Multiple lineages of monkeypox virus detected in the United States, 2021-2022.

Monkeypox is a viral zoonotic disease endemic in Central and West Africa. In May 2022, dozens of non-endemic countries reported hundreds of monkeypox cases, most with no epidemiological link to Africa. We identified two lineages of monkeypox virus (MPXV) among two 2021 and seven 2022 US monkeypox cases: the major 2022 outbreak variant called B.1 and a minor contemporaneously sampled variant called A.2. Analyses of mutations among these two variants revealed an extreme preference for GA-to-AA mutations indicative of human APOBEC3 cytosine deaminase activity among Clade IIb MPXV (previously West African, Nigeria) sampled since 2017. Such mutations were not enriched within other MPXV clades. These findings suggest that APOBEC3 editing may be a recurrent and a dominant driver of MPXV evolution within the current outbreak.

Preliminary Findings from an Investigation of Zika Virus Infection in a Patient with No Known Risk Factors - Utah, 2016.

On July 12, 2016, the Utah Department of Health (UDOH) was notified by a clinician caring for an adult (patient A) who was evaluated for fever, rash, and conjunctivitis that began on July 1. Patient A had not traveled to an area with ongoing Zika virus transmission; had not had sexual contact with a person who recently traveled; and had not received a blood transfusion, organ transplant, or mosquito bites (1). Patient A provided care over several days to an elderly male family contact (the index patient) who contracted Zika virus abroad. The index patient developed septic shock with multiple organ failure and died in the hospital on June 25, 2016. The index patient's blood specimen obtained 2 days before his death had a level of viremia approximately 100,000 times higher than the average level reported in persons infected with Zika virus (2). Zika virus infection was diagnosed in patient A by real-time reverse transcription-polymerase chain reaction (rRT-PCR) testing on a urine specimen collected 7 days after symptom onset. In addition, a serum specimen collected 11 days after symptom onset, after patient A's symptoms had resolved, was positive for antibodies to Zika virus by Zika immunoglobulin M (IgM) capture enzyme-linked immunosorbent assay (MAC-ELISA) and had neutralizing antibodies detected by plaque-reduction neutralization testing (PRNT). Working with Salt Lake and Davis County Health Departments, UDOH requested assistance from CDC with an investigation to determine patient A's exposures and determine a probable source of infection.

Human Rabies - Wyoming and Utah, 2015.

In September 2015, a Wyoming woman was admitted to a local hospital with a 5-day history of progressive weakness, ataxia, dysarthria, and dysphagia. Because of respiratory failure, she was transferred to a referral hospital in Utah, where she developed progressive encephalitis. On day 8 of hospitalization, the patient's family told clinicians they recalled that, 1 month before admission, the woman had found a bat on her neck upon waking, but had not sought medical care. The patient's husband subsequently had contacted county invasive species authorities about the incident, but he was not advised to seek health care for evaluation of his wife's risk for rabies. On October 2, CDC confirmed the patient was infected with a rabies virus variant that was enzootic to the silver-haired bat (Lasionycteris noctivagans). The patient died on October 3. Public understanding of rabies risk from bat contact needs to be improved; cooperation among public health and other agencies can aid in referring persons with possible bat exposure for assessment of rabies risk.

Survey of influenza and other respiratory viruses diagnostic testing in US hospitals, 2012-2013.

BACKGROUND: Little is known about laboratory capacity to routinely diagnose influenza and other respiratory viruses at clinical laboratories and hospitals. AIMS: We sought to assess diagnostic practices for influenza and other respiratory virus in a survey of hospitals and laboratories participating in the US Influenza Hospitalization Surveillance Network in 2012-2013. MATERIALS AND METHODS: All hospitals and their associated laboratories participating in the Influenza Hospitalization Surveillance Network (FluSurv-NET) were included in this evaluation. The network covers more than 80 counties in 15 states, CA, CO, CT, GA, MD, MN, NM, NY, OR, TN, IA, MI, OH, RI, and UT, with a catchment population of ~28 million people. We administered a standardized questionnaire to key personnel, including infection control practitioners and laboratory departments, at each hospital through telephone interviews. RESULTS: Of the 240 participating laboratories, 67% relied only on commercially available rapid influenza diagnostic tests to diagnose influenza. Few reported the availability of molecular diagnostic assays for detection of influenza (26%) and other viral pathogens (≤20%) in hospitals and commercial laboratories. CONCLUSION: Reliance on insensitive assays to detect influenza may detract from optimal clinical management of influenza infections in hospitals.

Improving Accuracy of Influenza-Associated Hospitalization Rate Estimates.

Diagnostic test sensitivity affects rate estimates for laboratory-confirmed influenza-associated hospitalizations. We used data from FluSurv-NET, a national population-based surveillance system for laboratory-confirmed influenza hospitalizations, to capture diagnostic test type by patient age and influenza season. We calculated observed rates by age group and adjusted rates by test sensitivity. Test sensitivity was lowest in adults >65 years of age. For all ages, reverse transcription PCR was the most sensitive test, and use increased from <10% during 2003-2008 to ≈70% during 2009-2013. Observed hospitalization rates per 100,000 persons varied by season: 7.3-50.5 for children <18 years of age, 3.0-30.3 for adults 18-64 years, and 13.6-181.8 for adults >65 years. After 2009, hospitalization rates adjusted by test sensitivity were ≈15% higher for children <18 years, ≈20% higher for adults 18-64 years, and ≈55% for adults >65 years of age. Test sensitivity adjustments improve the accuracy of hospitalization rate estimates.

Use of modified oligonucleotides to compensate for sequence polymorphisms in the real-time detection of norovirus.

Noroviruses are major causative agents of sporadic and outbreak-associated nonbacterial gastroenteritis worldwide. Real-time RT-PCR has rapidly become the principle means for norovirus detection due to its sensitivity and specificity; however sequence variations in the Norovirus genome can cause problems for real-time chemistries. Using a combination of modified bases and minor groove binder-conjugated Eclipse hybridization probes, a one step real-time RT-PCR assay was designed and optimized to detect norovirus genogroups I and II. Additionally, an RNA internal control was incorporated into the assay to monitor nucleic acid extraction and amplification inhibition. As part of this study, a combination of 36 stool and RNA samples were tested and results were compared to a previously described TaqMan assay. An overall correlation of 97% was obtained. After 7 months of clinical testing, a percent positive rate of 39% was determined, with genogroup II accounting for 98% of the positives. Overall, the Eclipse assay is a sensitive and robust method for detecting and typing norovirus genogroups I and II as well as useful for routine clinical testing. Incorporating modified bases helps overcome design limitations due to single nucleotide polymorphisms.