COVID-19 Scientific Publications From the Centers for Disease Control and Prevention, January 2020-January 2022.

OBJECTIVE: High-quality scientific evidence underpins public health decision making. The Centers for Disease Control and Prevention (CDC) agency provides scientific data, including during public health emergencies. To understand CDC's contributions to COVID-19 science, we conducted a bibliometric evaluation of publications authored by CDC scientists from January 20, 2020, through January 20, 2022, by using a quality improvement approach (SQUIRE 2.0). METHODS: We catalogued COVID-19 articles with ≥1 CDC-affiliated author published in a scientific journal and indexed in the World Health Organization's COVID-19 database. We identified priority topic areas from the agency's COVID-19 Public Health Science Agenda by using keyword scripts in EndNote and then assessed the impact of the published articles by using Scopus and Altmetric. RESULTS: During the first 2 years of the agency's pandemic response, CDC authors contributed to 1044 unique COVID-19 scientific publications in 208 journals. Publication topics included testing (n = 853, 82%); prevention strategies (n = 658, 63%); natural history, transmission, breakthrough infections, and reinfections (n = 587, 56%); vaccines (n = 567, 54%); health equity (n = 308, 30%); variants (n = 232, 22%); and post-COVID-19 conditions (n = 44, 4%). Publications were cited 40 427 times and received 81 921 news reports and 1 058 893 social media impressions. As the pandemic evolved, CDC adapted to address new scientific questions, including vaccine effectiveness, safety, and access; viral variants, including Delta and Omicron; and health equity. CONCLUSION: The agency's COVID-19 Public Health Science Agenda helped guide impactful scientific activities. CDC continues to evaluate COVID-19 priority topic areas and contribute to development of new scientific work. CDC is committed to monitoring emerging issues and addressing gaps in evidence needed to improve health.

Evaluation of the public health achievements made by projects supported by a federal contract mechanism at the Centers for Disease Control and Prevention (CDC), USA.

In 2012, the Centers for Disease Control and Prevention (CDC) established the Achieving Public Health Impact through Research (APHIR) contract mechanism. APHIR provides CDC's Centers, Institute, and Offices (CIOs) a mechanism that supports multiyear, high impact public health research. Awarded projects supported research on a wide range of topics (e.g., cancer surveillance, HIV education programs, development of biological assays, and evaluation of traumatic brain injury prevention programs) and achieved diverse outcomes (e.g., contribution to the body of knowledge in their field, changes in practice and health service delivery, and capacity building). This article describes how existing impact frameworks and a variety of methods and tools (key informant interviews, online survey, bibliometric analysis, Altmetric and document reviews) were used to identify the outcomes achieved by awarded projects. The approach discussed in this paper can be used to evaluate projects that involve a diversity of activities and outcomes.

Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.

The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.

Developing a cross-site evaluation tool for diverse health interventions.

The Prevention Research Center of Michigan provided technical assistance for the evaluation of 10 projects funded by the Michigan Department of Community Health's (MDCH) Health Disparities Reduction Program. These projects varied considerably in focus, methodology, geographical coverage, and populations served. The authors developed a cross-site evaluation tool to complement the internal evaluations of the projects. The tool contains four sections based on priorities identified by MDCH: evidence-based practice, research-based learning/evaluation (including process, impact, and outcomes indicators), cultural competence, and sustainability. Recognizing the diversity of programmatic efforts and organizational evaluation capacity, the authors sought to enable each project to create the best evaluation possible given the resources and data available. Each section contains a range of components from basic questions to more advanced evaluation techniques. The instrument attempts to use the highest quality of information available for each project. This evaluation tool can be used by programs with diverse goals and methodology.

Dynamics of oliveros virus infection in rodents in central Argentina.

Oliveros virus (OLV) is an arenavirus hosted by the sigmodontine rodent, Necromys benefactus, in central Argentina. We report a 3-year longitudinal field study of the dynamics of OLV infection in host populations from 15 localities in two provinces on the central Argentine pampa. There was an overall 3-year period immunofluorescent antibody prevalence of 25% in the host population, and infected hosts were found throughout the study area. Spill-over infection into common sympatric species was rare. Infection dynamics exhibited many of the patterns seen for other rodent-borne arenaviruses and hantaviruses, but had some unique characteristics. Host population density was highest in autumn and lowest in spring, while antibody prevalence was highest in spring and lowest in autumn. Virus transmission was horizontal: infection was strongly associated with age, reaching 45% prevalence in the oldest individuals, and prevalence of infection was equal among male and female hosts. Infection may have been associated with scars, which were also approximately equally distributed among male and female Necromys.

A longitudinal study of hantavirus infection in three sympatric reservoir species in agroecosystems on the Argentine Pampa.

Prevalence of antibody reactive with Sin Nombre hantavirus (SNV) was evaluated from rodents captured over 31 months (March 1988 to September 1990) from six mark-recapture grids on the central Argentine Pampa. The most frequently infected rodents were: Akodon azarae (31/459), Necromys benefactus (8/141), and Oligoryzomys flavescens (10/281), which are known hosts of Pergamino, Maciel, and Lechiguanas hantaviruses, respectively. Relative population density and antibody prevalence varied seasonally and from year to year, population densities were highest in fall and prevalences were highest in spring. A positive association between antibody prevalence and body weight corroborated findings from other studies suggesting that hantaviruses are maintained in reservoir populations by horizontal transmission. In two of three host species, transmission was more frequent among male than among female mice. We found no evidence for a detrimental effect of hantavirus infection on host body weight, growth, longevity, movement, or reproductive preparedness. This analysis, based on cryopreserved specimens, represents the earliest conducted longitudinal, mark-recapture study of the dynamics of infection of autochthonous American hantaviruses in their sigmodontine host populations.

Population genetic analysis of Bartonella bacilliformis isolates from areas of peru where Carrion's disease is endemic and epidemic.

Carrion's disease is caused by infection with the alpha-proteobacterium Bartonella bacilliformis. Distribution of the disease is considered coincident with the distribution of its known vector, the sand fly Lutzomyia verrucarum. Recent epidemics of B. bacilliformis infections associated with atypical symptomatology in nonendemic regions have raised questions regarding the historic and present distribution of this bacterium and the scope of disease that infection causes. Phylogenetic relationships and genomic diversity of 18 B. bacilliformis isolates (10 isolates from a region where Carrion's disease is epidemic, Cuzco, Peru, and 8 isolates from a region where Carrion's disease is endemic, Caraz, Peru) were assessed using genomic data generated by infrequent restriction site PCR and gene sequence analysis of the flagellin gltA and ialB genes. A population genetic analysis of the genomic diversity suggests that what was once considered an epidemic region of Peru did not result from the recent introduction of B. bacilliformis.

Ectoparasites of gray squirrels in two different habitats and screening of selected ectoparasites for bartonellae.

Gray squirrels, Sciurus carolinensis, were livetrapped in 2 different habitat types, woodland (67 squirrels) and parkland (53 squirrels), in southeastern Georgia. Ectoparasites were recovered from anesthetized squirrels and compared between hosts from the 2 habitats. Because of the absence of low vegetation in parkland habitats, it was hypothesized that the ectoparasite fauna, especially ticks and chiggers, would be more diverse on woodland squirrels. The results were generally in agreement with this hypothesis. Seventeen species of ectoparasites were recovered from woodland squirrels, compared with 6 species from parkland squirrels. Five species of ticks and 3 species of chiggers parasitized the woodland squirrels compared with no ticks or chiggers on the parkland squirrels. Significantly higher infestation prevalences were recorded on woodland compared with parkland squirrels for the flea Orchopeas howardi, the tick Amblyomma americanum, and the mesostigmatid mite Androlaelaps fahrenholzi. The mean intensity for O. howardi also was significantly higher on woodland than on parkland squirrels. Because a new strain of Bartonella sp. was isolated recently from S. carolinensis in Georgia, selected ectoparasites from this study were screened for bartonellae by polymerase chain reaction (PCR). Some of the fleas and lice, but none of the mites tested, were PCR positive, suggesting that fleas, or lice, or both, might be vectors of bartonellae between squirrels. Six distinct strains of Bartonella sp. were detected, 2 in fleas and 4 in lice.

Evaluation of an upper extremity student-role functioning scale using item response theory.

Millions of workers suffer from upper extremity (musculoskeletal) disorders. Many of these workers are predisposed to upper extremity musculoskeletal disorders because of early exposure to ergonomic risks as students. Computer usage for four or more hours remains the greatest risk for upper extremity musculoskeletal disorders for workers and students alike. Developing preventative methods to reduce student exposure, and thus protect future workers from upper extremity musculoskeletal disorders later in life, requires an appropriate measure for upper extremity musculoskeletal disorder prevalence and related limitations for student functioning. Item response theory analysis was used to evaluate and further develop a upper extremity functioning scale for the student role.

Molecular epidemiology of tuberculosis in a sentinel surveillance population.

We conducted a population-based study to assess demographic and risk-factor correlates for the most frequently occurring Mycobacterium tuberculosis genotypes from tuberculosis (TB) patients. The study included all incident, culture-positive TB patients from seven sentinel surveillance sites in the United States from 1996 to 2000. M. tuberculosis isolates were genotyped by IS6110-based restriction fragment length polymorphism and spoligotyping. Genotyping was available for 90% of 11923 TB patients. Overall, 48% of cases had isolates that matched those from another patient, including 64% of U.S.-born and 35% of foreign-born patients. By logistic regression analysis, risk factors for clustering of genotypes were being male, U.S.-born, black, homeless, and infected with HIV; having pulmonary disease with cavitations on chest radiograph and a sputum smear with acid-fast bacilli; and excessive drug or alcohol use. Molecular characterization of TB isolates permitted risk correlates for clusters and specific genotypes to be described and provided information regarding cluster dynamics over time.

Identifying the sources of tuberculosis in young children: a multistate investigation.

To better understand the molecular epidemiology of tuberculosis (TB) transmission for culture-confirmed patients <5 years of age, data were analyzed from a population-based study conducted in seven U.S. sites from 1996 to 2000. Mycobacterium tuberculosis isolates were genotyped with IS6110-based restriction fragment length polymorphism analysis and spoligotyping. Case-patient data were obtained from the Centers for Disease Control and Prevention s national tuberculosis registry and health department records. Routine public health investigations conducted by local health departments identified suspected source patients for 57 (51%) of 111 culture-confirmed patients <5 years of age. For 8 (15%) of 52 culture-confirmed patients <5 years of age and their suspected source patients with complete genotyping results, genotypes suggested infection with different TB strains. Potential differences between sources for patients <5 years of age and source patients that transmitted TB to adolescent and adult patients were identified.

DNA fingerprinting of Mycobacterium tuberculosis isolates from epidemiologically linked case pairs.

DNA fingerprinting was used to evaluate epidemiologically linked case pairs found during routine tuberculosis (TB) contact investigations in seven sentinel sites from 1996 to 2000. Transmission was confirmed when the DNA fingerprints of source and secondary cases matched. Of 538 case pairs identified, 156 (29%) did not have matching fingerprints. Case pairs from the same household were no more likely to have confirmed transmission than those linked elsewhere. Case pairs with unconfirmed transmission were more likely to include a smear-negative source case (odds ratio [OR] 2.0) or a foreign-born secondary case (OR 3.4) and less likely to include a secondary case <15 years old (OR 0.3). Our study suggests that contact investigations should focus not only on the household but also on all settings frequented by an index case. Foreign-born persons with TB may have been infected previously in high-prevalence countries; screening and preventive measures recommended by the Institute of Medicine could prevent TB reactivation in these cases.

Nutrient gain from wet and dry atmospheric deposition and rainfall acidity in southern California chaparral.

Ionic concentration and annual deposition of NO -3 -N, NH +4 -N, Ca2+, and Mg2+ from bulk precipitation and dry atmospheric deposition were studied for one year in southern California. Data were collected from an inland chaparral site at 1,300 m elevation, 75 km from the coast. The annual depositions of NO -3 -N and NH +4 -N amounted to 96.3 and 56.0 mg m-2 ground area yr-1, respectively. The corresponding values for calcium and magnesium ions were 207.4 and 57.4 mg m-2 yr-1. The average pH of rainwater was 3.74 (range 3.37 to 4.75), thus documenting acid rain for an inland site in California, distant from urban sources of air contamination. An estimate of nitrogen gains and losses indicated that the time between recurrent chaparral fires should be about 60 years in order to maintain a balanced nitrogen budget.