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EID Journal: Isolation of VEEV Genome from Human Swab Specimen, Peru

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  • EID Journal: Isolation of VEEV Genome from Human Swab Specimen, Peru

    EID Journal: Isolation of VEEV Genome from Human Swab Specimen, Peru
    Credit EID Journal


    Conventional wisdom - particularly when it comes to infectious diseases - isn't what it used to be. The more knowledge we glean, the more unexpected findings, and `exceptions to the rule', that end up in the scientific literature.

    A few recent examples include:

    Five years ago, it was generally accepted that Ebola was simply too debilitating, and too lethal, to have `legs’ . . . to spread beyond a limited geographic area. Those infected were believed `too sick to travel’, and therefore small outbreaks would inevitably `burn themselves out’ in relatively short order.
    And then, defying all expectations, we saw the first urban epidemic of Ebola spreading across three West African nations in 2014, resulting in more than 28,600 cases and causing at least 11,325 deaths (cite).
    Additionally, from this epidemic we learned that the Ebola virus can persist in a `recovered' patient for months (see Virus Evolution: Rapid Sequencing Reveals Rare Ebola Transmission Via Breast milk And Semen), adding new, and unexpected ways to reintroduce the virus back into the community.

    For forty years - since it famously sparked an infamous pneumonia outbreak at Philadelphia’s Bellevue Stratford Hotel during an American Legion convention in 1976 - Legionella pneumonia has been considered strictly an environmental illness.
    It was not believed transmissible from human-to-human (cite).
    And while that conventional wisdom is still probably true 99.99% of the time, in 2016's NEJM: Probable Person-to-Person Transmission Of Legionnaires’ Disease, we saw evidence presented that person-to-person transmission of Legionnaires Disease may have occurred in 2014 during an outbreak in Portugal.

    In 2015, an obscure vector borne arbovirus - Zika - was suddenly implicated in hundreds of severe birth defects in South America (see NEJM: CDC Concludes Zika Causes Microcephaly & Other Birth Defects)- an impact never before attributed to a mosquito borne virus.

    But Zika wasn't done confounding conventional wisdom, as we also learned in early 2016 that a Zika infection could be transmitted sexually. Something that had not been previously considered a serious public health risk (see WHO: Updated Interim Guidance On Prevention Of Sexual Transmission Of Zika Virus).
    The list of recent viral `surprises' is both lengthy and growing.
    Some of these events are extreme outliers - like H-2-H Legionella transmission - and probably don't have a great amount of real world implications - while others, like the surprises delivered by the Zika and Ebola viruses, do.
    Today via the CDC's EID Journal, we get yet another surprise finding, with a virus showing up in an unexpected part of a human host.
    While its real world significance is unknown right now, it involves a fascinating bit of scientific detective work based on the testing of a nasopharyngeal swab of a 16 year-old boy from Peru suffering from unexplained `flu-like' symptoms.

    A link and some excerpts follow, but you'll want to click the link to read it in its entirety.

    Volume 24, Number 8—August 2018
    Research Letter

    Isolation of Complete Equine Encephalitis Virus Genome from Human Swab Specimen, Peru

    Diana Juarez, Carolina Guevara, Michael Wiley, Armando Torre, Gustavo Palacios, Eric S. Halsey, Sonia Ampuero, and Mariana Leguia


    While studying respiratory infections in Peru, we identified Venezuelan equine encephalitis virus (VEEV) in a nasopharyngeal swab, indicating that this alphavirus can be present in human respiratory secretions. Because VEEV may be infectious when aerosolized, our finding is relevant for the management of VEEV-infected patients and for VEEV transmission studies.

    Venezuelan equine encephalitis virus (VEEV) is one of many alphaviruses transmitted through the bite of infected mosquitoes (1,2). VEEV primarily infects equine species, causing severe encephalitis and death. VEEV may also infect humans, causing fever and influenza-like symptoms that include headache, chills, myalgia, nausea, and vomiting. In severe cases, human VEEV infection may result in neurologic complications that lead to fatalities. Acute VEEV infection is usually confirmed by PCR, sequencing from blood (3), or both, or in the case of encephalitis, from spinal fluid. Nasopharyngeal swabs are rarely tested for alphaviruses like VEEV because they are considered nontraditional sample types for these kinds of pathogens.


    In 2013, in Iquitos, Peru, we identified a 16-year-old boy who reported a variety of undifferentiated illness symptoms, including fever, chills, general malaise, myalgia, headache, rhinorrhea, sore throat, nausea, vomiting, abdominal pain, retroorbital pain, rash, and photophobia. A field-administered rapid test for influenza on a nasopharyngeal swab specimen was negative. More thorough laboratory tests, including a highly multiplexed MassTag PCR assay that can detect >20 viral and bacterial pathogens (4), were also negative (Figure, panel A).

    The sample entered a pathogen discovery pipeline routinely used to amplify and identify unknown etiologies (5). In brief, we cultured 200 μL of the original nasopharyngeal sample in Vero-E6, LLCMK2, and MDCK cells. Cytopathic effect appeared by day 4 in Vero-E6 and LLCKM2 cells and by day 19 in MDCK cells. We used culture supernatant from day 4 LLCMK2 cells as starting material for NGS MiSeq libraries, which we prepared, sequenced, and processed as described (5). Sequencing generated 704,444 raw reads, from which 28,555 were de novo assembled into a single 11,412-nt contig (Figure, panel B). When blasted, the contig matched the complete genome of a VEEV-ID strain isolated in Peru from 1994 (GenBank accession no. KC344526.1) with 99% identity.


    Febrile surveillance studies have shown that VEEV is prevalent in many countries throughout Latin America (3,6). Although respiratory symptoms have been reported in association with VEEV infection (7), and there is >1 report of VEEV in throat swabs (8), human respiratory secretions are seldom tested for alphaviruses. In fact, the presence of VEEV in respiratory secretions, as well as its implications for health and biosafety, are rarely discussed.
    Although person-to-person transmission of VEEV has not been documented, VEEV can be infectious through aerosolized particles (9,10), so the potential for an alternate transmission route exists. This possibility should be considered both during individual management of VEEV-infected patients and in studies considering VEEV transmission dynamics or prevention strategies.

    Ms. Juarez has worked as a researcher at US Naval Medical Research Unit No. 6, in Lima, Peru. She is now with the Genomics Laboratory at Pontificia Universidad Cat?lica del Per?. Her work focuses on the characterization of emerging and novel pathogens.
    While this may end up being little more than a fascinating footnote in the VEEV literature, from tiny clues like these, bigger discoveries are often forged. Hopefully in the next year or two, we'll see some follow up studies.
    History has shown that the better scientists get at looking for things, the more strangeness they will find.
    Which is why - when it comes to predicting how infectious diseases will behave now - or in the future - it is probably prudent to never say `never'.

    All medical discussions are for educational purposes. I am not a doctor, just a retired paramedic. Nothing I post should be construed as specific medical advice. If you have a medical problem, see your physician.