Early Release

Perspective

• A Roadmap of Primary Pandemic Prevention Through Spillover Investigation
  E. S. Gurley and R. K. Plowright View Abstract

  Since the COVID-19 pandemic, attention and investment in pandemic preparedness have increased. Although there are many valiant plans around pandemic preparedness, they typically involve slowing the spread or mitigating the effects of a pathogen after it has already entered the human population. The task of stopping the pathogen from entering the human population in the first place, spillover prevention, remains a neglected area in discussions and planning for pandemic risk mitigation. Every spillover offers an opportunity to learn about an emerging public health threat and the conditions that aligned to enable spillover occurrence. In this article, we outline One Health approaches for use in spillover investigations, drawing from our experience investigating Hendra and Nipah virus spillovers. We present a roadmap for how findings from those investigations can lead to the development of interventions for spillover and ultimately pandemic prevention.

• Preparedness and Response Considerations for High-Consequence Infectious Disease
  J. Chan et al. View Abstract

  High-consequence infectious diseases (HCIDs) are acute human infectious diseases with high illness and case-fatality rates, few or no available effective treatment or prevention options, and the ability to spread in the community and within healthcare settings. Those characteristics lead to significant risks to patients and their close contacts, healthcare workers, laboratory personnel, and communities exposed to an outbreak. We describe aspects of healthcare system preparedness for and response to HCIDs, including the role of high-level isolation units, ensuring safe clinical laboratory capabilities and waste management, increasing availability of medical countermeasures, coordinating with stakeholders and systems of care, and communicating with the public. Finally, we discuss priority areas for further investment in HCID preparedness, care, and research. Effective and equitably disseminated medical countermeasures for HCIDs are urgently needed.

Synopses

• Surveillance of Viral Respiratory Infections within Maximum-Security Prison, Australia
  N. M. Legrand et al. View Abstract

  Limited surveillance data has hindered understanding of SARS-CoV-2 transmission within prisons. We integrated routine surveillance data with viral sequencing to investigate transmission dynamics and associated factors during a Delta variant outbreak in a maximum-security prison in Sydney, New South Wales, Australia. Infection incidence and associated factors were determined by using person-time and Cox regression. We generated transmission chains by integrating epidemiologic and viral sequencing data. Of 1,562 patients, SARS-CoV-2 infection was diagnosed in 169 (11%), predominantly acquired in prison and asymptomatic. Prisonwide testing identified substantial unrecognized transmission, and 4 subvariants indicated multiple viral introductions. Infection was associated with housing location, having a cellmate (regardless of infection status), and vaccination status. Our findings underscore the inadequacy of symptom-based testing and the efficacy of entry-quarantine, strategic housing, extensive testing, and vaccination in reducing transmission. This integrated approach to surveillance and genomic sequencing offers a valuable model for enhancing infectious disease surveillance in correctional settings.

• Emergence of Clade Ib Monkeypox Virus—Current State of Evidence
  P. S. Satheshkumar et al.

Research

• Rapid Emergence and Evolution of SARS-CoV-2 Intrahost Variants among COVID-19 Patients with Prolonged Infections, Singapore
  Y. Su et al. View Abstract

  The evolution and spread of SARS-CoV-2 variants have driven successive waves of global COVID-19 outbreaks, yet the longitudinal dynamics of intrahost variation within the same patient remain less clear. We conducted a longitudinal cohort study by deep sequencing 198 swab samples collected from COVID-19 patients with varying infection durations. Our analysis showed that prolonged infections enhanced viral genomic diversity, leading to emergence of co-occurring variants that maintained high (>20%) frequency and became dominant in virus populations. We observed heterogeneous intrahost dynamics among individual patients, 2 of whom exhibited a minor variant of the spike D614G substitution over the course of infection. The increase in intrahost variants strongly correlated with prolonged infections, highlighting the complex interplay between viral diversity and host factors. This study revealed the intricate evolutionary mechanisms driving the emergence of de novo variants and lineage dominance, which could inform development of effective vaccine candidates and strategies to protect public health.

• Scheffersomyces spartinae Fungemia among Pediatric Patients, Pakistan, 2020–2024
  K. Jabeen et al.
• Group A Streptococcus among American Indian Persons, White Mountain Apache Tribal Lands, United States, 2016–2019
  C. G. Sutcliffe et al. View Abstract

  American Indian populations have higher rates of invasive disease because of group A Streptococcus (GAS). This study describes the rates of severe and invasive GAS (siGAS) infections and the distribution of circulating emm types among nonsevere and siGAS cases in the White Mountain Apache Tribal lands in Arizona, USA, during 2016–2019. Isolates underwent whole-genome sequencing to determine emm type. Among siGAS cases, 36% of patients were female, the median age was 40.7 years, and 47.2% of patients were co-infected with Staphylococcus aureus. The age-standardized incidence rate during 2018–2019 was 554.2/100,000 persons. Among the pharyngitis isolates from 2017–2018, the most common emm types were 82 (36.3%), 6 (22.2%), and 60 (16.3%). Among the siGAS cases in 2017–2019, the most common emm type was 82 (65.5%) in the first year and 91 (36.2%) in the second year. Interventions are needed to address the high rates of GAS disease in this population.

• Multidisciplinary Tracking of Highly Pathogenic Avian Influenza A(H5N1) Outbreak in Griffon Vultures, Southern Europe, 2022
  J. Hirschinger et al. View Abstract

  Since 2021, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus has affected wild bird populations globally. Griffon vultures (Gyps fulvus), a species hitherto considered unexposed, experienced an HPAI H5N1 outbreak in 2022 in southern Europe, leading to moderate mortality and reduced breeding success. The integration of virological, serologic, phylogenetic, and ecologic data revealed a short yet intense viral circulation and a probable common source of infection. The dissemination across Spain and France was likely caused by frequent interpopulation movements of birds. This integrated overview of the 2022 HPAI outbreak in vultures provides novel insights into the role of large-scale movements of wild birds in the spread of such disease. Understanding the epidemiologic dynamics of HPAI H5N1 in these scavenger species is crucial because the birds play vital roles in ecosystem functioning. Their susceptibility to this virus highlights potential broader ecologic effects of the ongoing outbreaks.

• Estimated COVID-19 Periodicity and Correlation with SARS-CoV-2 Spike Protein S1 Antigenic Diversity, United States
  E. Rose et al. View Abstract

  Emergence of antigenically diverse SARS-CoV-2 variants may be correlated with temporal circulation patterns. We analyzed positive SARS-CoV-2 tests in the United States reported to a national, laboratory-based surveillance network and unique amino acid sequences of the S1 region of the spike protein reported to national genomic surveillance during October 2020–September 2024. We estimated SARS-CoV-2 dominant periodicities using a discrete Fourier transform, described S1 variation using the Simpson diversity index (SDI), and estimated Spearman cross-correlation coefficients between percentage change in SDI and percentage positivity. SARS-CoV-2 activity consistently peaked during July–September and December–February, and dominant periodicities were at weeks 52.2 and 26.1. Percentage positivity and percentage change in SDI were negatively correlated (ρ = −0.30; p<0.001). SARS-CoV-2 peaks occurred in late summer and winter, a pattern likely related to rapid SARS-CoV-2 evolution and cyclical diversity. Monitoring associations between percentage positivity and SDI can help forecast expected surges and optimize prevention and preparedness.

• Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N1) and A(H5N6) Viruses in Wild Birds, South Korea, 2023–2024
  Y. Seo et al. View Abstract

  We analyzed 15 cases of highly pathogenic avian influenza (HPAI) clade 2.3.4.4b virus infections detected in wild birds in South Korea during September 2023–March 2024. We isolated and sequenced 8 H5N1 and 7 H5N6 viruses. We investigated spatiotemporal transmission dynamics by using a Bayesian discrete trait phylodynamic model that incorporated geographic and host species information. Our source–sink dynamics support introductions of H5N1 viruses from northern Japan to South Korea and subsequent spread through multiple regions in South Korea. The H5N6 viruses were most likely introduced into southwestern South Korea and spread northeastward. Wild waterfowl, especially wild ducks, played a key role in transmission of both H5N1 and H5N6 viruses. Our data showed multiple introductions and extensive spread of HPAI clade 2.3.4.4b viruses and bidirectional transmission between Japan and South Korea. Our results highlight the value of enhanced active surveillance for monitoring HPAI viruses, which can provide insight into preventing future outbreaks.

Dispatches

• Gastric Submucosal Tumor in Patient Infected with Dioctophyme renale, South Korea
  D. Kim et al.
• Case Report of Clade Ib Monkeypox Virus Infection Linked to Travel to Democratic Republic of the Congo, Thailand, 2024
  D. Srithammavong et al. View Abstract

  We report clade Ib monkeypox virus infection in a patient who returned to Thailand from the Democratic Republic of the Congo, the subclade epicenter. Improved diagnostic testing, public health response, and surveillance systems for mpox are needed in Thailand, and preexposure mpox vaccination should be considered, especially for high-risk persons.

• Microsporidial Keratoconjunctivitis Caused by Vittaforma corneae, Sea of Galilee, Israel, 2022–2024
  A. Friehmann et al. View Abstract

  We describe a multiannual outbreak of keratoconjunctivitis caused by the microsporidium Vittaforma corneae in the Sea of Galilee, Israel. Patients had multifocal punctate corneal infiltrates and reduced visual acuity, confirmed by locally-developed pathogen-specific real-time PCR. Topical chlorhexidine, rather than traditional antimicrobial drugs, proved an effective and safe primary treatment.

• Progression from Candida auris Colonization Screening to Clinical Case Status, United States, 2016–2023
  A. D. Baker et al. View Abstract

  During 2016–2023, among 21,195 US patients who tested positive for Candida auris colonization, 6.9% were subsequently found to have a positive clinical specimen (2.8% from blood). Risk factors and strategies are needed to prevent invasive C. auris infections among patients with colonization (e.g., through patient decolonization).

• ACE2 Receptor Usage across Animal Species by SARS-CoV-2 Variants
  M. Hatta et al. View Abstract

  We analyzed the receptor-binding activity and infectivity of 6 representative SARS-CoV-2 lineages in cell lines expressing angiotensin-converting enzyme 2 proteins from 54 different animal species. All viruses demonstrated infectivity in a broad range of species. Susceptible animal species could serve as natural reservoirs or intermediate hosts for SARS-CoV-2.

• Genomic Surveillance Detection of SARS-CoV-1–Like Viruses in Rhinolophidae Bats, Bandarban Region, Bangladesh
  C. Bradburne et al. View Abstract

  We sequenced sarbecovirus from Rhinolophus spp. bats in Bandarban District, Bangladesh, in a genomic surveillance campaign during 2022–2023. Sequences shared identity with SARS-CoV-1 Tor2, which caused an outbreak of human illnesses in 2003. Describing the genetic diversity and zoonotic potential of reservoir pathogens can aid in identifying sources of future spillovers.

• Variance Among Public Health Agencies’ Boil Water Guidance
  M. Dorris et al. View Abstract

  We reviewed boil water guidance from 5 public health agencies and noted differences in boil definition, duration, and elevation adjustment. Publishing evidence-based models could clarify the scientific rationale, promote consensus, and minimize likelihood of incomplete water treatment or excess use of limited fuel resources during emergencies and in backcountry settings.

• Genetic Characterization of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b, Antarctica, 2024
  V. Neira et al. View Abstract

  In 2024, we sequenced highly pathogenic avian influenza virus A(H5N1) clade 2.3.4.4b genomes isolated from 5 brown skuas from James Ross Island, Antarctica. Phylogenetic analysis suggested the virus reached Antarctica through South America. Continued genetic surveillance will be critical to elucidate H5N1 virus transmission dynamics within Antarctica and surrounding areas.

• Identification of Co-Circulating Dengue and South America–Origin Zika Viruses, Pakistan, 2021–2022
  N. T. Iqbal et al. View Abstract

  We collected samples from febrile patients in Karachi, Pakistan, in 2021–2022. Sequencing, molecular, and serologic screens revealed dengue serotype 2 and Zika virus. The Zika lineage was inferred to be from Brazil in 2016, indicating unobserved circulation. We conclude that Zika virus contributes to perceived dengue outbreak burden in Pakistan.

• Neurologic Manifestations Associated with Parvovirus B19 Epidemic, Madrid, Spain, 2024
  C. Veintimilla et al. View Abstract

  A reemergence of parvovirus B19 infections in Spain in early 2024 prompted a 10-year review of the virus at a tertiary center. We identified 8 case-patients with neurologic manifestations who had parvovirus B19 in cerebrospinal fluid. Early recognition and management of parvovirus B19–associated neurologic conditions will help yield favorable outcomes.

• COVID-19 Predeparture Test Results and Vaccination Coverage among US-Bound Refugees, 2020–2022
  A. S. Judge et al. View Abstract

  We describe predeparture COVID-19 test positivity and vaccination coverage for US-bound refugees. During November 24, 2020–June 11, 2022, a total of 23,972 refugees received 28,465 tests (87% reverse transcription PCR); 2.6% of refugees tested positive. During November 24, 2020–December 31, 2022, vaccination coverage rose from 0% to 71% among 24,831 adult refugees.

• Recombinant Myxoma Virus in European Brown Hares, 2023–2024
  L. Fischer et al. View Abstract

  Recombinant myxoma virus has emerged in European brown hares (Lepus europaeus), causing increased deaths associated with swollen eyelids, head edema, and dermatitis at face, legs, and perineum. Introduction may date back as far as September 2020. As of August 2024, the disease is spreading radially from the Germany–Netherlands border area.

• Community-Scale Surveillance of SARS-CoV-2 and Influenza A Viruses in Wild Mammals, United States, 2022–2023
  G. Wilson-Henjum et al. View Abstract

  Sampling of mammal communities across the United States during 2022–2023 detected evidence of SARS-CoV-2 antibodies in 3 new species and 2 previously described species and evidence of influenza A antibodies in 2 previously described species. Our analysis provides surveillance and sampling guidance for detection of rare exposure events.

• Isolation of Highly Pathogenic Avian Influenza A(H5N1) Virus from Cat Urine after Raw Milk Ingestion, United States
  E. A. Frye et al. View Abstract

  In 2024, 3 domestic cats in California, USA consumed raw milk contaminated with highly pathogenic avian influenza A(H5N1) virus. Fever and neurologic signs developed; 2 cats died. The surviving cat’s urine tested positive for H5N1 virus by reverse transcription PCR. Raw dairy products pose a risk to both animal and human health.

Research Letters

• Complete Genome Analysis of African Swine Fever Virus Isolated from Wild Boar, India, 2021
  D. Senthilkumar et al. View Abstract

  Complete genome analysis of African swine fever virus isolated from a wild boar in Mizoram, India, revealed ≈99% nucleotide identity with those of domestic pig origin but with unique mutations. A One Health approach toward food security necessitates awareness among veterinary and public health professionals on virus evolution and domestic–wild pig transmission.

• Nipah Virus Antibodies in Bats, the Philippines, 2013–2022
  Y. Kaku et al. View Abstract

  In 2014, an outbreak of zoonotic Nipah virus (NiV) occurred on Mindanao Island, the Philippines. We investigated the prevalence of NiV in Philippine bats. Because neutralizing antibodies were detected in insectivorous bats on Siargao Island, public health officials should consider that the distribution range of NiV is not limited to Mindanao Island.

• Crimean-Congo Hemorrhagic Fever Virus Africa 1 Lineage in Hyalomma dromedarii Ticks, Algeria, 2023
  M. Temani et al. View Abstract

  We conducted a Crimean-Congo hemorrhagic fever virus (CCHFV) survey of Hyalomma spp. ticks collected from camels in southeastern Algeria. Of 138 tick pools, 1 was CCHFV positive; the sequenced strain belonged to the Africa 1 genotype. Healthcare professionals in Algeria should be aware of this detection of a circulating pathogenic CCHFV genotype.

• Seroprevalence of Rift Valley and Crimean-Congo Hemorrhagic Fever Viruses, Benin, 2022–2023
  N. Olk et al. View Abstract

  We screened 650 febrile patients from Benin for Rift Valley fever and Crimean-Congo hemorrhagic fever viruses during 2022–2023. None were positive by reverse transcription PCR; 1.1% and 0.3%, respectively, had virus-specific IgG. False-positive results from malaria-associated antibodies likely reacting with histidine-tagged viral antigens mandate careful validation of serologic tests in malaria-endemic regions.

• Emergence of Novel Fluoroquinolone Resistance Mutations in Mycoplasma bovis, China, 2008–2023
  S. Lan et al. View Abstract

  We investigated quinolone resistance in Mycoplasma bovis samples isolated in China during 2008–2023. Sequence type 52 was the dominant genotype; GyrA (S83F/Y) and ParC (S80R) protein double mutations caused high resistance to fluoroquinolones. Increased vigilance and surveillance of M. bovis infections in cattle will be needed to prevent disease.

• Molecular Characterization of Echinococcus vogeli from Human Case, Colombia, 2024
  J. Morcillo Muñoz et al. View Abstract

  In Colombia, 35 confirmed cases of neotropical polycystic echinococcosis were reported during 1978–2018. In most cases, Echinococcus vogeli was identified by means of morphologic identification. We describe a case of E. vogeli echinococcosis in a woman, diagnosed through PCR, mitochondrial DNA sequencing, and molecular characterization.

• Severe Fever with Thrombocytopenia Syndrome Acquired through Dog Bite, South Korea
  U. Kim et al. View Abstract

  A veterinary technician in South Korea contracted severe fever with thrombocytopenia syndrome virus from a dog bite. Molecular evidence, including PCR sequencing, supports dog-to-human transmission. The case underscores the zoonotic risks posed by companion animals and highlights the importance of preventive measures.

• Influenza D Virus in Domestic and Stray Cats, Northern China, 2024
  M. Shen et al. View Abstract

  Influenza D virus infects primarily cattle, but infrequent reports of infections in cats occur. We detected influenza D virus antibodies in 8 of 360 cats in northern China. Domestic cats showed higher susceptibility than strays. Our results suggest a previously overlooked aspect of epidemiology of this virus in companion animals.

• Crimean-Congo Hemorrhagic Fever Virus among Goats, Southern Bhutan
  S. Rinchen et al. View Abstract

  We conducted serosurveillance for Crimean-Congo hemorrhagic fever virus (CCHFV) among goats in southern Bhutan. Testing serum samples from 472 goats for CCHFV-specific IgG using an indirect fluorescent antibody test and ELISA, we found CCHFV antibody–positive goats along the analyzed border region with India, indicating widespread distribution of CCHFV in this area.

Letter

• Henipavirus in Northern Short-Tailed Shrew, Alabama, USA
  V. C. Haring et al.

Etymologia

• Mpox [em′poks] and Monkeypox Virus [muhng′kee poks′ vī-ruhs′]
  C. Partin

Online Report

• Optimal Timing for Expanding Diagnostic Laboratories, South Korea
  J. Park et al. View Abstract

  The rapid expansion of testing capacity is imperative for an adequate response to infectious diseases, such as COVID-19. South Korea rapidly secured large-scale testing during the early stages of COVID-19 in 2020 by leveraging the country’s experience with the 2015 Middle East respiratory syndrome outbreak; the initial response was relatively successful. A key difference between the 2 outbreak responses was the expansion from public to private testing laboratories during the COVID-19 pandemic. Expanding testing capacity during an infectious disease crisis should involve consideration of the overall response system and social conditions and not just the number of patients. If there are concerns about a crisis developing, testing capacity expansion should begin as soon as possible. Furthermore, accuracy should be ensured, especially when testing capacity is expanded. South Korea’s experience in developing diagnostic systems and adopting testing strategies underscores the value of proactive and well-timed preparedness for emerging infection disease outbreaks.

Corrections

• Correction: Vol. 30, No. 3
• Correction: Vol. 30, No. 2
• Correction: Vol. 31, No. 6

About the Cover

• The Pockmarked Face of the Comte de Mirabeau
  A. G. Nerlich et al.

Perspective

• Chagas Disease, an Endemic Disease in the United States
  N. L. Beatty et al.

Research

• Detection of Multiple Nosocomial Trichosporon asahii Transmission Events via Microsatellite Typing Assay, South America
  E. C. Francisco et al.
• Epidemiology of Sporothrix brasiliensis in Felids at Border of Brazil—Treatment Failure without Initial Elevated Itraconazole MICs
  C. do Prado et al.
• Drivers of Crimean-Congo Hemorrhagic Fever in Natural Host and Effects of Control Measures, Bulgaria
  G. Limon et al.
• Rickettsioses in Uganda: An Underrecognized Cause of Hospitalization Due to Febrile Illness
  P. W. Blair et al.
• Differences in Lyme Disease Diagnosis among Medicaid and Medicare Beneficiaries, United States, 2016–2021
  L. Gould et al.
• Surge in cumulative incidence of Candida auris skin colonization early in the COVID-19 Pandemic
  A. H. Dratch et al.
• Severe Group A Streptococcus Infection among Children, France, 2022–2024
  M. Colomina et al.
• New insights into infant strongyloidiasis in Papua New Guinea
  H. Zhao et al.
• Epidemiology of Chikungunya Hospitalizations, Brazil, 2014–2024
  V. Pedí et al.
• Theileria luwenshuni and Novel Babesia spp. Infections in Humans, Yunnan Province, China
  R. Xiang et al.

Dispatches

• CYP2D6 Genotype and Primaquine Treatment in Patients with Suspected Malaria, Venezuela
  C. Pacheco et al.
• Modeling Case Burden and Duration of Sudan Ebola Virus Disease Outbreak in Uganda, 2022
  D. Bisanzio et al.
• Emergence of Autochthonous Leishmania (Mundinia) martiniquensis Infections in Horses, Czech Republic and Austria, 2019–2023
  D. Modrý et al.
• Rapidly Progressing Melioidosis Outbreak in City Center Zoo, Hong Kong, 2024
  C. J. Brackman et al.
• Melioidosis cases with highly related Burkholderia pseudomallei whole genome sequences among 4 people with unknown exposure source, Georgia, USA, 1983–2024
  S. Brennan et al.

Research Letters

• Linezolid and Meropenem for Nocardia otitidiscaviarum Actinomycetoma
  K. Sardana et al.
• New World Screwworm Infestation in Wild Mountain Tapirs, Central Andes Mountains, Colombia
  J. Cepeda-Duque et al.
• Clinical and Molecular Characterization of Emerging Human Dirofilaria repens Infections, Estonia, 2023
  K. Nõupuu et al.
• Monkeypox Virus Clade IIa Infections, Liberia, 2023–2024
  D. Nyan et al.
• Detection of Rat Lungworms in Invasive Mollusks, Georgia, USA, 2024
  T. J. Achatz et al.
• Subarachnoid Neurocysticercosis Caused by Larval-Stage Taenia crassiceps Tapeworm, Slovenia
  B. Šoba et al.
• Pediatric Case Report and Overview of Autochthonous Tick-Borne Encephalitis, Belgium
  J. De Langhe et al.