Explanipedia

Clade I or clade II? Targeting essential viral genes to differentiate monkeypox virus clades by multiplex real-time PCR Open

William S. Probert, Alex Espinosa, Jill K. Hacker · 2025

The increasing incidence and global spread of mpox have prompted the World Health Organization to twice declare a Public Health Emergency of International Concern. Sustained human-to-human transmission, largely through sexual contact, and …

First Clade Ib Monkeypox Virus Infection Reported in the Americas — California, November 2024 Open

Vivian Levy, Anna Branzuela, Kristina Hsieh, Shiffen Getabecha, Ricardo Berumen , et al. · 2025

A clade I monkeypox virus (MPXV) outbreak is ongoing in the Democratic Republic of the Congo; travel-associated clade I MPXV infections have been reported in non-African countries. In November 2024, San Mateo County Health in California id…

Severe and Fatal Rocky Mountain Spotted Fever After Exposure in Tecate, Mexico — California, July 2023–January 2024 Open

Anne M. Kjemtrup, Jill K. Hacker, Michael W. Monroe, Vicki Williams, Charles Lines , et al. · 2024

Rocky Mountain spotted fever (RMSF) is a tickborne disease endemic in areas of the Americas. Persistent high incidence of the disease exists in northern Mexico, perpetuated by local populations of brown dog ticks (Rhipicephalus sanguineus …

Notes from the Field: Mpox Cluster Caused by Tecovirimat-Resistant Monkeypox Virus — Five States, October 2023–February 2024 Open

Crystal M. Gigante, Jade Takakuwa, D McGrath, C. Kling, Thomas A. Smith , et al. · 2024

The antiviral drug tecovirimat* has been used extensively to treat U.S. mpox cases since the start of a global outbreak in 2022. Mutations in the mpox viral protein target (F13 or VP37) that occur during treatment can result in resistance …

Duplex Reverse-Transcription Real-Time Polymerase Chain Reaction Assay Targeting 23S rRNA Single Nucleotide Polymorphisms for the Detection of Flea-Borne Rickettsioses Open

William S. Probert, Alexa C. Quintana, Anne M. Kjemtrup, Jill K. Hacker · 2024

Flea-borne spotted fever and flea-borne (murine) typhus are rickettsioses caused by Rickettsia felis and Rickettsia typhi , respectively, and typically present as undifferentiated febrile illnesses. The relative contribution of these agent…

Newly Recognized Spotted Fever Group Rickettsia as Cause of Severe Rocky Mountain Spotted Fever–Like Illness, Northern California, USA Open

Will Probert, Monica Haw, Aran C. Nichol, Carol Glaser, Sarah Y. Park , et al. · 2024

The incidence of spotted fever group (SFG) rickettsioses in the United States has tripled since 2010. Rocky Mountain spotted fever, the most severe SFG rickettsiosis, is caused by Rickettsia rickettsii. The lack of species-specific confirm…

Treatment of Mpox with Suspected Tecovirimat Resistance in Immunocompromised Patient, United States, 2022 Open

Caitlin A. Contag, Leah Mische, Isabel Fong, Abraar Karan, Akanksha Vaidya , et al. · 2023

Reports of tecovirimat-resistant mpox have emerged after widespread use of antiviral therapy during the 2022 mpox outbreak. Optimal management of patients with persistent infection with or without suspected resistance is yet to be establis…

Implementation of California COVIDNet – a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance Open

Debra A. Wadford, Nikki Baumrind, Elizabeth F. Baylis, John Bell, Ellen L. Bouchard , et al. · 2023

Introduction The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of Cal…

Community spread of a human monkeypox virus variant with a tecovirimat resistance-associated mutation Open

Jacob M. Garrigues, Peera Hemarajata, Alex Espinosa, Jill K. Hacker, Nhien T. Wynn , et al. · 2023

Fleaborne Typhus–Associated Deaths — Los Angeles County, California, 2022 Open

Jemma Alarcón, Armine Sanosyan, Zuelma A. Contreras, Van P. Ngo, Ann Carpenter , et al. · 2023

Fleaborne typhus (also known as murine typhus), a widely distributed vectorborne zoonosis caused by Rickettsia typhi, is a moderately severe, but infrequently fatal illness; among patients who receive doxycycline, the case-fatality rate is…

Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California’s SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet Open

Emily Smith, Kevin Libuit, Curtis J. Kapsak, Michelle R. Scribner, Sage M. Wright , et al. · 2023

The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did not have the infrastructure in place to handle the vast amount of severe …

Correction: A forty-year review of Rocky Mountain spotted fever cases in California shows clinical and epidemiologic changes Open

Anne M. Kjemtrup, Kerry A. Padgett, Christopher D. Paddock, Sharon Messenger, Jill K. Hacker , et al. · 2023

[This corrects the article DOI: 10.1371/journal.pntd.0010738.].

A forty-year review of Rocky Mountain spotted fever cases in California shows clinical and epidemiologic changes Open

Anne M. Kjemtrup, Kerry A. Padgett, Christopher D. Paddock, Sharon Messenger, Jill K. Hacker , et al. · 2022

Rocky Mountain spotted fever (RMSF) is a life-threatening tick-borne disease documented in North, Central, and South America. In California, RMSF is rare; nonetheless, recent fatal cases highlight ecological cycles of the two genera of tic…

Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant Open

Xianding Deng, Miguel Garcia-Knight, Mir M. Khalid, Venice Servellita, Candace Wang , et al. · 2021

Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation Open

Xianding Deng, Miguel Garcia-Knight, Mir M. Khalid, Venice Servellita, Candace Wang , et al. · 2021

We identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and in…

Use of Molecular Epidemiology to Inform Response to a Hepatitis A Outbreak — Los Angeles County, California, October 2018–April 2019 Open

Meredith Haddix, Rachel Civen, Jill K. Hacker, Will Probert, Sarah New , et al. · 2020

Los Angeles County comprises 4,058 square miles and is home to approximately 10 million residents (1), an estimated 59,000 (0.6%) of whom experience homelessness on a given night (2). In late 2018, Los Angeles County Department of Public H…

Public Health Responses to COVID-19 Outbreaks on Cruise Ships — Worldwide, February–March 2020 Open

Leah F. Moriarty, Mateusz M. Pluciński, Barbara J. Marston, Ekaterina V. Kurbatova, Barbara Knust , et al. · 2020

An estimated 30 million passengers are transported on 272 cruise ships worldwide each year* (1). Cruise ships bring diverse populations into proximity for many days, facilitating transmission of respiratory illness (2). SARS-CoV-2, the vir…

A Novel TaqMan Assay for Detection ofRickettsia364D, the Etiologic Agent of Pacific Coast Tick Fever Open

Sandor E. Karpathy, Alex Espinosa, Melissa Yoshimizu, Jill K. Hacker, Kerry A. Padgett , et al. · 2019

Pacific Coast tick fever is a febrile illness associated with the bite of Dermacentor occidentalis and results from an infection due to the intracellular pathogen Rickettsia 364D (also known by the proposed name “ Rickettsia philipii ”). C…

Molecular Genotyping of Hepatitis A Virus, California, USA, 2017–2018 Open

William S. Probert, Carlos González, Alex Espinosa, Jill K. Hacker · 2019

We implemented subgenomic and whole-genome sequencing to support the investigation of a large hepatitis A virus outbreak among persons experiencing homelessness, users of illicit drugs, or both in California, USA, during 2017-2018. Genotyp…

New Subgenotyping and Consensus Real-Time Reverse Transcription-PCR Assays for Hepatitis A Outbreak Surveillance Open

William S. Probert, Jill K. Hacker · 2019

Laboratory surveillance plays an important role in the detection and control of hepatitis A outbreaks and requires the application of rapid and accurate molecular diagnostic tools for hepatitis A virus (HAV) RNA detection, subgenotype iden…

Expanded Molecular Testing on Patients with Suspected West Nile Virus Disease Open

Nicole P. Lindsey, Sharon Messenger, Jill K. Hacker, María Salas, Christine Scott-Waldron , et al. · 2019

Most diagnostic testing for West Nile virus (WNV) disease is accomplished using serologic testing, which is subject to cross-reactivity, may require cumbersome confirmatory testing, and may fail to detect infection in specimens collected e…

Patients with laboratory evidence of West Nile virus disease without reported fever Open

Kimberly Landry, Ingrid B. Rabe, Sharon Messenger, Jill K. Hacker, María Salas , et al. · 2019

In 2013, the national surveillance case definition for West Nile virus (WNV) disease was revised to remove fever as a criterion for neuroinvasive disease and require at most subjective fever for non-neuroinvasive disease. The aims of this …

Rickettsia Species Isolated from Dermacentor occidentalis (Acari: Ixodidae) from California Open

Christopher D. Paddock, Melissa Yoshimizu, Maria L. Zambrano, Robert S. Lane, Bonnie M. Ryan , et al. · 2018

The Pacific Coast tick (Dermacentor occidentalis Marx, 1892) is one of the most widely distributed and frequently encountered tick species in California. This tick is the primary vector of an unclassified spotted fever group rickettsial pa…

Genotype-Specific Measles Transmissibility: A Branching Process Analysis Open

Sarah F. Ackley, Jill K. Hacker, Wayne Enanoria, Lee Worden, Seth Blumberg , et al. · 2017

Variability in measles transmissibility may have important implications for measles control; the vaccination threshold required for elimination may not be the same for all genotypes or age groups.

Complete Genome Sequences of Mumps and Measles Virus Isolates from Three States in the United States Open

Laura Cristal Magaña, Alex Espinosa, Rachel L. Marine, Terry Fei Fan Ng, Christina J. Castro , et al. · 2017

We report here the full coding sequence of nine paramyxovirus genomes, including two full-length mumps virus genomes (genotypes G and H) and seven measles virus genomes (genotypes B3 and D4, D8, and D9), from respiratory samples of patient…

Subacute Sclerosing Panencephalitis: The Devastating Measles Complication That Might Be More Common Than Previously Estimated Open

Kristen Wendorf, Kathleen Winter, Jennifer Zipprich, Rob Schechter, Jill K. Hacker , et al. · 2017

SSPE cases in California occurred at a high rate among unvaccinated children, particularly those infected during infancy. Protection of unvaccinated infants requires avoidance of travel to endemic areas, or early vaccination prior to trave…

Progress towards Rapid Detection of Measles Vaccine Strains: a Tool To Inform Public Health Interventions Open

Jill K. Hacker · 2016

Rapid differentiation of vaccine from wild-type strains in suspect measles cases is a valuable epidemiological tool that informs the public health response to this highly infectious disease. Few public health laboratories sequence measles …

Erratum to: Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens Open

Thuy Doan, Michael R. Wilson, Emily Crawford, Eric D. Chow, Lillian M. Khan , et al. · 2016

The Eco-epidemiology of Pacific Coast Tick Fever in California Open

Kerry A. Padgett, Denise L. Bonilla, Marina E. Eremeeva, Carol Glaser, Robert S. Lane , et al. · 2016

Rickettsia philipii (type strain "Rickettsia 364D"), the etiologic agent of Pacific Coast tick fever (PCTF), is transmitted to people by the Pacific Coast tick, Dermacentor occidentalis. Following the first confirmed human case of PCTF in …

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens Open

Thuy Doan, Michael R. Wilson, Emily Crawford, Eric D. Chow, Lillian M. Khan , et al. · 2016

MDS can identify fungi, parasites, and DNA and RNA viruses in minute volumes of intraocular fluid samples. The identification of chronic intraocular rubella virus infection highlights the eye's role as a long-term pathogen reservoir, which…

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