Early Release

Synopses

• Cross-Sectional Study of Clinical Predictors of Coccidioidomycosis, Arizona, USA
  F. A. Ramadan et al.
• Detection of SARS-CoV-2 B.1.351 (Beta) Variant through Wastewater Surveillance before Case Detection in a Community, Oregon, USA
  M. Sutton et al. View Abstract Email this Article

  Genomic surveillance has emerged as a critical monitoring tool during the SARS-CoV-2 pandemic. Wastewater surveillance has the potential to identify and track SARS-CoV-2 variants in the community, including emerging variants. We demonstrate the novel use of multilocus sequence typing to identify SARS-CoV-2 variants in wastewater. Using this technique, we observed the emergence of the B.1.351 (Beta) variant in Linn County, Oregon, USA, in wastewater 12 days before this variant was identified in individual clinical specimens. During the study period, we identified 42 B.1.351 clinical specimens that clustered into 3 phylogenetic clades. Eighteen of the 19 clinical specimens and all wastewater B.1.351 specimens from Linn County clustered into clade 1. Our results provide further evidence of the reliability of wastewater surveillance to report localized SARS-CoV-2 sequence information.

• Antimicrobial-Resistant Shigella spp. in San Diego, California, USA, 2017–2020
  T. Gaufin et al.
• Foodborne Illness Outbreaks Reported to National Surveillance, United States, 2009–2018
  A. E. White et al. View Abstract Email this Article

  Foodborne outbreaks reported to national surveillance systems represent a subset of all outbreaks in the United States; not all outbreaks are detected, investigated, and reported. We described the structural factors and outbreak characteristics of outbreaks reported during 2009–2018. We categorized states (plus DC) as high (highest quintile), middle (middle 3 quintiles), or low (lowest quintile) reporters on the basis of the number of reported outbreaks per 10 million population. Analysis revealed considerable variation across states in the number and types of foodborne outbreaks reported. High-reporting states reported 4 times more outbreaks than low reporters. Low reporters were more likely than high reporters to report larger outbreaks and less likely to implicate a setting or food vehicle; however, we did not observe a significant difference in the types of food vehicles identified. Per capita funding was strongly associated with increased reporting. Investments in public health programming have a measurable effect on outbreak reporting.

Research

• Divergent Rabies Virus Variant of Probable Bat Origin in 2 Gray Foxes, New Mexico, USA
  R. E. Condori et al. View Abstract Email this Article

  In the Western Hemisphere, bat-associated rabies viruses (RABVs) have established independent transmission cycles in multiple mammal hosts, forming genetically distinct lineages. In New Mexico, USA, skunks, bats, and gray foxes are rabies reservoir hosts and represent a public health risk because of encounters with humans. During 2015 and 2019, two previously undescribed RABVs were detected in 2 gray foxes (Urocyon cinereoargenteus) in Lincoln County, New Mexico. Phylogenetic analysis of the nucleoprotein gene indicated that the isolates are a novel RABV variant. These 2 cases probably represent repeated spillover events from an unknown bat reservoir to gray foxes. Molecular analysis of rabies cases across New Mexico identified that other cross-species transmission events were the result of viral variants previously known to be enzootic to New Mexico. Despite a robust rabies public health surveillance system in the United States, advances in testing and surveillance techniques continue to identify previously unrecognized zoonotic pathogens.

• Effects of Acute Dengue Infection on Sperm and Virus Clearance in Body Fluids of Men
  J. Mons et al. View Abstract Email this Article

  We investigated the effects of dengue virus (DENV) on semen using samples collected 7, 15, 30, 60, and 90 days after symptom onset from 10 infected volunteers on Réunion Island. We assessed characteristics of semen and reproductive hormones and isolated motile spermatozoa from semen. We assayed semen for DENV using reverse transcription PCR and searched for DENV RNA by virus isolation in Vero E6 cell cultures. Four volunteers had >1 DENV RNA-positive semen samples; 2 volunteers had DENV RNA–positive semen at day 15 and 1 at day 30. No motile sperm were DENV positive. After exposure to positive semen, few Vero E6 cells stained positive for DENV antigens, indicating low levels of replicative virus. We found DENV had shorter duration in semen than in blood. These findings support the possibilities that DENV is sexually transmissible for a short period after acute dengue illness and that acute dengue induces reversible alterations in sperm.

• Retrospective Genomic Characterization of a 2017 Dengue Virus Outbreak, Burkina Faso
  A. G. Letizia et al. View Abstract Email this Article

  Knowledge of contemporary genetic composition of dengue virus (DENV) in Africa is lacking. By using next-generation sequencing of samples from the 2017 DENV outbreak in Burkina Faso, we isolated 29 DENV genomes (5 serotype 1, 16 serotype 2 [DENV-2], and 8 serotype 3). Phylogenetic analysis demonstrated the endemic nature of DENV-2 in Burkina Faso. We noted discordant diagnostic results, probably related to genetic divergence between these genomes and the Trioplex PCR. Forward and reverse1 primers had a single mismatch when mapped to the DENV-2 genomes, probably explaining the insensitivity of the molecular test. Although we observed considerable homogeneity between the Dengvaxia and TetraVax-DV-TV003 vaccine strains as well as B cell epitopes compared with these genomes, we noted unique divergence. Continual surveillance of dengue virus in Africa is needed to clarify the ongoing novel evolutionary dynamics of circulating virus populations and support the development of effective diagnostic, therapeutic, and preventive countermeasures.

• Effect of Recombinant Vesicular Stomatitis Virus–Zaire Ebola Virus Vaccination on Ebola Virus Disease Illness and Death, Democratic Republic of the Congo
  N. Rupani et al. View Abstract Email this Article

  We conducted a retrospective cohort study to assess the effect vaccination with the live-attenuated recombinant vesicular stomatitis virus–Zaire Ebola virus vaccine had on deaths among patients who had laboratory-confirmed Ebola virus disease (EVD). We included EVD-positive patients coming to an Ebola Treatment Center in eastern Democratic Republic of the Congo during 2018–2020. Overall, 25% of patients vaccinated before symptom onset died compared with 63% of unvaccinated patients. Vaccinated patients reported fewer EVD-associated symptoms, had reduced time to clearance of viral load, and had reduced length of stay at the Ebola Treatment Center. After controlling for confounders, vaccination was strongly associated with decreased deaths. Reduction in deaths was not affected by timing of vaccination before or after EVD exposure. These findings support use of preexposure and postexposure recombinant vesicular stomatitis virus–Zaire Ebola virus vaccine as an intervention associated with improved death rates, illness, and recovery time among patients with EVD.

• Characterization of Healthcare-Associated and Community-Associated Clostridioides difficile Infections among Adults, Canada, 2015–2019
  T. Du et al. View Abstract Email this Article

  We investigated epidemiologic and molecular characteristics of healthcare-associated (HA) and community-associated (CA) Clostridioides difficile infection (CDI) among adult patients in Canadian Nosocomial Infection Surveillance Program hospitals during 2015–2019. The study encompassed 18,455 CDI cases, 13,735 (74.4%) HA and 4,720 (25.6%) CA. During 2015–2019, HA CDI rates decreased by 23.8%, whereas CA decreased by 18.8%. HA CDI was significantly associated with increased 30-day all-cause mortality as compared with CA CDI (p<0.01). Of 2,506 isolates analyzed, the most common ribotypes (RTs) were RT027, RT106, RT014, and RT020. RT027 was more often associated with CDI-attributable death than was non-RT027, regardless of acquisition type. Overall resistance C. difficile rates were similar for all drugs tested except moxifloxacin. Adult HA and CA CDI rates have declined, coinciding with changes in prevalence of RT027 and RT106. Infection prevention and control and continued national surveillance are integral to clarifying CDI epidemiology, investigation, and control.

• Economic Burden of Reported Lyme Disease in High-Incidence Areas, United States, 2014–2016
  S. A. Hook et al. View Abstract Email this Article

  Approximately 476,000 cases of Lyme disease are diagnosed in the United States annually, yet comprehensive economic evaluations are lacking. In a prospective study among reported cases in Lyme disease–endemic states, we estimated the total patient cost and total societal cost of the disease. In addition, we evaluated disease and demographic factors associated with total societal cost. Participants had a mean patient cost of ≈$1,200 (median $240) and a mean societal cost of ≈$2,000 (median $700). Patients with confirmed disseminated disease or probable disease had approximately double the societal cost of those with confirmed localized disease. The annual, aggregate cost of diagnosed Lyme disease could be $345–968 million (2016 US dollars) to US society. Our findings emphasize the importance of effective prevention and early diagnosis to reduce illness and associated costs. These results can be used in cost-effectiveness analyses of current and future prevention methods, such as a vaccine.

• Angiostrongylus cantonensis Nematode Invasion Pathway, Mallorca, Spain
  S. Delgado-Serra et al. View Abstract Email this Article

  Neural angiostrongyliasis is an emerging zoonosis caused by the rat lungworm, Angiostrongylus cantonensis. In humans, infection with this nematode often results in eosinophilic meningitis and other severe disorders of the central nervous system. Europe was deemed a nonendemic region until 2018, when A. cantonensis worms were detected on the Mediterranean island of Mallorca, Spain, a tourism hotspot. Since that time, a sentinel surveillance system and a molecular approach have been used to follow the invasion path of the rat lungworm on the island. A. cantonensis worms have been found in animals from 8 locations on the island over 3 consecutive years. Our preliminary results show a recognizable pattern of clinical signs in infected hedgehogs and a single mitochondrial haplotype circulating in Mallorca. We present strong evidence confirming that the rat lungworm have successfully established and colonized an island in Europe and discuss observations and possible strategies for its early detection across continental Europe.

• Risk Prediction Score for Pediatric Patients with Suspected Ebola Virus Disease
  A. E. Genisca et al. View Abstract Email this Article

  Rapid diagnostic tools for children with Ebola virus disease (EVD) are needed to expedite isolation and treatment. To evaluate a predictive diagnostic tool, we examined retrospective data (2014–2015) from the International Medical Corps Ebola Treatment Centers in West Africa. We incorporated statistically derived candidate predictors into a 7-point Pediatric Ebola Risk Score. Evidence of bleeding or having known or no known Ebola contacts was positively associated with an EVD diagnosis, whereas abdominal pain was negatively associated. Model discrimination using area under the curve (AUC) was 0.87, which outperforms the World Health Organization criteria (AUC 0.56). External validation, performed by using data from International Medical Corps Ebola Treatment Centers in the Democratic Republic of the Congo during 2018–2019, showed an AUC of 0.70. External validation showed that discrimination achieved by using World Health Organization criteria was similar; however, the Pediatric Ebola Risk Score is simpler to use.

• Geographic Origin and Vertical Transmission of Leishmania infantum Parasites in Hunting Hounds, United States
  S. U. Franssen et al. View Abstract Email this Article

  Vertical transmission of leishmaniasis is common but is difficult to study against the background of pervasive vector transmission. We present genomic data from dogs in the United States infected with Leishmania infantum parasites; these infections have persisted in the apparent absence of vector transmission. We demonstrate that these parasites were introduced from the Old World separately and more recently than L. infantum from South America. The parasite population shows unusual genetics consistent with a lack of meiosis: a high level of heterozygous sites shared across all isolates and no decrease in linkage with genomic distance between variants. Our data confirm that this parasite population has been evolving with little or no sexual reproduction. This demonstration of vertical transmission has profound implications for the population genetics of Leishmania parasites. When investigating transmission in complex natural settings, considering vertical transmission alongside vector transmission is vital.

• Risk Factors for SARS-CoV-2 Infection and Illness in Cats and Dogs
  D. Bienzle et al. View Abstract Email this Article

  We tested swab specimens from pets in households in Ontario, Canada, with human COVID-19 cases by quantitative PCR for SARS-CoV-2 and surveyed pet owners for risk factors associated with infection and seropositivity. We tested serum samples for to spike protein IgG and IgM in household pets and also in animals from shelters and low-cost neuter clinics. Among household pets, 2% (1/49) of swab specimens from dogs and 7.7% (5/65) from cats were PCR positive, but 41% of dog serum samples and 52% of cat serum samples were positive for SARS-CoV-2 IgG or IgM. The likelihood of SARS-CoV-2 seropositivity in pet samples was higher for cats but not dogs that slept on owners’ beds and for dogs and cats that contracted a new illness. Seropositivity in neuter-clinic samples was 16% (35/221); in shelter samples, 9.3% (7/75). Our findings indicate a high likelihood for pets in households of humans with COVID-19 to seroconvert and become ill.

Dispatches

• Dynamics of SARS-CoV-2 Antibody Response to CoronaVac followed by Booster Dose of BNT162b2 Vaccine
  M. Fonseca et al. View Abstract Email this Article

  We evaluated the longitudinal dynamics of antibody response to the SARS-CoV-2 vaccine CoronaVac and the effect of a booster dose of BNT162b2 vaccine. We found a robust antibody response after the second dose of CoronaVac that wanes over time. The response was recovered by BNT162b2, which boosted anti-spike antibody titers.

• Burkholderia pseudomallei in Environment of Adolescent Siblings with Melioidosis, Kerala, India, 2019
  P. Bhaskaran et al. View Abstract Email this Article

  In 2019, Burkholderia pseudomallei was isolated from the backyard of 2 siblings with melioidosis in Kerala, India,. This finding highlights the value of healthcare providers being aware of risk for melioidosis in febrile patients, of residents taking precautions when outside, and of increasing environmental surveillance for B. pseudomallei in this region.

• Outbreak of Imported Seventh Pandemic Vibrio cholerae O1 El Tor, Algeria, 2018
  N. Benamrouche et al. View Abstract Email this Article

  After a lull of >20 years, Algeria experienced a cholera outbreak in 2018 that included 291 suspected cases. We found that outbreak isolates were Vibrio cholerae O1 serotype Ogawa from seventh pandemic El Tor sublineage AFR14, which corresponds to a new introduction of cholera into Africa from South Asia.

• Lizards as Silent Hosts of Trypanosoma cruzi
  C. Botto-Mahan et al. View Abstract Email this Article

  We assessed 4 lizard species in Chile for Trypanosoma cruzi, the causative agent of Chagas disease, and 1 species for its ability to transmit the protozoan to uninfected kissing bugs. All lizard species were infected, and the tested species was capable of transmitting the protozoan, highlighting their role as T. cruzi reservoirs.

• Introduction and Rapid Spread of SARS-CoV-2 Omicron Variant and Dynamics of BA.1 and BA.1.1 Sublineages, Finland, December 2021
  H. Vauhkonen et al. View Abstract Email this Article

  Multiple introductions of SARS-COV-2 Omicron variant BA.1 and BA.1.1. lineages to Finland were detected in early December 2021. Within 3 weeks, Omicron overtook Delta as the most common variant in the capital region. Sequence analysis demonstrated the emergence and spread through community transmission of a large cluster of BA.1.1 virus.

• Rapid Increase of Community SARS-CoV-2 Seroprevalence during Second Wave of COVID-19, Yaoundé, Cameroon
  F. Ndongo et al. View Abstract Email this Article

  We conducted 2 independent population-based SARS-CoV-2 serosurveys in Yaoundé, Cameroon, during January 27–February 6 and April 24–May 19, 2021. Overall age-standardized SARS-CoV-2 IgG seroprevalence increased from 18.6% in the first survey to 51.3% in the second (p<0.001). This finding illustrates high community transmission during the second wave of COVID-19.

• Secondary Attack Rate, Transmission and Incubation Periods, and Serial Interval of SARS-CoV-2 Omicron Variant, Spain
  J. Del Águila-Mejía et al. View Abstract Email this Article

  Contact tracing data of SARS-CoV-2 Omicron variant cases during December 2021 in Cantabria, Spain, showed increased transmission (secondary attack rate 39%) compared with Delta cases (secondary attack rate 26%), uninfluenced by vaccination status. Incubation and serial interval periods were also reduced. Half of Omicron transmissions happened before symptom onset in the index case-patient.

• New Variant of Vibrio parahaemolyticus, Sequence Type 3, Serotype O10:K4, China, 2020
  Y. Huang et al. View Abstract Email this Article

  In 2020, a new serotype of Vibrio parahaemolyticus O10:K4 emerged and caused several outbreaks and sporadic cases in Guangxi, China. Phylogenetic analysis indicated that those strains are new variants of the sequence type 3 pandemic clone. The new serotype may become dominant, warranting enhanced investigations and surveillance.

• Identification of Human Case of Avian Influenza A(H5N1) Infection, India
  V. Potdar et al. View Abstract Email this Article

  A 11-year-old boy with acute myeloid leukemia was brought for treatment of severe acute respiratory infection in the National Capital Region, New Delhi, India. Avian influenza A(H5N1) infection was laboratory confirmed. Complete genome analysis indicated hemagglutinin gene clade 2.3.2.1a. We found the strain to be susceptible to amantadine and neuraminidase inhibitors.

• Fasciolopsis buski Detected in Humans in Bihar and Pigs in Assam, India
  D. Saikia et al. View Abstract Email this Article

  The foodborne intestinal trematode Fasciolopsis buski causes the neglected zoonotic disease fasciolopsiasis. We detected F. buski infection in 14 pediatric patients in Sitamarhi, Bihar, and in pigs in Sivasagar, Assam, India. Proper diagnostic methods and surveillance are urgently needed to accurately estimate the true burden of this disease in India.

• Zoonotic Transmission of Diphtheria from Domestic Animal Reservoir, Spain
  A. Hoefer et al. View Abstract Email this Article

  Toxigenic Corynebacterium ulcerans is as an emerging zoonotic agent of diphtheria. We describe the zoonotic transmission of diphtheria caused by toxigenic C. ulcerans from domestic animals in Spain, confirmed by core-genome multilocus sequence typing. Alongside an increasing number of recent publications, our findings highlight the public health threat posed by diphtheria reemergence.

• Public Health Response to Multistate Salmonella Typhimurium Outbreak Associated with Prepackaged Chicken Salad, United States, 2018
  B. Greening et al. View Abstract Email this Article

  Quantifying the effect of public health actions on population health is essential when justifying sustained public health investment. Using modeling, we conservatively estimated that rapid response to a multistate foodborne outbreak of Salmonella Typhimurium in the United States in 2018 potentially averted 106 cases and $715,458 in medical costs and productivity losses.

Research Letters

• Molecular Diagnosis of Pseudoterranova decipiens Sensu Stricto Infections, South Korea, 2002‒2020
  H. Song et al. View Abstract Email this Article

  Human Pseudoterranova decipiens larval infections were diagnosed by molecular analysis of mitochondrial cox1 and nd1 genes in 12 health check-up patients in South Korea during 2002–2020. Based on high genetic identity (99.3%–100% for cox1 and 96.7%–98.0% for nd1), we identified all 12 larvae as P. decipiens sensu stricto.

• Identifying Japanese Encephalitis Virus Using Metatranscriptomic Sequencing, Xinjiang Province, China
  Y. Yan et al. View Abstract Email this Article

  The treat of infectious disease epidemics has increased the critical need for continuous broad-ranging surveillance of pathogens with outbreak potential. Using metatranscriptomic sequencing of blood samples, we identified several cases of Japanese encephalitis virus infection from Xinjiang Province, China. This discovery highlights the risk for known viral diseases even in nonendemic areas.

• Detecting SARS-CoV-2 Omicron B.1.1.529 Variant in Wastewater Samples by Using Nanopore Sequencing
  L. D. Rasmussen et al. View Abstract Email this Article

  We report wastewater surveillance for SARS-CoV-2 variants of concern by using mutation-specific, real-time PCR and rapid nanopore sequencing. This surveillance might be useful for an early warning in a scenario in which a new variant is emerging, even in areas that have low virus incidences.

• Viral Zoonoses in Small Wild Mammals and Detection of Hantavirus, Spain
  S. Herrero-Cófreces et al. View Abstract Email this Article

  We screened 526 wild small mammals for zoonotic viruses in northwest Spain and found hantavirus in common voles (Microtus arvalis) (1.5%) and high prevalence (48%) of orthopoxvirus among western Mediterranean mice (Mus spretus). We also detected arenavirus among small mammals. These findings suggest novel risks for viral transmission in the region.

• Serum Neutralization of SARS-CoV-2 Omicron BA.1 and BA.2 after BNT162b2 Booster Vaccination
  R. M. Pedersen et al. View Abstract Email this Article

  The SARS-CoV-2 Omicron variant BA.2 sublineage is rapidly replacing earlier Omicron lineages, suggesting BA.2 has increased vaccine evasion properties. We measured neutralization titers of authentic BA.1 and BA.2 isolates in serum samples from persons who received the BNT162b2 booster vaccine. All samples neutralized BA.1 and BA.2 at equal median values.

• Recombinant BA.1/BA.2 SARS-CoV-2 Virus in Arriving Travelers, Hong Kong, February 2022
  H. Gu et al. View Abstract Email this Article

  We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021–February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5′ end of the spike gene in 2 epidemiologically linked case-patients. Continued surveillance for SARS-CoV-2 recombinants is needed.

• Experimental Infection of Mink with SARS-COV-2 Omicron Variant and Subsequent Clinical Disease
  J. Virtanen et al. View Abstract Email this Article

  We report an experimental infection of American mink with SARS-CoV-2 Omicron variant and show that mink remain positive for viral RNA for days, experience clinical signs and histopathologic changes, and transmit the virus to uninfected recipients. Preparedness is crucial to avoid spread among mink and spillover to human populations.

• Expansion of L452R-Positive SARS-CoV-2 Omicron Variant, Northern Lombardy, Italy
  F. Novazzi et al. View Abstract Email this Article

  We report 25 cases of infection with SARS-CoV-2 Omicron variant containing spike protein L452R mutation in northern Lombardy, Italy. Prevalence of this variant was >30% in this region, compared with <0.5% worldwide. Many laboratories are using previously developed L452R-specific PCRs to discriminate Omicron from Delta mutations, but these tests may be unreliable.

• Horse-Specific Cryptosporidium Genotype in Human with Crohn's Disease and Arthritis
  Ż. Zajączkowska et al. View Abstract Email this Article

  We identified an unusual subtype of a Cryptosporidium sp. horse genotype as the cause of cryptosporidiosis in a 13-year-old girl in Poland who was undergoing immunosuppressive treatment for juvenile rheumatoid arthritis and Crohn’s disease. The same subtype was identified in a horse the girl had ridden.

• Multistate Outbreak of Infection with SARS-CoV-2 Omicron Variant after Event in Chicago, Illinois, USA, 2021
  H. Spencer et al. View Abstract Email this Article

  Bars and restaurants are high-risk settings for SARS-CoV-2 transmission. A multistate outbreak after a bar gathering in Chicago, Illinois, USA, highlights Omicron variant transmissibility, the value of local genomic surveillance and interstate coordination, vaccination value, and the potential for rapid transmission of a novel variant across multiple states after 1 event.

• SARS-CoV-2 Breakthrough Infections among US Embassy Staff Members, Uganda, May–June 2021
  J. R. Harris et al. View Abstract Email this Article

  The SARS-CoV-2 Delta variant emerged shortly after COVID-19 vaccines became available in 2021. We describe SARS-CoV-2 breakthrough infections in a highly vaccinated, well-monitored US Embassy community in Kampala, Uganda. Defining breakthrough infection rates in highly vaccinated populations can help determine public health messaging, guidance, and policy globally.

• Lyme Disease, Anaplasmosis, and Babesiosis, Atlantic Canada
  Z. O. Allehebi et al. View Abstract Email this Article

  In July 2021, a PCR-confirmed case of locally acquired Babesia microti infection was reported in Atlantic Canada. Clinical features were consistent with babesiosis and resolved after treatment. In a region where Lyme disease and anaplasmosis are endemic, the occurrence of babesiosis emphasizes the need to enhance surveillance of tickborne infections.

Letters

• Association of Healthcare and Aesthetic Procedures with Infections Caused by Nontuberculous Mycobacteria, France, 2012–2020
  K. X. McNamara et al. Email this Article
• Association of Healthcare and Aesthetic Procedures with Infections Caused by Nontuberculous Mycobacteria, France, 2012‒2020
  C. Daniau Email this Article

Books and Media

• The New Microbiology: From Microbiomes to CRISPR
  T. Obe and N. W. Shariat Email this Article

Research

• Self-Reported and Physiologic Reactions to Third BNT162b2 mRNA COVID-19 (Booster) Vaccine Dose
  M. Mofaz et al.
• Epidemiologic, Clinical, and Genetic Characteristics of Human Infections with Influenza A(H5N6) Viruses, China
  W. Zhu et al. View Abstract Email this Article

  The recent rise in the frequency of influenza A(H5N6) infections in China has raised serious concerns about whether the risk for human infection has increased. We surveyed epidemiologic, clinical, and genetic data of human infections with A(H5N6) viruses. Severe disease occurred in 93.8% of cases, and the fatality rate was 55.4%. Median patient age was 51 years. Most H5N6 hemagglutinin (HA) genes in human isolates in 2021 originated from subclade 2.3.4.4b; we estimated the time to most recent common ancestor as June 16, 2020. A total of 13 genotypes with HA genes from multiple subclades in clade 2.3.4.4 were identified in human isolates. Of note, 4 new genotypes detected in 2021 were the major causes of increased H5N6 virus infections. Mammalian-adapted mutations were found in HA and internal genes. Although we found no evidence of human-to-human transmission, continuous evolution of H5N6 viruses may increase the risk for human infections.

• Nipah Virus Detection at Bat Roosts after Spillover Events, Bangladesh, 2012–2019
  C. D. McKee et al.
• Measuring Basic Reproduction Number to Assess Effects of Nonpharmaceutical Interventions on Nosocomial SARS-CoV-2 Transmission
  G. Shirreff et al. View Abstract Email this Article

  Outbreaks of SARS-CoV-2 infection frequently occur in hospitals. Preventing nosocomial infection requires insight into hospital transmission. However, estimates of the basic reproduction number (R₀) in care facilities are lacking. Analyzing a closely monitored SARS-CoV-2 outbreak in a hospital in early 2020, we estimated the patient-to-patient transmission rate and R₀. We developed a model for SARS-CoV-2 nosocomial transmission that accounts for stochastic effects and undetected infections and fit it to patient test results. The model formalizes changes in testing capacity over time, and accounts for evolving PCR sensitivity at different stages of infection. R₀ estimates varied considerably across wards, ranging from 3 to 15 in different wards. During the outbreak, the hospital introduced a contact precautions policy. Our results strongly support a reduction in the hospital-level R₀ after this policy was implemented, from 8.7 to 1.3, corresponding to a policy efficacy of 85% and demonstrating the effectiveness of nonpharmaceutical interventions.

• Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022
  M. T. Sofonea et al.
• One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016
  A. Bharat et al.
• Effect of Returning University Students on COVID–19 Infections in England, 2020
  D. Leeman et al.
• Outbreak of IncX8 Plasmid–Mediated KPC-3–Producing Enterobacterales, China
  L. Chen et al.
• Targeted Screening for Chronic Q Fever, the Netherlands
  D. Reukers et al.
• Novel Mycobacterium tuberculosis Complex Ecotype Related to M. caprae
  J. Shea et al.

Dispatches

• Potential Human Health Threats from Eurasian Avian-Like Swine Influenza A(H1N1) Virus and Its Reassortant Viruses
  S. Wang et al.
• Isolation and Characterisation of Novel Reassortant H10N7 Influenza A Virus in Harbor Seal in British Columbia, Canada
  Y. Berhane et al.
• Chronic Pulmonary Disease Caused by Tsukamurella toyonakaense
  T. Kuge et al.
• Detection of Highly Pathogenic Avian Influenza A(H5N8) Clade 2.3.4.4b Virus in Dust Samples from Poultry Farms, France, 2021
  F. Filaire et al.
• SARS-CoV-2 Delta–Omicron Recombinant Viruses, United States
  K. A. Lacek et al. View Abstract Email this Article

  To detect new and changing SARS-CoV-2 variants, we investigated candidate Delta–Omicron recombinant genomes from Centers for Disease Control and Prevention national genomic surveillance. Laboratory and bioinformatic investigations identified and validated 9 genetically related SARS-CoV-2 viruses with a hybrid Delta–Omicron spike protein.

• Multisystem Inflammatory Syndrome after Breakthrough SARS-CoV-2 Infection in 2 Immunized Adolescents
  L. D. Cole et al.
• Identifying Aortic Aneurysms Using Focused Detection of Helicobacter cinaedi
  S. Jien et al.
• Genetically Diverse Highly Pathogenic Avian Influenza A(H5N1/H5N8) Viruses among Wild Waterfowl and Domestic Poultry, Japan, 2021
  K. Okuya et al.
• Suspected Cat-to-Human Transmission of SARS-CoV-2
  T. Sila et al.
• Natural History and Dynamic Changes in Clinical Manifestation, Serology, and Treatment of Brucellosis, China
  H. Wang et al.
• Anncaliia algerae Microsporidiosis Diagnosed by Metagenomic Next-Generation Sequencing, China
  C. Liu et al.
• Use of Human Intestinal Enteroids to Evaluate Persistence of Infectious Human Norovirus in Seawater
  M. Desdouits et al.

Research Letters

• Type 1 Diabetes Mellitus Associated with Nivolumab after Second SARS-CoV-2 Vaccination, Japan
  T. Sato et al. View Abstract Email this Article

  Recently, along with increasing use of immune checkpoint inhibitors such as nivolumab, the incidence of immune-related adverse events, including type 1 diabetes mellitus, has become a serious problem. We report a patient who had immune checkpoint inhibitor‒associated type 1 diabetes mellitus that developed after a second mRNA-based SARS-CoV-2 vaccination.

• Circulation of Enterovirus D68 during Period of Increased Influenza-like Illness, Maryland, USA, 2021
  A. Fall et al.
• Persistent SARS-CoV-2 Alpha Variant Infection in Immunosuppressed Patient, France, February 2022
  S. Fourati et al. View Abstract Email this Article

  We describe persistent circulation of SARS-CoV-2 Alpha variant in an immunosuppressed patient in France during February 2022. The virus had a new pattern of mutation accumulation. The ongoing circulation of previous variants of concern could lead to reemergence of variants with the potential to propagate future waves of infection.

• SARS-CoV-2 Omicron BA.2 Infections among University Students and Staff, Arizona, USA, January 2022
  N. Fowle et al.
• Genomic Evidence of In-Flight SARS-CoV-2 Transmission, India to Australia, April 2021
  F. Hogarth et al. View Abstract Email this Article

  Epidemiologic and genomic investigation of SARS-CoV-2 infections associated with 2 repatriation flights from India to Australia in April 2021 indicated that 4 passengers transmitted SARS-CoV-2 to >11 other passengers. Results suggest transmission despite mandatory mask use and predeparture testing. For subsequent flights, predeparture quarantine and expanded predeparture testing were implemented.

• Increased Stability of SARS-CoV-2 Omicron Variant over Ancestral Strain
  A. Chin et al. View Abstract Email this Article

  As of April 2022, the Omicron BA.1 variant of concern of SARS-CoV-2 was spreading quickly around the world and outcompeting other circulating strains. We examined its stability on various surfaces and found that this Omicron variant is more stable than its ancestral strain on smooth and porous surfaces.

Another Dimension

• Emerging from an Isolation Cocoon, 2022
  R. Louie

In Memoriam

• In Memoriam: Karen Foster (1955–2022)
  B. Breedlove

Perspective

• Clinical and Economic Impact of COVID-19 on Agricultural Workers, Guatemala
  D. Olson et al.

Synopsis

• Enhancing Respiratory Disease Surveillance to Detect COVID-19 in Shelters for Displaced Persons, Thai-Myanmar Border, 2020–2021
  B. Knust et al.