A History of Outbreak Response

  • 2003


    CII developed the first sensitive PCR assay for SARS and Drs. Lipkin and Briese hand-delivered 10,000 test kits to Beijing at the height of the outbreak. This work was recognized by President Xi in 2016 with a gold medal and the China International Science and Technology Award and Consul General Ping Huang in 2020 with a medal of appreciation in celebration of the 70th year of the PRC.

  • 2006

    MassTag PCR

    MassTag PCR was utilized in 2006 as a rapid idenification of ten different causes of viral hemorrhagic fevers, which allows for early differential diagnosis that improves clinical management and containment. In 2008, multiplex MassTag-PCR illustrated previously unrecognized rhinoviruses may cause a significant amount of pediatric respiratory disease. Conventional diagnostic testing did not pick up the virus in any nasopharyngeal sample. The same technology was utilized for a pediatric unexplained respiratory illness study in Germany.

  • 2007

    Honey Bee Colony Collapse Disorder (CCD)

    First application of next-generation sequencing in an agricultural study showing the Israeli acute paralysis virus of bees was strongly correlated with CCD. A follow up 2009 study utilized pyrosequencing to analyze the negative impact of the microsporidian pathogen Nosema ceranae.

  • 2008

    Novel Bornavirus in Psittacines

    Discovery of a novel bornavirus as the cause of proventricular dilatation disease (PDD) using pyrosequencing of cDNA from the brains of parrots. Discovery of the two strains involved were discovered in a two-week period, whereas the initial bornavirus discovery in the late-1980s required a two year investment in subtractive cloning.

  • 2008

    Dandenong Virus

    The use of high-throughput sequencing revealed a new arenavirus transmitted through solid-organ transplantation, marking the first application of next-generation sequecing in an infectious disease outbreak. Specific PCR assays based on a unique sequence confirmed viral presence in the kidneys, liver, blood, and cerebrospinal fluid of transplant recipients.

  • 2008


    Discovery of a novel arenavirus (LuJo virus) as the cause of an outbreak of unexplained hemorrhagic fever in Southern Africa. Four of five patients died until identification via RT-PCR enabled treatment and survival of the final victim. Mice are strongly considered to be the viral source and humans become infected via contaminated food or household items.

  • 2010

    Novel Polyradiculoneuropathy

    Identification of a novel polyradiculoneuropathy associated with removing porcine brains via compressed air, which liquifed the brain and generated aerosolized droplets from the CNS tissue, easily exposing workers. The finding changed methods for meat processing and eliminated the exposure risk and earned the group the 2011 Charles C. Shepard Science Award from the CDC.

  • 2010

    Piscine Reovirus

    Discovery of a novel orthoreovirus (Piscine reovirus, PRV) as the cause of a fatal heart and skeletal muscle inflammation threatening farms and wild salmon worldwide. The study prompted global measures to be taken to control PRV to ensure food security and prevent economic disruption.

  • 2014


    One fecal sample from an Egyptian Tomb Bat (Taphozous perforatus) collected within a few kilometers of the first known MERS victim's home contained sequences of a virus identical to those recovered from the victim. Nasal samples collected during a countrywide survey of dromedary camels matched MERS-CoV found in humans, indicating that the virus in camels is capable of infecting humans and that camels are a likely source of the outbreak.

  • 2016

    Tilapia Lake Virus (TiLV)

    We reported the characterization of a novel orthomyxo-like virus as the causative agent in TiLV, which is implicated in the mass die-off in two continents. The Food and Agricultural Organization of the United Nations acknowledged this poses a global threat to food as well as economic security. The Binational Agricultural Research and Development Fund, who sponsored the research, selected the TiLV research as one of the top three most successful and impactful scientific projects (out of 1,330 total) in the 40 year history of the organization.

  • 2017


    A pentaplex rRT-PCR assay was developed for specific and sensitive detection of the African and American genotypes of Zika, dengue, chikungunya, West Nile virus. The CII-ArboViroPlex rRT-PCR assay received and FDA EUA and has been using in guiding clinical management of at-risk pregnant women.

  • 2017

    Tick-borne Disease

    Building upon the MassTag PCR technology a decade prior, the TBD-Serochip was designed to discriminate antibody responses to eight major tick-borne pathogens present in the US. As capture sequencing technology improved, the TBDCapSeq assay was able to test at higher sensitivity and identify unknown infections from prior PCR testing.

  • 2018


    Identification of rickettsia as the cause of unexplained encephalitis in Musahar children in India. Discovery that the infection can be treated with inexpensive antibiotics resulted in a dramatic decrease in morbidity and mortality.

  • 2019

    Acute Flaccid Myelitis (AFM)

    Utilizing VirCapSeq and peptide arrays, a 2019 study demonstrates the implication of enterovirus D68 as a plausible link between infection and AFM. Several other research groups around the world confirmed the same correlation using different techniques.

  • 2020

    Infant Hydrocephalus

    Paenibacillus infection along with a frequent viral cofinection contributes to postinfectious hyrocephalus in infants. It often follows neonatal sepsis and is the most common cause of pediatric phydrocephalus worldwide.

  • 2020

    SARS-CoV-2 Array

    Our team utilized proteome-wide high-density peptide microarray technology to detect specific humoral immune responses to SARS-CoV-2 and other human coronaviruses. The technology was granted an FDA EUA and used in more than 100 million tests by the Los Angeles County School District (San Jose/Santa Cruz, California).

  • 2021

    SARS-CoV-2 Convalescent Plasma

    In adults hospitalized with severe COVID-19, use of convalescent plasma was not associated with significant improvement in day 28 clinical status. However, convalescent plasma was associated with significantly improved survival.

  • 2022

    Human Polyomavirus 9

    Researchers found that a human polyomavirus (HPyV9) was associated with the deaths of three solid organ transplant recipients who developed a severe skin rash and then died about a year later from pulmonary and multiorgan failure. Using VirCapSeq-VERT, HPyV9 was detected and found the virus was present in the skin, blood, and lungs of the three patients. Additional tests showed the virus was not just present in the patients but was actively replicating, causing the initial skin rash and damaging the lungs.