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.

• Considerations for Preparedness and Response to High Consequence Infectious Disease
  J. Chan et al.

Synopses

• Enhancing surveillance of viral respiratory infections: Lessons learnt from a SARS-CoV-2 outbreak in a maximum-security Australian prison
  N. M. Legrand et al.
• 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.
• The burden and molecular epidemiology of group A Streptococcus among American Indian individuals in the White Mountain Apache Tribal lands, 2016–2019
  C. G. Sutcliffe et al.
• Multidisciplinary Tracking of Highly Pathogenic Avian Influenza A(H5N1) Outbreak in Griffon Vultures, Southern Europe, 2022
  J. Hirschinger et al.
• 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.
• Genomic Surveillance Detection of SARS-CoV-1–Like Virus Taxa in Rhinolophidae Bats, Bandarban Region, Bangladesh
  C. Bradburne et al.
• 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.

• Co-circulation of Dengue and South American–origin Zika Viruses, Pakistan
  N. T. Iqbal et al.
• Neurologic Manifestations Associated with Parvovirus B19 Epidemic, Madrid, Spain, 2024
  C. Veintimilla et al.
• COVID-19 Predeparture Test Results and Vaccination Coverage among United States–Bound Refugees, 2020–2022
  A. S. Judge et al.
• 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
  G. Wilson-Henjum et al.

Research Letters

• Complete Genome Analysis of African Swine Fever Virus Isolated from Wild Boar, India, 2021
  D. Senthilkumar et al.
• Nipah Virus Antibodies in Bats, Philippines, 2013–2022
  Y. Kaku et al.
• 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.

• Detection Rates of Rift Valley and Crimean-Congo Hemorrhagic Fever Virus Antibodies, Benin, 2023
  N. Olk et al.
• Emergence of Novel Fluoroquinolone Resistance Mutations in Mycoplasma bovis, China, 2008–2023
  S. Lan et al.
• Molecular Characterization of Echinococcus vogeli from Human Case, Colombia, 2024
  J. A. Morcillo Muñoz et al.
• Severe Fever with Thrombocytopenia Syndrome Acquired through Dog Bite, South Korea
  U. Kim et al.
• Influenza D Virus in Domestic and Stray Cats, Northern China
  M. Shen et al.

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.

Corrections

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

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.

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.

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.