Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.
Volume 27, Number 10—October 2021
Antimicrobial Resistance in Africa—How to Relieve the Burden on Family Farmers
Although currently available data indicate that Africa has the lowest usage of antimicrobials in animals in the world (adjusted by animal biomass), data show a high prevalence of antimicrobial resistance in foodborne pathogens isolated from animals and animal products. Apart from the lack of solid data on antimicrobial use in many countries in Africa, different hypotheses could explain this situation. Qualitative interviews of farmers show a lack of knowledge and uninformed use of antimicrobials. Considering the development of animal farming to meet an increasing demand for proteins, this deficiency represents a serious public health issue. We advocate for policies that consider the specific challenges faced by family farmers in Africa, to simultaneously improve access to veterinary drugs while strengthening the regulation of their use. We propose a global approach targeting the agri-food system, offering innovative social and technical interventions on antimicrobial usage, adapted to family farmers.
Characteristics, Comorbidities, and Data Gaps for Coronavirus Disease Deaths, Tennessee, USA
As of March 2021, coronavirus disease (COVID-19) had led to >500,000 deaths in the United States, and the state of Tennessee had the fifth highest number of cases per capita. We reviewed the Tennessee Department of Health COVID-19 surveillance and chart-abstraction data during March 15‒August 15, 2020. Patients who died from COVID-19 were more likely to be older, male, and Black and to have underlying conditions (hereafter comorbidities) than case-patients who survived. We found 30.4% of surviving case-patients and 20.3% of deceased patients had no comorbidity information recorded. Chart-abstraction captured a higher proportion of deceased case-patients with >1 comorbidity (96.3%) compared with standard surveillance deaths (79.0%). Chart-abstraction detected higher rates of each comorbidity except for diabetes, which had similar rates among standard surveillance and chart-abstraction. Investing in public health data collection infrastructure will be beneficial for the COVID-19 pandemic and future disease outbreaks.
Fatal Exacerbations of Systemic Capillary Leak Syndrome Complicating Coronavirus Disease
We report 2 fatal exacerbations of systemic capillary leak syndrome (SCLS), also known as Clarkson disease, associated with coronavirus disease (COVID-19) in the United States. One patient carried an established diagnosis of SCLS and the other sought treatment for new-onset hypotensive shock, hemoconcentration, and anasarca, classic symptoms indicative of an SCLS flare. Both patients had only mild-to-moderate symptoms of COVID-19. This clinical picture suggests that these patients succumbed to complications of SCLS induced by infection with severe acute respiratory syndrome coronavirus 2. Persons with known or suspected SCLS may be at increased risk for developing a disease flare in the setting of mild-to-moderate COVID-19 infection.
Distribution and Characteristics of Human Plague Cases and Yersinia pestis Isolates from 4 Marmota Plague Foci, China, 1950–2019
We analyzed epidemiologic characteristics and distribution of 1,067 human plague cases and 5,958 Yersinia pestis isolates collected from humans, host animals, and insect vectors during 1950–2019 in 4 Marmota plague foci in China. The case-fatality rate for plague in humans was 68.88%; the overall trend slowly decreased over time but fluctuated greatly. Most human cases (98.31%) and isolates (82.06%) identified from any source were from the Marmota himalayana plague focus. The tendency among human cases could be divided into 3 stages: 1950–1969, 1970–2003, and 2004–2019. The Marmota sibirica plague focus has not had identified human cases nor isolates since 1926. However, in the other 3 foci, Y. pestis continues to circulate among animal hosts; ecologic factors might affect local Y. pestis activity. Marmota plague foci are active in China, and the epidemic boundary is constantly expanding, posing a potential threat to domestic and global public health.
Severe Acute Respiratory Syndrome Coronavirus 2 and Pregnancy Outcomes According to Gestational Age at Time of Infection
We conducted an international multicenter retrospective cohort study, PregOuTCOV, to examine the effect of gestational age at time of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on obstetric and neonatal outcomes. We included all singleton pregnancies with a live fetus at 10 weeks’ gestation in which pregnancy outcomes were known. The exposed group consisted of patients infected with SARS-CoV-2, whereas the unexposed group consisted of all remaining patients during the same period. Primary outcomes were defined as composite adverse obstetric outcomes and composite adverse neonatal outcomes. Of 10,925 pregnant women, 393 (3.60%) were infected with SARS-CoV-2 (exposed group). After matching for possible confounders, we identified statistically significant increases in the exposed group of composite adverse obstetric outcomes at >20 weeks’ gestation and of composite adverse neonatal outcomes at >26 weeks’ gestation (p<0.001). Vaccination programs should target women early in pregnancy or before conception, if possible.
Novel Outbreak-Associated Food Vehicles, United States
Novel outbreak-associated food vehicles (i.e., foods not implicated in past outbreaks) can emerge as a result of evolving pathogens and changing consumption trends. To identify these foods, we examined data from the Centers for Disease Control and Prevention Foodborne Disease Outbreak Surveillance System and found 14,216 reported outbreaks with information on implicated foods. We compared foods implicated in outbreaks during 2007–2016 with those implicated in outbreaks during 1973–2006. We identified 28 novel food vehicles, of which the most common types were fish, nuts, fruits, and vegetables; one third were imported. Compared with other outbreaks, those associated with novel food vehicles were more likely to involve illnesses in multiple states and food recalls and were larger in terms of cases, hospitalizations, and deaths. Two thirds of novel foods did not require cooking after purchase. Prevention efforts targeting novel foods cannot rely solely on consumer education but require industry preventive measures.
Bloodstream Infection Risk, Incidence, and Deaths for Hospitalized Patients during Coronavirus Disease Pandemic
Hospital-acquired infections are emerging major concurrent conditions during the coronavirus disease (COVID-19) pandemic. We conducted a retrospective review of hospitalizations during March‒October 2020 of adults tested by reverse transcription PCR for severe acute respiratory syndrome coronavirus 2. We evaluated associations of COVID-19 diagnosis with risk for laboratory-confirmed bloodstream infections (LCBIs, primary outcome), time to LCBI, and risk for death by using logistic and competing risks regression with adjustment for relevant covariates. A total of 10,848 patients were included in the analysis: 918 (8.5%) were given a diagnosis of COVID-19, and 232 (2.1%) had LCBIs during their hospitalization. Of these patients, 58 (25%) were classified as having central line‒associated bloodstream infections. After adjusting for covariates, COVID-19‒positive status was associated with higher risk for LCBI and death. Reinforcement of infection control practices should be implemented in COVID-19 wards, and review of superiority and inferiority ranking methods by National Healthcare Safety Network criteria might be needed.
Direct and Indirect Effectiveness of mRNA Vaccination against Severe Acute Respiratory Syndrome Coronavirus 2 in Long-Term Care Facilities, Spain
We conducted a registries-based cohort study of long-term care facility residents >65 years of age offered vaccination against severe acute respiratory syndrome coronavirus 2 before March 10, 2021, in Spain. Risk for infection in vaccinated and nonvaccinated persons was compared with risk in the same persons in a period before the vaccination campaign, adjusted by daily-varying incidence and reproduction number. We selected 299,209 persons; 99.0% had >1 dose, 92.6% had 2 doses, and 99.8% of vaccines were Pfizer/BioNTech (BNT162b2). For vaccinated persons with no previous infection, vaccine effectiveness was 81.8% (95% CI 81.0%–82.7%), and 11.6 (95% CI 11.3–11.9) cases were prevented per 10,000 vaccinated/day. In those with previous infection, effectiveness was 56.8% (95% CI 47.1%–67.7%). In nonvaccinated residents with no previous infection, risk decreased by up to 81.4% (95% CI 73.3%–90.3%). Our results confirm vaccine effectiveness in this population and suggest indirect protection in nonvaccinated persons.
Predictors of Test Positivity, Mortality, and Seropositivity during the Early Coronavirus Disease Epidemic, Orange County, California, USA
We conducted a detailed analysis of coronavirus disease in a large population center in southern California, USA (Orange County, population 3.2 million), to determine heterogeneity in risks for infection, test positivity, and death. We used a combination of datasets, including a population-representative seroprevalence survey, to assess the actual burden of disease and testing intensity, test positivity, and mortality. In the first month of the local epidemic (March 2020), case incidence clustered in high-income areas. This pattern quickly shifted, and cases next clustered in much higher rates in the north-central area of the county, which has a lower socioeconomic status. Beginning in April 2020, a concentration of reported cases, test positivity, testing intensity, and seropositivity in a north-central area persisted. At the individual level, several factors (e.g., age, race or ethnicity, and ZIP codes with low educational attainment) strongly affected risk for seropositivity and death.
Fatal Cowpox Virus Infection in Human Fetus, France, 2017
Cowpox virus (CPXV) has an animal reservoir and is typically transmitted to humans by contact with infected animals. In 2017, CPXV infection of a pregnant woman in France led to the death of her fetus. Fetal death after maternal orthopoxvirus (smallpox) vaccination has been reported; however, this patient had not been vaccinated. Investigation of the patient’s domestic animals failed to demonstrate prevalence of CPXV infection among them. The patient’s diagnosis was confirmed by identifying CPXV DNA in all fetal and maternal biopsy samples and infectious CPXV in biopsy but not plasma samples. This case of fetal death highlights the risk for complications of orthopoxvirus infection during pregnancy. Among orthopoxviruses, fetal infection has been reported for variola virus and vaccinia virus; our findings suggest that CPXV poses the same threats for infection complications as vaccinia virus.
Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in Georgia, USA, February 1–July 13, 2020
The serial interval and effective reproduction number for coronavirus disease (COVID-19) are heterogenous, varying by demographic characteristics, region, and period. During February 1–July 13, 2020, we identified 4,080 transmission pairs in Georgia, USA, by using contact tracing information from COVID-19 cases reported to the Georgia Department of Public Health. We examined how various transmission characteristics were affected by symptoms, demographics, and period (during shelter-in-place and after subsequent reopening) and estimated the time course of reproduction numbers for all 159 Georgia counties. Transmission varied by time and place but also by persons’ sex and race. The mean serial interval decreased from 5.97 days in February–April to 4.40 days in June–July. Younger adults (20–50 years of age) were involved in most transmission events occurring during or after reopening. The shelter-in-place period was not long enough to prevent sustained virus transmission in densely populated urban areas connected by major transportation links.
Risk Assessment for Highly Pathogenic Avian Influenza A(H5N6/H5N8) Clade 18.104.22.168 Viruses
The numerous global outbreaks and continuous reassortments of highly pathogenic avian influenza (HPAI) A(H5N6/H5N8) clade 22.214.171.124 viruses in birds pose a major risk to the public health. We investigated the tropism and innate host responses of 5 recent HPAI A(H5N6/H5N8) avian isolates of clades 126.96.36.199b, e, and h in human airway organoids and primary human alveolar epithelial cells. The HPAI A(H5N6/H5N8) avian isolates replicated productively but with lower competence than the influenza A(H1N1)pdm09, HPAI A(H5N1), and HPAI A(H5N6) isolates from humans in both or either models. They showed differential cellular tropism in human airway organoids; some infected all 4 major epithelial cell types: ciliated cells, club cells, goblet cells, and basal cells. Our results suggest zoonotic potential but low transmissibility of the HPAI A(H5N6/H5N8) avian isolates among humans. These viruses induced low levels of proinflammatory cytokines/chemokines, which are unlikely to contribute to the pathogenesis of severe disease.
Medscape CME Activity
Population-Based Study of Bloodstream Infection Incidence and Mortality Rates, Finland, 2004–2018
We evaluated the incidence, outcomes, and causative agents of bloodstream infections (BSI) in Finland during 2004–2018 by using data from the national registries. We identified a total of 173,715 BSIs; annual incidence increased from 150 to 309 cases/100,000 population. BSI incidence rose most sharply among persons >80 years of age. The 1-month case-fatality rate decreased from 13.0% to 12.6%, but the 1-month all-cause mortality rate rose from 20 to 39 deaths/100,000 population. BSIs caused by Escherichia coli increased from 26% to 30% of all BSIs. BSIs caused by multidrug-resistant microbes rose from 0.4% to 2.8%, mostly caused by extended-spectrum β-lactamase-producing E. coli. We observed an increase in community-acquired BSIs, from 67% to 78%. The proportion of patients with severe underlying conditions rose from 14% to 23%. Additional public health and healthcare prevention efforts are needed to curb the increasing trend in community-acquired BSIs and antimicrobial drug–resistant E. coli.
New Delhi Metallo-β-Lactamase–Producing Enterobacterales Bacteria, Switzerland, 2019–2020
Carbapenemase-producing Enterobacterales (CPE) bacteria are a critical global health concern; New Delhi metallo-β-lactamase (NDM) enzymes account for >25% of all CPE found in Switzerland. We characterized NDM-positive CPE submitted to the Swiss National Reference Center for Emerging Antibiotic Resistance during a 2-year period (January 2019–December 2020) phenotypically and by using whole-genome sequencing. Most isolates were either Klebsiella pneumoniae (59/141) or Escherichia coli (52/141), and >50% were obtained from screening swabs. Among the 108 sequenced isolates, NDM-1 was the most prevalent variant, occurring in 56 isolates, mostly K. pneumoniae (34/56); the next most prevalent was NDM-5, which occurred in 49 isolates, mostly E. coli (40/49). Fourteen isolates coproduced a second carbapenemase, predominantly an OXA-48-like enzyme, and almost one third of isolates produced a 16S rRNA methylase conferring panresistance to aminoglycosides. We identified successful plasmids and global lineages as major factors contributing to the increasing prevalence of NDMs in Switzerland.
New Perspective on the Geographic Distribution and Evolution of Lymphocytic Choriomeningitis Virus, Central Europe
Lymphocytic choriomeningitis virus (LCMV) is an Old World mammarenavirus found worldwide because of its association with the house mouse. When LCMV spills over to immunocompetent humans, the virus can cause aseptic meningitis; in immunocompromised persons, systemic infection and death can occur. Central Europe is a strategic location for the study of LCMV evolutionary history and host specificity because of the presence of a hybrid zone (genetic barrier) between 2 house mouse subspecies, Mus musculus musculus and M. musculus domesticus. We report LCMV prevalence in natural mouse populations from a Czech Republic–Germany transect and genomic characterization of 2 new LCMV variants from the Czech Republic. We demonstrate that the main division in the LCMV phylogenetic tree corresponds to mouse host subspecies and, when the virus is found in human hosts, the mouse subspecies found at the spillover location. Therefore, LCMV strains infecting humans can be predicted by the genetic structure of house mice.
Burden of Influenza-Associated Respiratory Hospitalizations, Vietnam, 2014–2016
Influenza burden estimates are essential to informing prevention and control policies. To complement recent influenza vaccine production capacity in Vietnam, we used acute respiratory infection (ARI) hospitalization data, severe acute respiratory infection (SARI) surveillance data, and provincial population data from 4 provinces representing Vietnam’s major regions during 2014–2016 to calculate provincial and national influenza-associated ARI and SARI hospitalization rates. We determined the proportion of ARI admissions meeting the World Health Organization SARI case definition through medical record review. The mean influenza-associated hospitalization rates per 100,000 population were 218 (95% uncertainty interval [UI] 197–238) for ARI and 134 (95% UI 119–149) for SARI. Influenza-associated SARI hospitalization rates per 100,000 population were highest among children <5 years of age (1,123; 95% UI 946–1,301) and adults >65 years of age (207; 95% UI 186–227), underscoring the need for prevention and control measures, such as vaccination, in these at-risk populations.
Widespread Disease in Hedgehogs (Erinaceus europaeus) Caused by Toxigenic Corynebacterium ulcerans
Toxin-producing Corynebacterium ulcerans, a causative agent of diphtheria in humans, was isolated from 53 hedgehogs in Belgium during the spring of 2020. Isolates showed low levels of acquired antimicrobial drug resistance. Strain diversity suggests emergence from an endemic situation. These findings stress the need for raising public awareness and improved wildlife disease surveillance.
Genetic Diversity of SARS-CoV-2 among Travelers Arriving in Hong Kong
We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our results suggest that international or regional travel hubs might be useful surveillance sites to monitor sequence diversity.
Point-of-Care Antigen Test for SARS-CoV-2 in Asymptomatic College Students
We used the BinaxNOW COVID-19 Ag Card to screen 1,540 asymptomatic college students for severe acute respiratory syndrome coronavirus 2 in a low-prevalence setting. Compared with reverse transcription PCR, BinaxNOW showed 20% overall sensitivity; among participants with culturable virus, sensitivity was 60%. BinaxNOW provides point-of-care screening but misses many infections.
Medscape CME Activity
Recurrence of Human Babesiosis Caused by Reinfection
Babesiosis developed in a 62-year-old immunocompetent physician, who had an uneventful recovery after receiving atovaquone and azithromycin. Three years later, babesiosis developed again, and he was again successfully given treatment. Clinical and laboratory evidence were highly supportive of Babesia reinfection. Healthcare professionals should be aware that reinfection might occur in babesiosis.
Breakthrough Infections of SARS-CoV-2 Gamma Variant in Fully Vaccinated Gold Miners, French Guiana, 2021
An outbreak of severe acute respiratory syndrome coronavirus 2 caused by the Gamma variant of concern infected 24/44 (55%) employees of a gold mine in French Guiana (87% symptomatic, no severe forms). The attack rate was 60% (15/25) among fully vaccinated miners and 75% (3/4) among unvaccinated miners without a history of infection.
Seoul Virus Associated with Pet Rats, Scotland, UK, 2019
We describe a case of hemorrhagic fever with renal syndrome caused by Seoul virus in a woman in Scotland, UK. Whole-genome sequencing showed the virus belonged to a lineage characterized by recent international expansion, probably driven by trade in pet rats.
Natural Plasmodium inui Infections in Humans and Anopheles cracens Mosquito, Malaysia
We detected 2 natural, asymptomatic Plasmodium inui monoinfections in humans in Malaysia by using nested PCR on concentrated high-volume blood samples. We found a P. inui–positive Anopheles cracens mosquito in the same site as the human infections. Investigators should use ultrasensitive detection methods to identify simian malaria parasite transmission in humans.
Outbreak of Oropouche Virus in French Guiana
Oropouche fever is a zoonotic dengue-like syndrome caused by Oropouche virus. In August–September 2020, dengue-like syndrome developed in 41 patients in a remote rainforest village in French Guiana. By PCR or microneutralization, 23 (82.1%) of 28 tested patients were positive for Oropouche virus, documenting its emergence in French Guiana.
Rapid Increase in Lymphogranuloma Venereum among HIV-Negative Men Who Have Sex with Men, England, 2019
Incidence of lymphogranuloma venereum increased in England during 2018–2019, after a period of decline. Our retrospective analysis of national surveillance data identified a rapid increase in diagnoses among HIV-negative men who have sex with men. These findings indicate a need for sustained surveillance and targeted public health action.
Confirmation of Rickettsia conorii Subspecies indica Infection by Next-Generation Sequencing, Shandong, China
We describe 3 similar cases of rickettsial disease that occurred after tick bites in a mountainous rural area of Shandong Province, China. Next-generation sequencing indicated the etiologic agent of 1 patient was Rickettsia conorii subspecies indica. This agent may be more widely distributed across China than previously thought.
- Relapsing Fever Infection Manifesting as Aseptic Meningitis
Genetic Characterization of Seoul Virus in the Seaport of Cotonou, Benin
Seoul virus is a zoonotic pathogen carried by the brown rat Rattus norvegicus. Information on its circulation in Africa is limited. In this study, the virus was detected in 37.5% of brown rats captured in the Autonomous Port of Cotonou, Benin. Phylogenetic analyses place this virus in Seoul virus lineage 7.
Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020
In fall 2020, a coronavirus disease cluster comprising 16 cases occurred in Connecticut, USA. Epidemiologic and genomic evidence supported transmission among persons at a school and fitness center but not a workplace. The multiple transmission chains identified within this cluster highlight the necessity of a combined investigatory approach.
Therapeutic Efficacy of Human Monoclonal Antibodies against Andes Virus Infection in Syrian Hamsters
Andes virus, an orthohantavirus endemic to South America, causes severe hantavirus cardiopulmonary syndrome associated with human-to-human transmission. No approved treatments or vaccines against this virus are available. We show that a combined treatment with 2 monoclonal antibodies protected Syrian hamsters when administered at midstage or late-stage disease.
Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA
Genomic surveillance can provide early insights into new circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. While conducting genomic surveillance (1,663 cases) from December 2020–April 2021 in Arizona, USA, we detected an emergent E484K-harboring variant, B.1.243.1. This finding demonstrates the importance of real-time SARS-CoV-2 surveillance to better inform public health responses.
Autochthonous Case of Rickettsia slovaca Infection in Russia
We describe an autochthonous case of Rickettsia slovaca infection in a man 35 years of age from Russia who had tickborne lymphadenopathy. We used ELISA and quantitative PCR testing to further identify DNA and confirm diagnosis. Physicians in Russia should consider similar diseases in differential diagnoses after tick bites.
Indoor and Outdoor Rodent Hosts of Orientia tsutsugamushi, Shandong Province, China
During December 2012–July 2016, we tested small indoor and outdoor mammals in Qingdao, China, for Orientia tsutsugamushi infection. We found that outdoor Apodemus agrarius mice, Cricetulus barabensis hamsters, and Niviventer confucianus rats, as well as indoor Mus musculus mice, tested positive for O. tsutsugamushi by PCR.
SARS-CoV-2 Neutralization Resistance Mutations in Patient with HIV/AIDS, California, USA
We report persistent severe acute respiratory syndrome coronavirus 2 infection in a patient with HIV/AIDS; the virus developed spike N terminal domain and receptor binding domain neutralization resistance mutations. Our findings suggest that immunocompromised patients can harbor emerging variants of severe acute respiratory syndrome coronavirus 2.
Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19
We report in vivo selection of a severe acute respiratory syndrome coronavirus 2 spike mutation (Q493R) conferring simultaneous resistance to bamlanivimab and etesivimab. This mutation was isolated from a patient who had coronavirus disease and was treated with these drugs.
SARS-CoV-2 Variants in Immunocompromised Patient Given Antibody Monotherapy
A 72-year-old immunocompromised man infected with severe acute respiratory syndrome coronavirus 2 received bamlanivimab monotherapy. Viral evolution was monitored in nasopharyngeal and blood samples by melting curve analysis of single-nucleotide polymorphisms and whole-genome sequencing. Rapid emergence of spike receptor binding domain mutations was found, associated with a compartmentalization of viral populations.
Effects of COVID-19 Pandemic on Reported Lyme Disease, United States, 2020
Surveys indicate US residents spent more time outdoors in 2020 than in 2019, but fewer tick bite–related emergency department visits and Lyme disease laboratory tests were reported. Despite ongoing exposure, Lyme disease case reporting for 2020 might be artificially reduced due to coronavirus disease–associated changes in healthcare-seeking behavior.
Equine Herpesvirus 1 Variant and New Marker for Epidemiologic Surveillance, Europe, 2021
Equine herpesvirus 1 isolates from a 2021 outbreak of neurologic disease in Europe have a mutation, A713G, in open reading frame 11 not detected in 249 other sequences from equine herpesvirus 1 isolates. This single-nucleotide polymorphism could help identify horses infected with the virus strain linked to this outbreak.
Nocardiosis in Immunocompromised Patients on Alternative Pneumocystis Prophylaxis
Prophylactic trimethoprim/sulfamethoxazole (TMP/SMX) prevents Pneumocystis jirovecii pneumonia and nocardiosis in immunocompromised patients but sometimes is avoided because of purported allergies or side effects. Of 25 immunocompromised patients receiving alternative prophylaxis in whom nocardiosis developed, 16 subsequently tolerated TMP/SMX treatment. Clinicians should consider TMP/SMX allergy evaluation and rechallenging to assess patient tolerance.
Emergomyces orientalis Emergomycosis Diagnosed by Metagenomic Next-Generation Sequencing
Emergomyces is a newly described dimorphic fungus genus; it may cause fatal infections in immunocompromised patients, but diagnosis is often delayed. We report a case of disseminated emergomycosis caused by the novel species Emergomyces orientalis in a kidney transplant recipient from Tibet. Infection was diagnosed early by metagenomic next-generation sequencing.
Human Infection with Avian Influenza A(H9N2) Virus, Cambodia, February 2021
In February 2021, routine sentinel surveillance for influenza-like illness in Cambodia detected a human avian influenza A(H9N2) virus infection. Investigations identified no recent H9N2 virus infections in 43 close contacts. One chicken sample from the infected child’s house was positive for H9N2 virus and genetically similar to the human virus.
SARS-CoV-2 Delta Variant among Asiatic Lions, India
In May 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in Asiatic lions in a zoological park in India. Sequence and phylogenetic analyses showed the SARS-CoV-2 strains were the B.1.617.2 (Delta) variant. To reduce transmission of variants of concern, surveillance of SARS-CoV-2 in wild animal populations should be increased.
About the Cover
Proactive Engagement of the Expert Meeting in Managing the Early Phase of the COVID-19 Epidemic, Japan, February–June 2020
To deal with the risk of emerging diseases with many unknowns, close and timely collaboration and communication between science experts and policymakers are crucial to developing and implementing an effective science-based intervention strategy. The Expert Meeting, an ad hoc medical advisory body, was established in February 2020 to advise Japan’s COVID-19 Response Headquarters. The group played an important role in the policymaking process, promoting timely situation awareness and developing science-based proposals on interventions that were promptly reflected in government actions. However, this expert group may have been overly proactive in taking on the government’s role in crisis management. For the next stage of managing the coronavirus disease pandemic and future pandemics, the respective roles of the government and its advisory bodies need to be clearly defined. Leadership and strategic risk communication by the government are key.
Volume 27, Number 11—November 2021
Policy Review and Modeling Analysis of Mitigation Measures for Coronavirus Disease Epidemic Control, Health System, and Disease Burden, South Korea
We reviewed the timeline of key policies for control of the coronavirus disease epidemic and determined their impact on the epidemic and hospital burden in South Korea. Using a discrete stochastic transmission model, we estimated that multilevel policies, including extensive testing, contact tracing, and quarantine, reduced contact rates by 90% and rapidly decreased the epidemic in Daegu and nationwide during February‒March 2020. Absence of these prompt responses could have resulted in a >10-fold increase in infections, hospitalizations, and deaths by May 15, 2020, relative to the status quo. The model suggests that reallocation of persons who have mild or asymptomatic cases to community treatment centers helped avoid overwhelming hospital capacity and enabled healthcare workers to provide care for more severely and critically ill patients in hospital beds and negative-pressure intensive care units. As small outbreaks continue to occur, contact tracing and maintenance of hospital capacity are needed.
Effectiveness of Abbott BinaxNOW Rapid Antigen Test for Detection of SARS-CoV-2 Infections in Outbreak among Horse Racetrack Workers, California, USA
The Abbott BinaxNOW rapid antigen test is cheaper and faster than real-time reverse transcription PCR (rRT-PCR) for detecting severe acute respiratory syndrome coronavirus 2. We compared BinaxNOW with rRT-PCR in 769 paired specimens from 342 persons during a coronavirus disease outbreak among horse racetrack workers in California, USA. We found positive percent agreement was 43.3% (95% CI 34.6%–52.4%), negative percent agreement 100% (95% CI 99.4%–100%), positive predictive value 100% (95% CI 93.5%–100%), and negative predictive value 89.9% (95% CI 87.5%–92.0%). Among 127 rRT-PCR–positive specimens, the 55 with paired BinaxNOW-positive results had a lower mean cycle threshold than the 72 with paired BinaxNOW-negative results (17.8 vs. 28.5; p<0.001). Of 100 specimens with cycle threshold <30, a total of 51 resulted in positive virus isolation; 45 (88.2%) of those were BinaxNOW-positive. Our comparison supports immediate isolation for BinaxNOW-positive persons and confirmatory testing for negative persons.
- Ehrlichiosis and Anaplasmosis among Transfusion and Transplant Recipients in the United States
- Interventions to Disrupt COVID-19 Transmission at a University, Wisconsin, USA, August–October 2020
- Genomic Profiling of Mycobacterium tuberculosis Strains, Myanmar
- Incidence Rates for Hepatitis A Virus and Biomarker Dynamics in Plasma Donors, United States
Probability-Based Estimates of Severe Acute Respiratory Syndrome Coronavirus 2 Seroprevalence and Detection Fraction, Utah, USA
We aimed to generate an unbiased estimate of the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 4 urban counties in Utah, USA. We used a multistage sampling design to randomly select community-representative participants >12 years of age. During May 4–June 30, 2020, we collected serum samples and survey responses from 8,108 persons belonging to 5,125 households. We used a qualitative chemiluminescent microparticle immunoassay to detect SARS-CoV-2 IgG in serum samples. We estimated the overall seroprevalence to be 0.8%. The estimated seroprevalence-to-case count ratio was 2.5, corresponding to a detection fraction of 40%. Only 0.2% of participants from whom we collected nasopharyngeal swab samples had SARS-CoV-2–positive reverse transcription PCR results. SARS-CoV-2 antibody prevalence during the study was low, and prevalence of PCR-positive cases was even lower. The comparatively high SARS-CoV-2 detection rate (40%) demonstrates the effectiveness of Utah’s testing strategy and public health response.
Seroprevalence of SARS-CoV-2–Specific Antibodies among Quarantined Close Contacts of COVID-19 Patients, Faroe Islands, 2020
Close contacts of coronavirus disease (COVID-19) patients are at high risk for severe acute respiratory syndrome 2 (SARS-CoV-2) infection. We assessed the seroprevalence of SARS-CoV-2–specific antibodies among quarantined close contacts of COVID-19 patients in the Faroe Islands. We invited quarantined close contacts of COVID-19 index patients identified during March 3–April 22, 2020, to participate in this study; 584 (81%) contacts consented and underwent serologic testing. Among the 584 participants, 32 (5.5%) were seropositive for total antibody against SARS-CoV-2. Household and young or elderly contacts had higher risk for seropositivity than other contacts. We found a secondary attack rate of 19.2%. Seroprevalence among close contacts was almost 10-fold higher than among the general population of the Faroe Islands. Regularly testing household close contacts of COVID-19 patients might help track the transmission of SARS-CoV-2.
Rapid Increase in SARS-CoV-2 P.1 Lineage Leading to Codominance with B.1.1.7 Lineage, British Columbia, Canada, January–April 2021
Several severe acute respiratory syndrome coronavirus 2 variants of concern (VoCs) emerged in late 2020; lineage B.1.1.7 initially dominated globally. However, lineages B.1.351 and P.1 represent potentially greater risk for transmission and immune escape. In British Columbia, Canada, B.1.1.7 and B.1.351 were first identified in December 2020 and P.1 in February 2021. We combined quantitative PCR and whole-genome sequencing to assess relative contribution of VoCs in nearly 67,000 infections during the first 16 weeks of 2021 in British Columbia. B.1.1.7 accounted for <10% of screened or sequenced specimens early on, increasing to >50% by week 8. P.1 accounted for <10% until week 10, increased rapidly to peak at week 12, and by week 13 codominated within 10% of rates of B.1.1.7. B.1.351 was a minority throughout. This rapid expansion of P.1 but suppression of B.1.351 expands our understanding of population-level VoC patterns and might provide clues to fitness determinants for emerging VoCs.
- Multidrug-Resistant MRSA Associated with Bacteremia and Monocyte Evasion, Rio de Janeiro, Brazil
- Changing Patterns of Disease Severity in Blastomyces dermatitidis Infection, Quebec, Canada
- Encephalitis and Death in Wild Mammals at Rehabilitation Center after Systemic Infection with Highly Pathogenic Avian Influenza A(H5N8), United Kingdom
- Population Genomics and Inference of Mycobacterium avium Complex Clusters in Cystic Fibrosis Centers, United States
Bordetella hinzii Pneumonia and Bacteremia in a Patient with SARS-CoV-2 Infection
Patients with severe acute respiratory syndrome coronavirus 2 infection may have bacterial co-infections, including pneumonia and bacteremia. Bordetella hinzii infections are rare, may be associated with exposure to poultry, and have been reported mostly among immunocompromised patients. We describe B. hinzii pneumonia and bacteremia in a severe acute respiratory syndrome coronavirus 2 patient.
Mutations Associated with SARS-CoV-2 Variants of Concern, Benin, Early 2021
Intense transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa might promote emergence of variants. We describe 10 SARS-CoV-2 lineages in Benin during early 2021 that harbored mutations associated with variants of concern. Benin-derived SARS-CoV-2 strains were more efficiently neutralized by antibodies derived from vaccinees than patients, warranting accelerated vaccination in Africa.
- Genetically Divergent Highly Pathogenic Avian Influenza A(H5N8) Viruses in Wild Birds, Eastern China
Prevalence of SARS-CoV-2 Antibodies after First 6 Months of COVID-19 Pandemic, Portugal
In September 2020, we tested 13,398 persons in Portugal for antibodies against severe acute respiratory syndrome coronavirus 2 by using a quota sample stratified by age and population density. We found a seroprevalence of 2.2%, 3–4 times larger than the official number of cases at the end of the first wave of the pandemic.
Co-infection with Legionella and SARS-CoV-2, France, March 2020
We describe a March 2020 co-occurrence of Legionnaires’ disease (LD) and coronavirus disease in France. Severe acute respiratory syndrome coronavirus 2 co-infections were identified in 7 of 49 patients from LD case notifications. Most were elderly men with underlying conditions who had contracted severe pneumonia, illustrating the relevance of co-infection screening.
Correlation of SARS-CoV-2 Subgenomic RNA with Antigen Detection in Nasal Midturbinate Swab Specimens
Among symptomatic outpatients, subgenomic RNA of severe acute respiratory syndrome coronavirus 2 in nasal midturbinate swab specimens was concordant with antigen detection but remained detectable in 13 (82.1%) of 16 nasopharyngeal swab specimens from antigen-negative persons. Subgenomic RNA in midturbinate swab specimens might be useful for routine diagnostics to identify active virus replication.
Multinational Observational Cohort Study of COVID-19–Associated Pulmonary Aspergillosis
We performed an observational study to investigate intensive care unit incidence, risk factors, and outcomes of coronavirus disease–associated pulmonary aspergillosis (CAPA). We found 10%–15% CAPA incidence among 823 patients in 2 cohorts. Several factors were independently associated with CAPA in 1 cohort and mortality rates were 43%–52%.
- Isolation of Mycobacterium camsnse sp. nov. from skin infection in an immunocompromised person
- Epidemiologic Analysis of Efforts to Sustain Malaria Elimination along the China–Myanmar Border, 2013–2019
- COVID-19 Vaccination Coverage, Intent, and Knowledge, Attitudes, and Beliefs among Essential Workers, United States
Socioeconomic Patterns of COVID-19 Clusters in Low-Incidence City, Hong Kong
Although coronavirus disease (COVID-19) outbreaks have been relatively well controlled in Hong Kong, containment remains challenging among socioeconomically disadvantaged persons. They are at higher risk for widespread COVID-19 transmission through sizable clustering, probably because of exposure to social settings in which existing mitigation policies had differential socioeconomic effects.
- Fatal Multisystem Inflammatory Syndrome in Adult after SARS-CoV-2 Natural Infection and COVID-19 Vaccination
- Influenza and SARS-CoV-2 Co-infection, California, USA, 2020–2021
- Emergence of Vibrio cholerae O1 Sequence Type 75, South Africa, 2018–2020
- Association of Shared Living Spaces and COVID-19 in University Students, Wisconsin, USA, 2020
Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay
We developed a genomic surveillance program for real-time monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARS-CoV-2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of the SARS-CoV-2 P.1 VOC in Uruguay.
Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka
A melioidosis case cluster of 10 blood culture–positive patients occurred in eastern Sri Lanka after an extreme weather event. Four infections were caused by Burkholderia pseudomallei isolates of sequence type 594. Whole-genome analysis showed that the isolates were genetically diverse and the case cluster was nonclonal.
Resurgence of Respiratory Syncytial Virus Infections during COVID-19 Pandemic, Tokyo, Japan
More than a year into the coronavirus-19 pandemic, intensified infection control measures have controlled most viral respiratory infections in Tokyo, Japan. As of July 2021, however, an unusually high number of respiratory syncytial virus infections were reported in Tokyo. This resurgence may have resulted from restarting social activities for children.
Online Registry of COVID-19–Associated Mucormycosis Cases, India, 2021
We established an online registry of coronavirus disease–associated mucormycosis cases in India. We analyzed data from 65 cases diagnosed during April–June 2021, when the Delta variant predominated, and found that patients frequently received antibacterial drugs and zinc supplementation. Online registries rapidly provide relevant data for emerging infections.
Fatal Systemic Capillary Leak Syndrome after SARS-CoV-2 Vaccination in Patient with Multiple Myeloma
A young man with smoldering multiple myeloma died of hypotensive shock 2.5 days after severe acute respiratory syndrome coronavirus 2 vaccination. Clinical findings suggested systemic capillary leak syndrome (SCLS); the patient had experienced a previous suspected flare episode. History of SCLS may indicate higher risk for SCLS after receiving this vaccine.
Spontaneous Bacterial Peritonitis Caused by Bordetella hinzii
Although Bordetella hinzii coccobacilli is most commonly identified in respiratory tracts of birds and rodents, this organism has occasionally been isolated in human infections. We describe a case of B. hinzii spontaneous bacterial peritonitis in Missouri, USA. Whole-genome sequencing of blood and peritoneal fluid isolates confirmed B. hinzii infection.
- Tracing the Origin, Spread, and Molecular Evolution of Zika Virus, Puerto Rico, 2016–2017
Books and Media
- The COVID Catastrophe: What’s Gone Wrong and How To Stop It Happening Again
Volume 27, Number 12—December 2021
- Use of a Novel Serological Assay to Measure the Seroprevalence of Zika Virus in the Philippines
- Surface‒Aerosol Stability and Pathogenicity of Diverse Middle East Respiratory Syndrome Coronavirus Strains, 2012‒2018
SARS-CoV-2 Seroprevalence in a Rural and Urban Household Cohort during First and Second Waves of Infections, South Africa, July 2020–March 2021
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may be underestimated because of limited access to testing. We measured SARS-CoV-2 seroprevalence in South Africa every 2 months during July 2020–March 2021 in randomly selected household cohorts in 2 communities. We compared seroprevalence to reported laboratory-confirmed infections, hospitalizations, and deaths to calculate infection–case, infection–hospitalization, and infection–fatality ratios in 2 waves of infection. Post–second wave seroprevalence ranged from 18% in the rural community children <5 years of age, to 59% in urban community adults 35–59 years of age. The second wave saw a shift in age distribution of case-patients in the urban community (from persons 35–59 years of age to persons at the extremes of age), higher attack rates in the rural community, and a higher infection–fatality ratio in the urban community. Approximately 95% of SARS-CoV-2 infections were not reported to national surveillance.
- Coronavirus Disease Contact Tracing Outcomes and Cost, Salt Lake County, Utah, United States, March–May 2020
- Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in Households with Children, Southwest Germany, May–August 2020
- Novel Transmission of Burkholderia pseudomallei from Freshwater Home Aquarium Causing Human Melioidosis, United States
- Heartland Virus Transmission, Suffolk County, New York, USA
- Experimental Oronasal Transmission of Chronic Wasting Disease Agent from White-Tailed Deer to Suffolk Sheep
Detection of SARS-CoV-2 in Wastewater at Residential College, Maine, USA, August–November 2020
We used wastewater surveillance to identify 2 coronavirus disease outbreaks at a college in Maine, USA. Cumulative increases of >1 log10 severe acute respiratory syndrome coronavirus 2 RNA in consecutive 24-hour composite samples preceded the outbreaks. For 76% of cases, RNA was identified in grab samples from residence halls <7 days before case discovery.
- SARS-CoV-2–Specific Antibodies in Domestic Cats during First COVID-19 Wave, Europe
- Incidence Trends for SARS-CoV2 Alpha and Beta Variants, Finland, Spring 2021
- SARS-CoV-2 Variants, South Sudan, January–March 2021
Large-Scale Screening of Asymptomatic Persons for SARS-CoV-2 Variants of Concern and Gamma Takeover, Brazil
We performed a large-scale severe acute respiratory syndrome coronavirus 2 screening campaign using 2 PCR-based approaches, coupled with variant genotyping, aiming to provide a safer environment for employees of Federal University in Curitiba, Brazil. We observed the rapid spread of the Gamma variant of concern, which replaced other variants in <3 months.
- Septic Polyarthritis Caused by Streptobacillus moniliformis
- SARS-CoV-2 Lineage B.1.1.7 Infection in Malayan Tigers, Virginia, United States
Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy
The Delta variant of concern of severe acute respiratory syndrome coronavirus 2 is dominant worldwide. We report a case cluster caused by Delta sublineage B.1.617.2 harboring the mutation E484K in Italy during July 11–July 29, 2021. This mutation appears to affect immune response and vaccine efficacy; monitoring its appearance is urgent.
- Coxiella burnetii in 3 Species of Turtles in the Upper Midwest, United States
- Real-time Projections of the SARS-CoV-2 B.1.1.7 Variant in a University Setting, Texas, USA
- Neutralizing Titers in Serum of Coronavirus Vaccine Recipients against Wuhan Strain and Multiple Variants
Volume 28, Number 1—January 2022
- Global Genome Diversity and Recombination in Mycoplasma pneumoniae