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.

COVID-19-related health outcomes in people with primary immunodeficiency: A systematic review.

A better understanding of COVID-19 in people with primary immunodeficiency (PI), rare inherited defects in the immune system, is important for protecting this population, especially as population-wide approaches to mitigation change. COVID-19 outcomes in the PI population could have broader public health implications because some people with PI might be more likely to have extended illnesses, which could lead to increased transmission and emergence of variants. We performed a systematic review on COVID-19-associated morbidity and mortality in people with PI. Of the 1114 articles identified through the literature search, we included 68 articles in the review after removing 1046 articles because they were duplicates, did not involve COVID-19, did not involve PI, were not in English, were commentaries, were gene association or gene discovery studies, or could not be accessed. The 68 articles included outcomes for 459 people with PI and COVID-19. Using data from these 459 people, we calculated a case fatality rate of 9%, hospitalization rate of 49%, and oxygen supplementation rate of 29%. Studies have indicated that a number of people with PI showed at least some immune response to COVID-19 vaccination, with responses varying by type of PI and other factors, although vaccine effectiveness against hospitalization was lower in the PI population than in the general population. In addition to being up-to-date on vaccinations, current strategies for optimizing protection for people with PI can include pre-exposure prophylaxis for those eligible and use of therapeutics. Overall, people with PI, when infected, tested positive and showed symptoms for similar lengths of time as the general population. However, a number of people with X-linked agammaglobulinemia (XLA) or other B-cell pathway defects were reported to have prolonged infections, measured by time from first positive SARS-CoV-2 test to first negative test. As prolonged infections might increase the likelihood of genetic variants emerging, SARS-CoV2 isolates from people with PI and extended illness would be good candidates to prioritize for whole genome sequencing.

Publication and Impact of Preprints Included in the First 100 Editions of the CDC COVID-19 Science Update: Content Analysis.

BACKGROUND: Preprints are publicly available manuscripts posted to various servers that have not been peer reviewed. Although preprints have existed since 1961, they have gained increased popularity during the COVID-19 pandemic due to the need for immediate, relevant information. OBJECTIVE: The aim of this study is to evaluate the publication rate and impact of preprints included in the Centers for Disease Control and Prevention (CDC) COVID-19 Science Update and assess the performance of the COVID-19 Science Update team in selecting impactful preprints. METHODS: All preprints in the first 100 editions (April 1, 2020, to July 30, 2021) of the Science Update were included in the study. Preprints that were not published were categorized as "unpublished preprints." Preprints that were subsequently published exist in 2 versions (in a peer-reviewed journal and on the original preprint server), which were analyzed separately and referred to as "peer-reviewed preprint" and "original preprint," respectively. Time to publish was the time interval between the date on which a preprint was first posted and the date on which it was first available as a peer-reviewed article. Impact was quantified by Altmetric Attention Score and citation count for all available manuscripts on August 6, 2021. Preprints were analyzed by publication status, publication rate, preprint server, and time to publication. RESULTS: Of the 275 preprints included in the CDC COVID-19 Science Update during the study period, most came from three servers: medRxiv (n=201, 73.1%), bioRxiv (n=41, 14.9%), and SSRN (n=25, 9.1%), with 8 (2.9%) coming from other sources. Additionally, 152 (55.3%) were eventually published. The median time to publish was 2.3 (IQR 1.4-3.7). When preprints posted in the last 2.3 months were excluded (to account for the time to publish), the publication rate was 67.8%. Moreover, 76 journals published at least one preprint from the CDC COVID-19 Science Update, and 18 journals published at least three. The median Altmetric Attention Score for unpublished preprints (n=123, 44.7%) was 146 (IQR 22-552) with a median citation count of 2 (IQR 0-8); for original preprints (n=152, 55.2%), these values were 212 (IQR 22-1164) and 14 (IQR 2-40), respectively; for peer-review preprints, these values were 265 (IQR 29-1896) and 19 (IQR 3-101), respectively. CONCLUSIONS: Prior studies of COVID-19 preprints found publication rates between 5.4% and 21.1%. Preprints included in the CDC COVID-19 Science Update were published at a higher rate than overall COVID-19 preprints, and those that were ultimately published were published within months and received higher attention scores than unpublished preprints. These findings indicate that the Science Update process for selecting preprints had a high fidelity in terms of their likelihood to be published and their impact. The incorporation of high-quality preprints into the CDC COVID-19 Science Update improves this activity's capacity to inform meaningful public health decision-making.

Occupational Safety and Health and Illicit Opioids: State of the Research on Protecting Against the Threat of Occupational Exposure.

The nationwide opioid crisis continues to affect not only people who use opioids but also communities at large by increasing the risk of accidental occupational exposure to illicit opioids. In addition, the emergence of highly potent synthetic opioids such as fentanyl and carfentanil increases the need to protect workers who may encounter unknown drug substances during job activities. To support the National Institute for Occupational Safety and Health Opioids Research Gaps Working Group, we examined the state of the literature concerning methods to protect workers against accidental occupational exposure to illicit opioids, and have identified unmet research needs concerning personal protective equipment, decontamination methods, and engineering controls. Additional studies are needed to overcome gaps in technical knowledge about personal protective equipment, decontamination, and control methods, and gaps in understanding how these measures are utilized by workers. Increasing our knowledge of how to protect against exposure to illicit opioids has the potential to improve occupational health across communities.

Diagnosis of Progressive Disseminated Histoplasmosis in Advanced HIV: A Meta-Analysis of Assay Analytical Performance.

Histoplasmosis is an important cause of mortality in people with advanced HIV, especially in countries with limited access to diagnostic assays. Histoplasmosis can be diagnosed using culture, histopathology, and antibody, antigen, and molecular assays. Several factors may affect the analytical performance of these laboratory assays, including sample type, clinical stage of the disease, and previous use of antifungal treatment, among others. Here we describe the results of a systematic literature review, followed by a meta-analysis of the analytical performances of the diagnostic laboratory assays employed. Our initial search identified 1631 references, of which 1559 references were excluded after title and abstract screening, leaving 72 references identified as studies relevant to the validation of histoplasmosis diagnostic assays. After evaluating the full text, 30 studies were selected for final review, including one paper not identified in the initial search. The meta-analysis for assay analytical performance shows the following results for the overall sensitivity (Sen) and specificity (Spe) of the various methods evaluated: Culture, Sen 77% (no data for specificity calculation); antibody detection assays, Sen 58%/Spe 100%; antigen detection assays, Sen 95%/Spe 97%; and DNA detection assays (molecular), Sen 95%/Spe 99%. Of the 30 studies reviewed, nearly half (n = 13) evaluated Histoplasma antigen assays, which were determined to be the most accurate methodology for diagnosis of progressive disseminated histoplasmosis in advanced HIV (inverse of the negative likelihood ratio was 13.2). Molecular assays appear promising for accurate diagnosis of histoplasmosis, but consensus on exact techniques is needed. Cultures showed variable sensitivity related to sample type and laboratory handling. Finally, antibody assays presented high specificity but low sensitivity. This poor sensitivity is most likely due the highly immunosuppressed state of this patient population. Diagnostic assays are crucial for accurate diagnosis of progressive disseminated histoplasmosis (PDH) with advanced HIV disease.