslated Region (UTR)] of the viral genome. [...] During active infection the ratio of positive to negative strands is roughly 100:1, whereas chronic infections display a ratio closer to 1:1. [...] The 5′UTR of [enteroviruses (EV)] contains a cloverleaf secondary structure, [...] as well as an internal ribosome entry site (IRES). [...] The viral encoded RNA polymerase is error-prone due to lack of a proof-reading mechanism, resulting in high mutation rates throughout enteroviral evolution.
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Steady-state infections are characterized by all cells in culture having low levels of non-lytic viral replication. [...] To date, multiple studies have shown a subset of enterovirus serotypes, including coxsackieviruses and echoviruses, are able to produce low replicative steady-state infections without cytopathic effect. This phenomenon may be caused by a number of factors including but not limited to 5′UTR terminal deletions that lead to replication deficiencies or reduced type I interferon response elicitation, faulty virion capsid formation due to incomplete capsid polypeptide processing, and alternative EV RNA mutations that lead to abnormalities such as stable and atypical double-stranded RNA complex formation that inhibits further viral positive strand synthesis. In the context of ME/CFS, 5′UTR terminal deletions and/or atypical dsRNA complex formation are notable, as they have been shown to occur in a proportion of ME/CFS patient cohorts in multiple studies. [...] Low levels of viral replication result in EV RNA levels so small that they may be past the lower limit of detection.
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Detection of Enteroviruses
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Across the enterovirus and virus literature at large, a number of methodologies are used to detect the presence of enteroviral infection in patients. In the early years of virus detection, biological approaches such as serological testing and cell culture methods were employed. [...] The main disadvantages to cell culture are that inoculation depends on quality of the patient sample and requires variable and sometimes extended time periods to allow detection. Some enteroviruses, especially persistent enterovirus variants, do not produce [Cytopathic Effect (CPE)] in cell culture. Without CPE, screening for viral nucleic acid or protein would be necessary.
Serological testing is confounded by several factors. First, enteroviruses often produce clinical disease before the appearance of antibodies, making their detection retrospective. Furthermore, enteroviruses and rhinoviruses have extensive antigenic heterogeneity and lack cross-reacting antigens, so that many different antigens would be needed to detect anti-EV antibodies. [...] Commercial labs with serological tests for EVs are far from comprehensive. For instance, the Enterovirus [...] kits sold via Virotech Diagnostics detects 14 [...] of the roughly 120 known EV serotypes. The Enterovirus Antibody Panel lab test provided by ARUP Laboratories similarly detects 14 EV serotypes [...] although the serotypes differ slightly. Negative detection of EVs via these commercially available serological tests does not conclusively eliminate the possibility of an EV infection.
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The most popular detection method for identification of enteroviruses is RT-PCR, with amplification directed at conserved regions of the enterovirus genome, including those encoding the 5′UTR, 3Dpol and VP1. VP1 is the region of choice to conduct enterovirus typing. However, low sequence similarity amidst the approximately 120 enterovirus serotypes means that no one primer set is robustly comprehensive so that RT-PCR methods would have a lower chance of identifying novel EV serotypes than unbiased sequencing. RT-PCR experiments that use primers directed at the 5′UTR of enteroviruses can be problematic if the enterovirus contains mutations within the primer binding region, as is known to happen during persistent infection. Traditional RT-PCR approaches have reduced ability to identify novel enteroviruses that could be etiological agents in new diseases.
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To date, ME/CFS studies reporting the use of tissue culture for EV detection have used [Cerebrospinal Fluid (CSF)] and feces in 1 and 4 studies, respectively. The singular CSF study reported two EV infections in a cohort of 4 patients, while the 4 fecal studies reported an increased EV infection prevalence in 2 of 4 studies, with cohorts ranging from a 22–25% prevalence across patient cohorts. [...] Although the prevalence of EV infections in these studies was generally shown to be significantly increased compared to healthy control cohorts, limitations in patient sample types and cell culture models may have led to findings that underrepresent the prevalence of EV infections in patient cohorts. Of the five cell culture studies, one study used only one cell type, 3 studies used two cell types and one study used three cell types. [...] Furthermore, the investigators were searching for [Cytopathic Effect (CPE)], and EVs present in chronic infections commonly undergo genetic changes which reduce CPE. An example of the inadequacy of CPE is a report that inoculated cell cultures were negative for CPE production in human fetal lung fibroblast and tertiary monkey kidney cell cultures but were nevertheless positive upon RT-PCR. [...] Studies reporting the absence of enterovirus infections in ME/CFS patient cohorts using tissue culture approaches had small sample sizes and incomprehensive cell culture systems. Small sample sizes along with the fact that EVs harboring 5′UTR deletions do not produce CPE means that no definitive conclusion can be made about the absence of EVs from the data in these studies. Furthermore, fecal samples usually identify only acute enterovirus infections and not chronic ones that might be in secondary infection sites.
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Studies between the 1970s and late 1990s that screened for EV infections in ME/CFS patients largely focused on serological testing. The diversity of testing employed in a total of 20 serological-based ME/CFS studies included neutralization, complement fixation, micro-metabolic inhibition, ELISA, indirect immunofluorescence, and VP1 antigen detection tests. In total, 16 of the 20 studies found an increased prevalence of [Coxsackievirus B (CVB)] signals in ME/CFS cohorts with positive findings ranging from 8 to 90% compared to the positive findings in healthy control cohorts that ranged from 0 to 65%. The vast majority of studies evaluated the presence of antibodies directed only against CVB enteroviruses, with a few exceptions. [...] A notable study was performed in 1997, in which neutralization tests for 11 enteroviruses [...] found that 100 out of 200 tested patients had elevated enteroviral titers. Although serological testing in ME/CFS cohorts generally shows an increase in the prevalence of EV antibodies, the findings often lack clinical specificity as a high prevalence of EV antibodies are found in the general population from previous exposure. In a retrospective study, it cannot be known whether the enterovirus infection occurred before or after ME/CFS disease onset without having paired sera from both time periods.
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The enteroviral capsid protein VP1 is commonly used for [immunohistochemical] identification of enteroviral virions in ME/CFS patient tissues. In total, 5 studies have used this technique on a variety of patient sample types, including muscle, gastrointestinal, and brain tissue. Of these, 4 out of 5 studies identified the presence of VP1 capsid proteins in patient tissue. The muscle tissue study did not detect VP1 staining in samples of a cohort of 30 ME/CFS patients, despite RT-PCR signals that indicated the presence of EV RNA in 13 of the same 30 patients. The authors suggested that the difference in PCR and VP1 immunochemistry resulted from persistent but latent enteroviral infection in patient muscle tissues, in which no detectable amount of virion particles were being produced. The remaining 4 studies showed positive VP1 staining in both gastrointestinal and brain tissues. Gastrointestinal samples exhibited positive staining rate of 82% in two patient cohorts. [...] The ME/CFS [cohort] showed dsRNA staining for 64% [...] of patients. [...] Because persistent/chronic EV infections with reduced CPE and viral replication typically have a 1:1 ratio between enteroviral positive and negative RNA strands, finding a high rate of dsRNA in patient tissues indicates the likely presence of persistent enteroviral infections.
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The 4 Northern blot studies used muscle tissue biopsies and were all positive for viral RNA, indicating an EV prevalence between 21 and 50% in ME/CFS with control cohorts showing a prevalence between 0 and 1%. The two RNAseq studies were negative for the presence of EV in blood, whether or not blood was taken before or after an exercise stress that exacerbated subject symptoms. While RNAseq is a more comprehensive approach to enterovirus detection than Northern blots, these studies cannot be directly compared since one used muscle tissue and the other assayed blood samples. With regard to EV studies that applied RT-PCR methods, 5 of the 17 reports indicated no significant difference in EV prevalence between ME/CFS and control cohorts. [...] A list of all 8 PCR approaches/methods, indicating the primer sets employed in RT-PCR experiments, was first compiled, and then each PCR set was examined for its effectiveness for detection of all 117 known EV serotypes. [...] As mentioned earlier, EVs are known to exhibit mutations in the 5′UTR that result in replication deficiencies. Interestingly, all 8 PCR methodologies used primer pairs targeting the 5′UTR with the exception of method 5. [...] This is an important consideration as patients infected with EV variants exhibiting 5′UTR deletions may not be successfully targeted by the primer sets employed across these PCR methodologies. In conclusion, PCR studies aimed at identifying EVs in ME/CFS have been crippled by the use of incomprehensive primer sets that target potentially deleted portions of the viral genome.