Last data update: Sep 16, 2024. (Total: 47680 publications since 2009)
Records 1-30 (of 1275 Records) |
Query Trace: Johnson N [original query] |
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Efficacy of internet recruitment and HIV self-testing for diagnosing HIV infections among black and Hispanic/Latino MSM and transgender women in 11 US states, 2020-2021
MacGowan RJ , Chavez PR , Dana R , Hannah M , Raiford JL , Caldwell JA , Wall KM , Johnson JA , Sharma A , Hightow-Weidman L , Stephenson R , Sanchez T , Smith AJ , Sullivan S , Jones J , Sullivan PS . J Acquir Immune Defic Syndr 2024 97 (2) 133-141 INTRODUCTION: We evaluated internet platforms for distributing HIV self-tests (HIVSTs) to Black or African American (Black) and Hispanic or Latino men who have sex with men (MSM) and transgender women (TGW). METHODS: We recruited MSM and TGW from general interest, dating, and lesbian, gay, bisexual, and transgender platforms. Two HIVSTs were mailed to all MSM and TGW. Surveys (screening, baseline, 4-month, and results reporting) were completed online. After 4 months, participants were mailed another HIVST and a dried blood spot card. All HIVST interpretations and images of HIVST devices were reported online. RESULTS: Of 2093 MSM and 102 TGW, most were recruited through general interest and dating platforms. Over 50% were 18-29 years old, most identified as gay or bisexual. Overall, 45% had not tested for HIV in the past 12 months, and 9.1% of MSM reported a positive (reactive for HIV antibodies) HIVST result, with the highest percentage among Black MSM (11.5%). Dating platforms recruited higher percentages of MSM who recorded positive results compared with MSM from general interest platforms during the intervention period (11.9% vs 5.5% (P < 0.0001)), and MSM who had never tested for HIV reported a greater percentage of positive HIVST results compared with MSM who had been tested for HIV before enrollment (16.1% vs. 7.1%; P < 0.0001). MSM were able to correctly interpret and report HIVST results. Of TGW, 7% reported a positive HIVST result. CONCLUSIONS: Internet dating and general interest platforms can be key to increasing awareness of infection among BMSM, HMSM, and TGW persons, including those who do not use existing HIV services. TRIAL REGISTRATION: www.clinicaltrials.gov Identifier: NCT04219878. |
Reduced risk of SARS-CoV-2 infection among household contacts with recent vaccination and past COVID-19 infection: Results from two multi-site case-ascertained household transmission studies
Rolfes MA , Talbot HK , Morrissey KG , Stockwell MS , Maldonado Y , McLean HQ , Lutrick K , Bowman NM , Rao S , Izurieta HS , Zhu Y , Chappell J , Battan-Wraith S , Merrill LS , McClaren S , Sano E , Petrie JG , Biddle J , Johnson S , Salvatore P , Smith-Jeffcoat SE , Asturias EJ , Lin JT , Ellingson KD , Belongia EA , Olivo V , Mellis AM , Grijalva CG . Am J Epidemiol 2024 Households are a primary setting for transmission of SARS-CoV-2. We examined the role of prior SARS-CoV-2 immunity on the risk of infection in household close contacts. Households in the United States with an individual who tested positive for SARS-CoV-2 during September 2021-May 2023 were enrolled if the index case's illness began ≤6 days prior. Household members had daily self-collected nasal swabs tested by RT-PCR for SARS-CoV-2. The effects of prior SARS-CoV-2 immunity (vaccination, prior infection, or hybrid immunity) on SARS-CoV-2 infection risk among household contacts were assessed by robust, clustered multivariable Poisson regression. Of 1,532 contacts (905 households), 8% had immunity from prior infection alone, 51% from vaccination alone, 29% hybrid immunity, and 11% had no prior immunity. Sixty percent of contacts tested SARS-CoV-2-positive during follow-up. The adjusted risk of SARS-CoV-2 infection was lowest among contacts with vaccination and prior infection (aRR: 0.81, 95% CI: 0.70, 0.93, compared with contacts with no prior immunity) and was lowest when the last immunizing event occurred ≤6 months before COVID-19 affected the household (aRR: 0.69, 95% CI: 0.57, 0.83). In high-transmission settings like households, immunity from COVID-19 vaccination and prior infection was synergistic in protecting household contacts from SARS-CoV-2 infection. |
RSV vaccine effectiveness against hospitalization among US adults 60 years and older
Surie D , Self WH , Zhu Y , Yuengling KA , Johnson CA , Grijalva CG , Dawood FS . Jama 2024 This study evaluates the effectiveness of the respiratory syncytial virus vaccine against hospitalization for acute respiratory illness among US adults aged 60 years and older. | eng |
Respiratory Viral Infections from 2015 to 2022 in the HIVE Cohort of American Households: Incidence, illness characteristics, and seasonality
Monto AS , Foster-Tucker JE , Callear AP , Leis AM , Godonou ET , Smith M , Truscon R , Johnson E , Thomas LJ , Thompson MS , Fry AM , Flannery B , Malosh RE , Petrie JG , Lauring AS , Martin ET . J Infect Dis 2024 BACKGROUND: Viral respiratory illnesses are the most common acute illnesses experienced and generally follow a predicted pattern over time. The SARS-CoV-2 pandemic interrupted that pattern. METHODS: The HIVE (Household Influenza Vaccine Evaluation) study was established in 2010 to follow a cohort of Southeast Michigan households over time. Initially focused on influenza, surveillance was expanded to include other major respiratory pathogens, and, starting in 2015, the population was followed year-round. Symptoms of acute illness were reported, and respiratory specimens were collected and tested to identify viral infections. Based on the known population being followed, virus-specific incidence was calculated. RESULTS: From 2015 to 2022, 1755 participants were followed in HIVE for 7785 person-years with 7833 illnesses documented. Before the pandemic, rhinovirus (RV) and common cold human coronaviruses (HCoVs) were the viruses most frequently identified, and incidence decreased with increasing age. Type A influenza was next but with comparable incidence by age. Parainfluenza and respiratory syncytial viruses were less frequent overall, followed by human metapneumoviruses. Incidence was highest in young children, but infections were frequently documented in all age groups. Seasonality followed patterns established decades ago. The SARS-CoV-2 pandemic disrupted these patterns, except for RV and, to a lesser extent, HCoVs. In the first two years of the pandemic, RV incidence far exceeded that of SARS-CoV-2. CONCLUSION: Longitudinal cohort studies are important in comparing the incidence, seasonality, and characteristics of different respiratory viral infections. Studies documented the differential effect of the pandemic on the incidence of respiratory viruses in addition to SARS-CoV-2. |
Effectiveness of updated 2023-2024 (monovalent XBB.1.5) COVID-19 vaccination against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineage hospitalization and a comparison of clinical severity-IVY Network, 26 hospitals, October 18, 2023-March 9, 2024
Ma KC , Surie D , Lauring AS , Martin ET , Leis AM , Papalambros L , Gaglani M , Columbus C , Gottlieb RL , Ghamande S , Peltan ID , Brown SM , Ginde AA , Mohr NM , Gibbs KW , Hager DN , Saeed S , Prekker ME , Gong MN , Mohamed A , Johnson NJ , Srinivasan V , Steingrub JS , Khan A , Hough CL , Duggal A , Wilson JG , Qadir N , Chang SY , Mallow C , Kwon JH , Parikh B , Exline MC , Vaughn IA , Ramesh M , Safdar B , Mosier J , Harris ES , Shapiro NI , Felzer J , Zhu Y , Grijalva CG , Halasa N , Chappell JD , Womack KN , Rhoads JP , Baughman A , Swan SA , Johnson CA , Rice TW , Casey JD , Blair PW , Han JH , Ellington S , Lewis NM , Thornburg N , Paden CR , Atherton LJ , Self WH , Dawood FS , DeCuir J . Clin Infect Dis 2024 BACKGROUND: Assessing variant-specific COVID-19 vaccine effectiveness (VE) and severity can inform public health risk assessments and decisions about vaccine composition. BA.2.86 and its descendants, including JN.1 (referred to collectively as "JN lineages"), emerged in late 2023 and exhibited substantial divergence from co-circulating XBB lineages. METHODS: We analyzed patients hospitalized with COVID-19-like illness at 26 hospitals in 20 U.S. states admitted October 18, 2023-March 9, 2024. Using a test-negative, case-control design, we estimated effectiveness of an updated 2023-2024 (Monovalent XBB.1.5) COVID-19 vaccine dose against sequence-confirmed XBB and JN lineage hospitalization using logistic regression. Odds of severe outcomes, including intensive care unit (ICU) admission and invasive mechanical ventilation (IMV) or death, were compared for JN versus XBB lineage hospitalizations using logistic regression. RESULTS: 585 case-patients with XBB lineages, 397 case-patients with JN lineages, and 4,580 control-patients were included. VE in the first 7-89 days after receipt of an updated dose was 54.2% (95% CI = 36.1%-67.1%) against XBB lineage hospitalization and 32.7% (95% CI = 1.9%-53.8%) against JN lineage hospitalization. Odds of ICU admission (adjusted odds ratio [aOR] 0.80; 95% CI = 0.46-1.38) and IMV or death (aOR 0.69; 95% CI = 0.34-1.40) were not significantly different among JN compared to XBB lineage hospitalizations. CONCLUSIONS: Updated 2023-2024 COVID-19 vaccination provided protection against both XBB and JN lineage hospitalization, but protection against the latter may be attenuated by immune escape. Clinical severity of JN lineage hospitalizations was not higher relative to XBB. |
HIV immunocapture reveals particles expressed in semen under integrase strand transfer inhibitor-based therapy are largely myeloid cell-derived and disparate
Johnson JA , Li JF , Politch JA , Lipscomb JT , Tino AS , DeFelice J , Gelman M , Anderson DJ , Mayer KH . J Infect Dis 2024 230 (1) 78-85 As use of human immunodeficiency virus (HIV) integrase strand transfer inhibitors (INSTI) increases and formulations are being developed for maintenance therapies and chemoprophylaxis, assessing virus suppression under INSTI-based regimens in prevention-relevant biologic compartments, such as the male genital tract, is timely. We used cell-source marker virion immunocapture to examine amplification of particle RNA then assessed the phylogenetic relatedness of seminal and blood viral sequences from men with HIV who were prescribed INSTI-based regimens. Seminal plasma immunocaptures yielded amplifiable virion RNA from 13 of 24 (54%) men, and the sequences were primarily associated with markers indicative of macrophage and resident dendritic cell sources. Genetic distances were greatest (>2%) between seminal virions and circulating proviruses, pointing to ongoing low-level expression from tissue-resident cells. While the low levels in semen predict an improbable likelihood of transmission, viruses with large genetic distances are expressed under potent INSTI therapy and have implications for determining epidemiologic linkages if adherence is suboptimal. |
Asymptomatic and mildly symptomatic influenza virus infections by season -- Case-ascertained household transmission studies, United States, 2017-2023
Biddle JE , Nguyen HQ , Talbot HK , Rolfes MA , Biggerstaff M , Johnson S , Reed C , Belongia EA , Grijalva CG , Mellis AM . medRxiv 2024 Asymptomatic influenza virus infection occurs but may vary by factors such as age, influenza vaccination status, or influenza season. We examined the frequency of influenza virus infection and associated symptoms using data from two case-ascertained household transmission studies (conducted from 2017-2023) with prospective, systematic collection of respiratory specimens and symptoms. From the 426 influenza virus infected household contacts that met our inclusion criteria, 8% were asymptomatic, 6% had non-respiratory symptoms, 23% had acute respiratory symptoms, and 62% had influenza-like illness symptoms. Understanding the prevalence of asymptomatic and mildly symptomatic influenza cases is important for implementing effective influenza prevention strategies and enhancing the effectiveness of symptom-based surveillance systems. |
Notes from the field: Illnesses after administration of presumed counterfeit botulinum toxin in nonmedical settings - Tennessee and New York City, March 2024
Thomas CM , McElroy R , Yackley J , Fill MA , Goonewardene D , Mackley C , Roth E , Ackelsberg J , Slavinski S , Habrun C , Hodge B , Rush C , Brown CM , Waltenburg MA , Bertling LH , McGorty M , Johnson R , Schaffner W , Jones TF , Dunn JR . MMWR Morb Mortal Wkly Rep 2024 73 (27) 609-611 |
Using the index of concentration at the extremes to evaluate associations of economic and Hispanic/Latino-White racial segregation with HIV outcomes among adults aged ≥ 18 years with diagnosed HIV - United States, 2021
Gant Sumner Z , Dailey A , Beer L , Dong X , Morales J , Johnson Lyons S , Satcher Johnson A . J Racial Ethn Health Disparities 2024 OBJECTIVE(S): To examine associations between Index of Concentration at the Extremes (ICE) measures (proxy for structural racism) for economic and Hispanic/Latino-White racial segregation and HIV outcomes among adults in the U.S. METHODS: Census tract-level HIV diagnoses, linkage to HIV medical care within 1 month of diagnosis (linkage), and viral suppression within 6 months of diagnosis (viral suppression) data for 2021 from the National HIV Surveillance System were used. Three ICE measures were obtained from the American Community Survey: ICEincome (income segregation), ICErace (Hispanic/Latino-White racial segregation), and ICEincome + race (Hispanic/Latino-White racialized economic segregation). Rate ratios (RRs) for HIV diagnosis and prevalence ratios (PRs) for linkage and viral suppression were used to examine differences in HIV outcomes across ICE quintiles with Quintile5 (Q5: most privileged) as reference group and adjusted by selected characteristics. RESULTS: Among the 32,529 adults, diagnosis rates were highest in Quintile1 (Q1: most deprived) for ICEincome (28.7) and ICEincome + race (28.4) and Q2 for ICErace (27.0). We also observed higher RRs in HIV diagnosis and lower PRs in linkage and viral suppression (except for ICErace for linkage) in Q1 compared to Q5. Higher RRs and lower PRs in ICE measures were observed among males (diagnosis), adults aged 18‒34 (diagnosis and linkage) and aged ≥ 45 (viral suppression), and among adults in the South (all 3 HIV outcomes). CONCLUSIONS: Barriers in access to care/treatment in more Hispanic/Latino-White racialized economic segregated communities perpetuate the disproportionate impact of HIV on the population. Removing barriers to HIV care/treatment created by systemic racism/segregation may improve HIV outcomes and reduce disparities. |
Diversifying Doulas Initiative: Improving maternal health outcomes in people of color through doula care
Livingston S , Hamblin C , Johnson C , Chatman L , Bolden K . Health Equity 2024 8 (1) 455-460 The Diversifying Doulas Initiative (DDI) aims to improve maternal health outcomes in Black and Brown people through doula care in Lancaster County. DDI trained 28 Black and Brown doulas and provided fully subsidized doula care to over 200 patients of color giving birth in Lancaster County. The perinatal workforce comprises community birth workers, doulas, midwives, nurses, students, and physicians. By diversifying the perinatal workforce and increasing access to doulas, patients of color benefit from a proven intervention. |
Performance of a rapid recency assay for detection of early HIV infection
Di Germanio C , Deng X , Grebe E , Johnson JA , Masciotra S , Busch MP , Norris PJ . J Clin Virol 2024 174 105708 The Asanté HIV-1 Rapid Recency assay's 'verification' line detected HIV infection a median of 18 days later than a nucleic acid detection assay and performed similarly to 19 other existing rapid HIV antibody tests. Pending regulatory approval, the assay could be an option with other rapid tests in national HIV-1 testing algorithms, which would allow collection of HIV recency data as part of a national screening program without requiring additional testing. |
CDC prioritizes HIV prevention and treatment to reduce HIV disparities among cis-gender black women
Raiford JL , DiNenno E , Beer L , Bowman S , Johnson Lyons S , Anderson SKE , Powell N , Nickson R , Hall G , Neblett Fanfair R . J Womens Health (Larchmt) 2024 To succeed in ending the HIV epidemic in the United States, the Centers for Disease Control and Prevention (CDC) focuses on delivering combinations of scientifically proven, cost-effective, and scalable interventions to priority populations. Systemic factors continue to contribute to persistent health disparities and disproportionately higher rates of HIV diagnosis in some communities. The National HIV/AIDS Strategy has designated cis-gender Black women (CgBW) as a priority population to address the racial and ethnic inequities in HIV. This report presents the portfolio of projects, programs, and initiatives funded by the CDC's Division of HIV Prevention (DHP) to address disparities in HIV and improve health and QOL among CgBW. These funded activities include the development, planning, and implementation of HIV prevention programs, mass media campaigns, and behavioral interventions focused on CgBW. This report also summarizes DHP's community engagement, capacity building, and partnership efforts, and highlights research and surveillance activities focusing on CgBW. Finally, this report outlines future directions for CDC's efforts to improve access to HIV testing, treatment, and prevention for CgBW in the United States. |
Notes from the field: Multidisciplinary approach to investigating Brucella canis exposures - South Carolina, September 2023
Moore TS , Lancaster A , Nelson J , Sanders J , Johnson M , Moore A , Tori M . MMWR Morb Mortal Wkly Rep 2024 73 (25) 581-582 |
An evaluation of translife care: A locally developed structural HIV prevention intervention for transgender women in Chicago, Illinois
Kuhns LM , Perloff J , Johnson AK , Paul JL , Pleasant K , Evans K , Denson DJ , Gelaude DJ , Bessler PA , Cervantes M , Muldoon AL , Garofalo R , Hotton AL . AIDS Educ Prev 2024 36 (3) 155-167 Transgender women are disproportionately impacted by HIV infection. We report herein the findings of a pre-post evaluation of the TransLife Care (TLC) project in Chicago, Illinois, on behaviors associated with HIV transmission among transgender women. Participants who received any TLC component versus those who did not were compared using mixed-effects logistic regression with random intercepts across follow-up time points. Ninety-seven participants aged 18 to 59 (median age 24) enrolled; 76.3% were transgender women of color. There was a decrease in condomless sex without consistent PrEP use at 8 months, which was not significantly different between those who did and did not receive the TLC intervention, controlling for calendar time. Evidence does not indicate that the TLC reduces condomless sex without PrEP protection among urban transgender women. However, given the preponderance of evidence of the influence of structural barriers on condomless sex, future research should continue to test the efficacy of structural interventions. |
Population percentage and population size of men who have sex with men in the United States, 2017-2021: Meta-analysis of 5 population-based surveys
Bennett BW , DuBose S , Huang YA , Johnson CH , Hoover KW , Wiener J , Purcell DW , Sullivan PS . JMIR Public Health Surveill 2024 10 e56643 BACKGROUND: Male-to-male sexual transmission continues to account for the greatest proportion of new HIV diagnoses in the United States. However, calculating population-specific surveillance metrics for HIV and other sexually transmitted infections requires regularly updated estimates of the number and proportion of men who have sex with men (MSM) in the United States, which are not collected by census surveys. OBJECTIVE: The purpose of this analysis was to estimate the number and percentage of MSM in the United States from population-based surveys. METHODS: We used data from 5 population-based surveys to calculate weighted estimates of the proportion of MSM in the United States and pooled these estimates using meta-analytic procedures. We estimated the proportion of MSM using sexual behavior-based questions (encompassing anal or oral sex) for 3 recall periods-past 12 months, past 5 years, and lifetime. In addition, we estimated the proportion of MSM using self-reported identity and attraction survey responses. The total number of MSM and non-MSM in the United States were calculated from estimates of the percentage of MSM who reported sex with another man in the past 12 months. RESULTS: The percentage of MSM varied by recall period: 3.3% (95% CI 1.7%-4.9%) indicated sex with another male in the past 12 months, 4.7% (95% CI 0.0%-33.8%) in the past 5 years, and 6.2% (95% CI 2.9%-9.5%) in their lifetime. There were comparable percentages of men who identified as gay or bisexual (3.4%, 95% CI 2.2%-4.6%) or who indicated that they are attracted to other men (4.9%, 95% CI 3.1%-6.7%) based on pooled estimates. Our estimate of the total number of MSM in the United States is 4,230,000 (95% CI 2,179,000-6,281,000) based on the history of recent sexual behavior (sex with another man in the past 12 months). CONCLUSIONS: We calculated the pooled percentage and number of MSM in the United States from a meta-analysis of population-based surveys collected from 2017 to 2021. These estimates update and expand upon those derived from the Centers for Disease Control and Prevention in 2012 by including estimates of the percentage of MSM based on sexual identity and sexual attraction. The percentage and number of MSM in the United States is an important indicator for calculating population-specific disease rates and eligibility for preventive interventions such as pre-exposure prophylaxis. |
Symptoms, viral loads, and rebound among COVID-19 outpatients treated with nirmatrelvir/ritonavir compared to propensity score matched untreated individuals
Smith-Jeffcoat SE , Biddle JE , Talbot HK , Morrissey KG , Stockwell MS , Maldonado Y , McLean HQ , Ellingson KD , Bowman NM , Asturias E , Mellis AM , Johnson S , Kirking HL , Rolfes MAR , Olivo V , Merrill L , Battan-Wraith S , Sano E , McLaren SH , Vargas CY , Goodman S , Sarnquist CC , Govindaranjan P , Petrie JG , Belongia EA , Ledezma K , Pryor K , Lutrick K , Bullock A , Yang A , Haehnel Q , Rao S , Zhu Y , Schmitz J , Hart K , Grijalva CG , Salvatore PP . Clin Infect Dis 2024 78 (5) 1175-1184 BACKGROUND: Nirmatrelvir/ritonavir (N/R) reduces severe outcomes from coronavirus disease 2019 (COVID-19); however, rebound after treatment has been reported. We compared symptom and viral dynamics in individuals with COVID-19 who completed N/R treatment and similar untreated individuals. METHODS: We identified symptomatic participants who tested severe acute respiratory syndrome coronavirus 2-positive and were N/R eligible from a COVID-19 household transmission study. Index cases from ambulatory settings and their households contacts were enrolled. We collected daily symptoms, medication use, and respiratory specimens for quantitative polymerase chain reaction for 10 days during March 2022-May 2023. Participants who completed N/R treatment (treated) were propensity score matched to untreated participants. We compared symptom rebound, viral load (VL) rebound, average daily symptoms, and average daily VL by treatment status measured after N/R treatment completion or 7 days after symptom onset if untreated. RESULTS: Treated (n = 130) and untreated participants (n = 241) had similar baseline characteristics. After treatment completion, treated participants had greater occurrence of symptom rebound (32% vs 20%; P = .009) and VL rebound (27% vs 7%; P < .001). Average daily symptoms were lower among treated participants without symptom rebound (1.0 vs 1.6; P < .01) but not statistically lower with symptom rebound (3.0 vs 3.4; P = .5). Treated participants had lower average daily VLs without VL rebound (0.9 vs 2.6; P < .01) but not statistically lower with VL rebound (4.8 vs 5.1; P = .7). CONCLUSIONS: Individuals who completed N/R treatment experienced fewer symptoms and lower VL but rebound occured more often compared with untreated individuals. Providers should prescribe N/R, when indicated, and communicate rebound risk to patients. |
Clinical and treatment characteristics of infants and toddlers less than 2 years of age with hemophilia
Han JH , Dupervil B , Mahajerin A , Kulkarni R , Manco-Johnson M , Thornburg C . Blood Adv 2024 8 (11) 2707-2717 Infants and toddlers (ITs) with hemophilia have unique bleeding features. Factor prophylaxis has been shown to decrease the risk of intracranial hemorrhage (ICH), which supports recommendations to begin at a young age. Clinical and demographic characteristics were analyzed for 883 ITs ≤2 years old with hemophilia A and B, seen at US Hemophilia Treatment Centers and enrolled in the Community Counts Registry, a surveillance program of the Centers for Disease Control and Prevention. ICH in the first 2 years of life was seen in 68 of 883 (7.7%) ITs, of whom 8 of 68 (11.8%) were on continuous prophylaxis at the time of ICH. ITs in this study usually started prophylaxis within the first year of life (mean, 10.3 months), with earlier ages of prophylaxis initiation in later birth cohorts in ITs with hemophilia A. Compared with those without a family history (FH) of hemophilia, known positive FH of hemophilia was associated with earlier age of diagnosis (P ≤ .0001) and decreased rates of vaginal delivery (P = .0006). The use of factor VIII mimetics and extended half-life clotting factor prophylaxis increased with later birth cohorts for ITs with hemophilia A and B. The study highlights that ICH rates in ITs with hemophilia remains substantial and underscores the need for further research to identify modifiable risk factors to prevent ICH by earlier diagnosis and initiating prophylaxis early, even within the first month of life. |
Enhancements to the National HIV Surveillance System, United States, 2013-2023
Satcher Johnson A , Peruski A , Oster AM , Balaji A , Siddiqi AE , Sweeney P , Hernandez AL . Public Health Rep 2024 333549241253092 HIV infection is monitored through the National HIV Surveillance System (NHSS) to help improve the health of people with HIV and reduce transmission. NHSS data are routinely used at federal, state, and local levels to monitor the distribution and transmission of HIV, plan and evaluate prevention and care programs, allocate resources, inform policy development, and identify and respond to rapid transmission in the United States. We describe the expanded use of HIV surveillance data since the 2013 NHSS status update, during which time the Centers for Disease Control and Prevention (CDC) coordinated to revise the HIV surveillance case definition to support the detection of early infection and reporting of laboratory data, expanded data collection to include information on sexual orientation and gender identity, enhanced data deduplication processes to improve quality, and expanded reporting to include social determinants of health and health equity measures. CDC maximized the effects of federal funding by integrating funding for HIV prevention and surveillance into a single program; the integration of program funding has expanded the use of HIV surveillance data and strengthened surveillance, resulting in enhanced cluster response capacity and intensified data-to-care activities to ensure sustained viral suppression. NHSS data serve as the primary source for monitoring HIV trends and progress toward achieving national initiatives, including the US Department of Health and Human Services' Ending the HIV Epidemic in the United States initiative, the White House's National HIV/AIDS Strategy (2022-2025), and Healthy People 2030. The NHSS will continue to modernize, adapt, and broaden its scope as the need for high-quality HIV surveillance data remains. |
The women's health needs study among women from countries with high prevalence of female genital mutilation living in the United States: Design, methods, and participant characteristics
Besera G , Snead MC , Goodwin M , Smoots A , Bish CL , Ruiz A , Sayyad A , Avripas S , Ubri P , Ahn R , Pineau V , Warren N , Mukangu D , Johnson-Agbakwu CE , Goldberg H , Okoroh E . PLoS One 2024 19 (5) e0302820 BACKGROUND: The Women's Health Needs Study (WHNS) collected information on the health characteristics, needs, and experiences, including female genital mutilation (FGM) experiences, attitudes, and beliefs, of women aged 18 to 49 years who were born, or whose mothers were born, in a country where FGM is prevalent living in the US. The purpose of this paper is to describe the WHNS design, methods, strengths and limitations, as well as select demographic and health-related characteristics of participants. METHODS: We conducted a cross-sectional survey from November 2020 -June 2021 in four US metropolitan areas, using a hybrid venue-based sampling (VBS) and respondent-driven sampling (RDS) approach to identify women for recruitment. RESULTS: Of 1,132 participants, 395 were recruited via VBS and 737 RDS. Most were born, or their mothers were born, in either a West African country (Burkina Faso, Guinea, Mali, Mauritania, Sierra Leone, The Gambia) (39.0%) or Ethiopia (30.7%). More than a third were aged 30-39 years (37.5%) with a majority who immigrated at ages ≥13 years (86.6%) and had lived in the United States for ≥5 years (68.9%). Medicaid was the top health insurer (52.5%), followed by private health insurance (30.5%); 17% of participants had no insurance. Nearly half of women reported 1-2 healthcare visits within the past 12 months (47.7%). One in seven did not get needed health care due to cost (14.8%). Over half have ever used contraception (52.1%) to delay or avoid pregnancy and 76.9% had their last pelvic and/or Papanicolaou (pap) exam within the past 3 years. More than half experienced FGM (55.0%). Nearly all women believed that FGM should be stopped (92.0%). CONCLUSION: The VBS/RDS approach enabled recruitment of a diverse study population. WHNS advances research related to the health characteristics, needs, and experiences of women living in the US from countries where FGM is prevalent. |
Antigenic characterization of circulating and emerging SARS-CoV-2 variants in the U.S. Throughout the Delta to Omicron waves
Di H , Pusch EA , Jones J , Kovacs NA , Hassell N , Sheth M , Lynn KS , Keller MW , Wilson MM , Keong LM , Cui D , Park SH , Chau R , Lacek KA , Liddell JD , Kirby MK , Yang G , Johnson M , Thor S , Zanders N , Feng C , Surie D , DeCuir J , Lester SN , Atherton L , Hicks H , Tamin A , Harcourt JL , Coughlin MM , Self WH , Rhoads JP , Gibbs KW , Hager DN , Shapiro NI , Exline MC , Lauring AS , Rambo-Martin B , Paden CR , Kondor RJ , Lee JS , Barnes JR , Thornburg NJ , Zhou B , Wentworth DE , Davis CT . Vaccines (Basel) 2024 12 (5) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into numerous lineages with unique spike mutations and caused multiple epidemics domestically and globally. Although COVID-19 vaccines are available, new variants with the capacity for immune evasion continue to emerge. To understand and characterize the evolution of circulating SARS-CoV-2 variants in the U.S., the Centers for Disease Control and Prevention (CDC) initiated the National SARS-CoV-2 Strain Surveillance (NS3) program and has received thousands of SARS-CoV-2 clinical specimens from across the nation as part of a genotype to phenotype characterization process. Focus reduction neutralization with various antisera was used to antigenically characterize 143 SARS-CoV-2 Delta, Mu and Omicron subvariants from selected clinical specimens received between May 2021 and February 2023, representing a total of 59 unique spike protein sequences. BA.4/5 subvariants BU.1, BQ.1.1, CR.1.1, CQ.2 and BA.4/5 + D420N + K444T; BA.2.75 subvariants BM.4.1.1, BA.2.75.2, CV.1; and recombinant Omicron variants XBF, XBB.1, XBB.1.5 showed the greatest escape from neutralizing antibodies when analyzed against post third-dose original monovalent vaccinee sera. Post fourth-dose bivalent vaccinee sera provided better protection against those subvariants, but substantial reductions in neutralization titers were still observed, especially among BA.4/5 subvariants with both an N-terminal domain (NTD) deletion and receptor binding domain (RBD) substitutions K444M + N460K and recombinant Omicron variants. This analysis demonstrated a framework for long-term systematic genotype to antigenic characterization of circulating and emerging SARS-CoV-2 variants in the U.S., which is critical to assessing their potential impact on the effectiveness of current vaccines and antigen recommendations for future updates. |
Accelerating COVID-19 vaccination among people living with HIV and health care workers in Tanzania: A case study
Jalloh MF , Tinuga F , Dahoma M , Rwebembera A , Kapologwe NA , Magesa D , Mukurasi K , Rwabiyago OE , Kazitanga J , Miller A , Sando D , Maruyama H , Mbatia R , Temu F , Matiko E , Kazaura K , Njau P , Imaa J , Pinto T , Nur SA , Schaad N , Malero A , Damian D , Grund J , Mgomella GS , Johnson A , Cole G , Mmari E , Gatei W , Swaminathan M . Glob Health Sci Pract 2024 BACKGROUND: There is limited evidence on COVID-19 vaccination uptake among people living with HIV (PLHIV) and health care workers (HCWs), with the current evidence concentrated in high-income countries. There is also limited documentation in the published literature regarding the feasibility and lessons from implementing targeted vaccination strategies to reach PLHIV and HCWs in low- and middle-income countries. PROGRAM DEVELOPMENT, PILOTING, AND IMPLEMENTATION: We designed and implemented multifaceted strategies to scale up targeted COVID-19 vaccination among PLHIV and HCWs in 11 administrative regions on the mainland of Tanzania plus Zanzibar. An initial 6-week intensification strategy was implemented using a diverse partnership model comprising key stakeholders at the national- and subnational levels. A layered package of strategies included expanding the number of certified vaccinators, creating vaccination points within HIV clinics, engaging HCWs to address their concerns, and building the capacity of HCWs as "champions" to promote and facilitate vaccination. We then closely monitored COVID-19 vaccination uptake in 562 high-volume HIV clinics. Between September 2021 and September 2022, the proportion of fully vaccinated adult PLHIV increased from <1% to 97% and fully vaccinated HCWs increased from 23% to 80%. LESSONS AND IMPLICATIONS: Our intra-action review highlighted the importance of leveraging a strong foundation of existing partnerships and platforms, integrating COVID-19 vaccination points within HIV clinics, and refining strategies to increase vaccination demand while ensuring continuity of vaccine supply to meet the increased demand. Lessons from Tanzania can inform targeted vaccination of vulnerable groups in future health emergencies. |
Carbapenem-resistant Acinetobacter baumannii complex in the United States - an epidemiological and molecular description of isolates collected through the Emerging Infections Program, 2019
Bulens SN , Campbell D , McKay SL , Vlachos N , Burgin A , Burroughs M , Padila J , Grass JE , Jacob JT , Smith G , Muleta DB , Maloney M , Macierowski B , Wilson LE , Vaeth E , Lynfield R , O'Malley S , Snippes Vagnone PM , Dale J , Janelle SJ , Czaja CA , Johnson H , Phipps EC , Flores KG , Dumyati G , Tsay R , Beldavs ZG , Maureen Cassidy P , Hall A , Walters MS , Guh AY , Magill SS , Lutgring JD . Am J Infect Control 2024 BACKGROUND: Understanding the epidemiology of carbapenem-resistant A. baumannii complex (CRAB) and the patients impacted is an important step towards informing better infection prevention and control practices and improving public health response. METHODS: Active, population-based surveillance was conducted for CRAB in 9 U.S. sites from January 1-December 31, 2019. Medical records were reviewed, isolates were collected and characterized including antimicrobial susceptibility testing and whole genome sequencing. RESULTS: Among 136 incident cases in 2019, 66 isolates were collected and characterized; 56.5% were from cases who were male, 54.5% were from persons of Black or African American race with non-Hispanic ethnicity, and the median age was 63.5 years. Most isolates, 77.2%, were isolated from urine, and 50.0% were collected in the outpatient setting; 72.7% of isolates harbored an acquired carbapenemase gene (aCP), predominantly bla(OXA-23) or bla(OXA-24/40); however, an isolate with bla(NDM) was identified. The antimicrobial agent with the most in vitro activity was cefiderocol (96.9% of isolates were susceptible). CONCLUSIONS: Our surveillance found that CRAB isolates in the U.S. commonly harbor an aCP, have an antimicrobial susceptibility profile that is defined as difficult-to-treat resistance, and epidemiologically are similar regardless of the presence of an aCP. |
Descriptive epidemiology of pathogens associated with acute respiratory infection in a community-based study of K-12 school children (2015-2023)
Bell C , Goss M , Norton D , Barlow S , Temte E , He C , Hamer C , Walters S , Sabry A , Johnson K , Chen G , Uzicanin A , Temte J . Pathogens 2024 13 (4) School-based outbreaks often precede increased incidence of acute respiratory infections in the greater community. We conducted acute respiratory infection surveillance among children to elucidate commonly detected pathogens in school settings and their unique characteristics and epidemiological patterns. The ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) is a longitudinal, laboratory-supported, school-based, acute respiratory illness (ARI) surveillance study designed to evaluate the utility of cause-specific student absenteeism monitoring for early detection of increased activity of influenza and other respiratory viruses in schools from kindergarten through 12th grade. Eligible participants with ARIs provided demographic, epidemiologic, and symptom data, along with a nasal swab or oropharyngeal specimen. Multipathogen testing using reverse-transcription polymerase chain reaction (RT-PCR) was performed on all specimens for 18 respiratory viruses and 2 atypical bacterial pathogens (Chlamydia pneumoniae and Mycoplasma pneumoniae). Between 5 January 2015 and 9 June 2023, 3498 children participated. Pathogens were detected in 2455 of 3498 (70%) specimens. Rhinovirus/enteroviruses (36%) and influenza viruses A/B (35%) were most commonly identified in positive specimens. Rhinovirus/enteroviruses and parainfluenza viruses occurred early in the academic year, followed by seasonal coronaviruses, RSV, influenza viruses A/B, and human metapneumovirus. Since its emergence in 2020, SARS-CoV-2 was detected year-round and had a higher median age than the other pathogens. A better understanding of the etiologies, presentations, and patterns of pediatric acute respiratory infections can help inform medical and public health system responses. |
Use of Ebola vaccines - worldwide, 2021-2023
Kallay R , Doshi RH , Muhoza P , Choi MJ , Legand A , Aberle-Grasse E , Bagayoko A , Hyde TB , Formenty P , Costa A . MMWR Morb Mortal Wkly Rep 2024 73 (16) 360-364 Ebola virus disease (Ebola) is a rare but severe illness in humans, with an average case fatality rate of approximately 50%. Two licensed vaccines are currently available against Orthoebolavirus zairense, the virus that causes Ebola: the 1-dose rVSVΔG-ZEBOV-GP (ERVEBO [Merck]) and the 2-dose regimen of Ad26.ZEBOV and MVA-BN-Filo (Zabdeno/Mvabea [Johnson & Johnson]). The Strategic Advisory Group of Experts on Immunization recommends the use of 1-dose ERVEBO during Ebola outbreaks, and in 2021, a global stockpile of ERVEBO was established to ensure equitable, timely, and targeted access to vaccine doses for future Ebola outbreaks. This report describes the use of Ebola vaccines and the role of the stockpile developed and managed by the International Coordinating Group (ICG) on Vaccine Provision during 2021-2023. A total of 145,690 doses have been shipped from the ICG stockpile since 2021. However, because outbreaks since 2021 have been limited and rapidly contained, most doses (139,120; 95%) shipped from the ICG stockpile have been repurposed for preventive vaccination of high-risk groups, compared with 6,570 (5%) used for outbreak response. Repurposing doses for preventive vaccination could be prioritized in the absence of Ebola outbreaks to prevent transmission and maximize the cost-efficiency and benefits of the stockpile. |
Predicting state level suicide fatalities in the United States with realtime data and machine learning
Patel D , Sumner SA , Bowen D , Zwald M , Yard E , Wang J , Law R , Holland K , Nguyen T , Mower G , Chen Y , Johnson JI , Jespersen M , Mytty E , Lee JM , Bauer M , Caine E , De Choudhury M . Npj Ment Health Res 2024 3 (1) 3 Digital trace data and machine learning techniques are increasingly being adopted to predict suicide-related outcomes at the individual level; however, there is also considerable public health need for timely data about suicide trends at the population level. Although significant geographic variation in suicide rates exist by state within the United States, national systems for reporting state suicide trends typically lag by one or more years. We developed and validated a deep learning based approach to utilize real-time, state-level online (Mental Health America web-based depression screenings; Google and YouTube Search Trends), social media (Twitter), and health administrative data (National Syndromic Surveillance Program emergency department visits) to estimate weekly suicide counts in four participating states. Specifically, per state, we built a long short-term memory (LSTM) neural network model to combine signals from the real-time data sources and compared predicted values of suicide deaths from our model to observed values in the same state. Our LSTM model produced accurate estimates of state-specific suicide rates in all four states (percentage error in suicide rate of -2.768% for Utah, -2.823% for Louisiana, -3.449% for New York, and -5.323% for Colorado). Furthermore, our deep learning based approach outperformed current gold-standard baseline autoregressive models that use historical death data alone. We demonstrate an approach to incorporate signals from multiple proxy real-time data sources that can potentially provide more timely estimates of suicide trends at the state level. Timely suicide data at the state level has the potential to improve suicide prevention planning and response tailored to the needs of specific geographic communities. |
Telemedicine-based risk program to prevent falls among older adults: Study protocol for a randomized quality improvement trial
Rein DB , Hackney ME , Haddad YK , Sublett FA , Moreland B , Imhof L , Peterson C , Legha JK , Mark J , Vaughan CP , Johnson Ii TM , Bergen G . JMIR Res Protoc 2024 13 e54395 BACKGROUND: The Center for Disease Control and Prevention's Stopping Elderly Accidents, Deaths, and Injuries (STEADI) initiative offers health care providers tools and resources to assist with fall risk screening and multifactorial fall risk assessment and interventions. Its effectiveness has never been evaluated in a randomized trial. OBJECTIVE: This study aims to describe the protocol for the STEADI Options Randomized Quality Improvement Trial (RQIT), which was designed to evaluate the impact on falls and all-cause health expenditures of a telemedicine-based form of STEADI implemented among older adults aged 65 years and older, within a primary care setting. METHODS: STEADI Options was a pragmatic RQIT implemented within a health system comparing a telemedicine version of the STEADI fall risk assessment to the standard of care (SOC). Before screening, we randomized all eligible patients in participating clinics into the STEADI arm or SOC arm based on their scheduled provider. All received the Stay Independent screener (SIS) to determine fall risk. Patients were considered at risk for falls if they scored 4 or more on the SIS or answered affirmatively to any 1 of the 3 key questions within the SIS. Patients screened at risk for falls and randomized to the STEADI arm were offered a registered nurse (RN)-led STEADI assessment through telemedicine; the RN provided assessment results and recommendations to the providers, who were advised to discuss fall-prevention strategies with their patients. Patients screened at risk for falls and randomized to the SOC arm were asked to participate in study data collection only. Data on recruitment, STEADI assessments, use of recommended prevention services, medications, and fall occurrences were collected using electronic health records and patient surveys. Using staff time diaries and administrative records, the study prospectively collected data on STEADI implementation costs and all-cause outpatient and inpatient charges incurred over the year following enrollment. RESULTS: The study enrolled 720 patients (n=307, 42.6% STEADI arm; n=353, 49% SOC arm; and n=60, 8.3% discontinued arm) from September 2020 to December 2021. Follow-up data collection was completed in January 2023. As of February 2024, data analysis is complete, and results are expected to be published by the end of 2025. CONCLUSIONS: The STEADI RQIT evaluates the impact of a telemedicine-based, STEADI-based fall risk assessment on falls and all-cause health expenditures and can provide information on the intervention's effectiveness and cost-effectiveness. TRIAL REGISTRATION: ClinicalTrials.gov NCT05390736, http://clinicaltrials.gov/ct2/show/NCT05390736. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR1-10.2196/54395. |
Acute hepatitis due to primary human immunodeficiency virus infection
Elliott EI , Smith D , Lipscomb J , Banini B , Meurer L , Vanderford TH , Johnson JA , Jain D , Achhra A . Open Forum Infect Dis 2024 11 (4) ofae170 The acute retroviral syndrome may present with diverse systemic manifestations and laboratory abnormalities. Here we present a rare case of primary human immunodeficiency virus (HIV) infection causing severe acute hepatitis. Liver histopathology demonstrated a pattern of lymphocytic inflammation consistent with acute hepatitis, high levels of HIV proviral DNA were detected within liver tissue, and immunofluorescence showed HIV p24 antigen within immune and parenchymal cells including hepatocytes. We review the literature pertaining to HIV infection of cell compartments within the liver and discuss the implications for HIV-associated acute liver disease. |
Surveillance to track progress toward polio eradication - Worldwide, 2022-2023
Kishore N , Krow-Lucal E , Diop OM , Jorba J , Avagnan T , Grabovac V , Kfutwah AKW , Johnson T , Joshi S , Sangal L , Sharif S , Wahdan A , Tallis GF , Kovacs SD . MMWR Morb Mortal Wkly Rep 2024 73 (13) 278-285 The reliable and timely detection of poliovirus cases through surveillance for acute flaccid paralysis (AFP), supplemented by environmental surveillance of sewage samples, is a critical component of the polio eradication program. Since 1988, the number of polio cases caused by wild poliovirus (WPV) has declined by >99.9%, and eradication of WPV serotypes 2 and 3 has been certified; only serotype 1 (WPV1) continues to circulate, and transmission remains endemic in Afghanistan and Pakistan. This surveillance update evaluated indicators from AFP surveillance, environmental surveillance for polioviruses, and Global Polio Laboratory Network performance data provided by 28 priority countries for the program during 2022-2023. No WPV1 cases have been detected outside of Afghanistan and Pakistan since August 2022, when an importation into Malawi and Mozambique resulted in an outbreak during 2021-2022. During 2022-2023, among 28 priority countries, 20 (71.4%) met national AFP surveillance indicator targets, and the number of environmental surveillance sites increased. However, low national rates of reported AFP cases in priority countries in 2023 might have resulted from surveillance reporting lags; substantial national and subnational AFP surveillance gaps persist. Maintaining high-quality surveillance is critical to achieving the goal of global polio eradication. Monitoring surveillance indicators is important to identifying gaps and guiding surveillance-strengthening activities, particularly in countries at high risk for poliovirus circulation. |
Severity of respiratory syncytial virus vs COVID-19 and influenza among hospitalized US adults
Surie D , Yuengling KA , DeCuir J , Zhu Y , Lauring AS , Gaglani M , Ghamande S , Peltan ID , Brown SM , Ginde AA , Martinez A , Mohr NM , Gibbs KW , Hager DN , Ali H , Prekker ME , Gong MN , Mohamed A , Johnson NJ , Srinivasan V , Steingrub JS , Leis AM , Khan A , Hough CL , Bender WS , Duggal A , Bendall EE , Wilson JG , Qadir N , Chang SY , Mallow C , Kwon JH , Exline MC , Shapiro NI , Columbus C , Vaughn IA , Ramesh M , Mosier JM , Safdar B , Casey JD , Talbot HK , Rice TW , Halasa N , Chappell JD , Grijalva CG , Baughman A , Womack KN , Swan SA , Johnson CA , Lwin CT , Lewis NM , Ellington S , McMorrow ML , Martin ET , Self WH . JAMA Netw Open 2024 7 (4) e244954 IMPORTANCE: On June 21, 2023, the Centers for Disease Control and Prevention recommended the first respiratory syncytial virus (RSV) vaccines for adults aged 60 years and older using shared clinical decision-making. Understanding the severity of RSV disease in adults can help guide this clinical decision-making. OBJECTIVE: To describe disease severity among adults hospitalized with RSV and compare it with the severity of COVID-19 and influenza disease by vaccination status. DESIGN, SETTING, AND PARTICIPANTS: In this cohort study, adults aged 18 years and older admitted to the hospital with acute respiratory illness and laboratory-confirmed RSV, SARS-CoV-2, or influenza infection were prospectively enrolled from 25 hospitals in 20 US states from February 1, 2022, to May 31, 2023. Clinical data during each patient's hospitalization were collected using standardized forms. Data were analyzed from August to October 2023. EXPOSURES: RSV, SARS-CoV-2, or influenza infection. MAIN OUTCOMES AND MEASURES: Using multivariable logistic regression, severity of RSV disease was compared with COVID-19 and influenza severity, by COVID-19 and influenza vaccination status, for a range of clinical outcomes, including the composite of invasive mechanical ventilation (IMV) and in-hospital death. RESULTS: Of 7998 adults (median [IQR] age, 67 [54-78] years; 4047 [50.6%] female) included, 484 (6.1%) were hospitalized with RSV, 6422 (80.3%) were hospitalized with COVID-19, and 1092 (13.7%) were hospitalized with influenza. Among patients with RSV, 58 (12.0%) experienced IMV or death, compared with 201 of 1422 unvaccinated patients with COVID-19 (14.1%) and 458 of 5000 vaccinated patients with COVID-19 (9.2%), as well as 72 of 699 unvaccinated patients with influenza (10.3%) and 20 of 393 vaccinated patients with influenza (5.1%). In adjusted analyses, the odds of IMV or in-hospital death were not significantly different among patients hospitalized with RSV and unvaccinated patients hospitalized with COVID-19 (adjusted odds ratio [aOR], 0.82; 95% CI, 0.59-1.13; P = .22) or influenza (aOR, 1.20; 95% CI, 0.82-1.76; P = .35); however, the odds of IMV or death were significantly higher among patients hospitalized with RSV compared with vaccinated patients hospitalized with COVID-19 (aOR, 1.38; 95% CI, 1.02-1.86; P = .03) or influenza disease (aOR, 2.81; 95% CI, 1.62-4.86; P < .001). CONCLUSIONS AND RELEVANCE: Among adults hospitalized in this US cohort during the 16 months before the first RSV vaccine recommendations, RSV disease was less common but similar in severity compared with COVID-19 or influenza disease among unvaccinated patients and more severe than COVID-19 or influenza disease among vaccinated patients for the most serious outcomes of IMV or death. |
A compendium of multi-omics data illuminating host responses to lethal human virus infections
Eisfeld AJ , Anderson LN , Fan S , Walters KB , Halfmann PJ , Westhoff Smith D , Thackray LB , Tan Q , Sims AC , Menachery VD , Schäfer A , Sheahan TP , Cockrell AS , Stratton KG , Webb-Robertson BM , Kyle JE , Burnum-Johnson KE , Kim YM , Nicora CD , Peralta Z , N'Jai A U , Sahr F , van Bakel H , Diamond MS , Baric RS , Metz TO , Smith RD , Kawaoka Y , Waters KM . Sci Data 2024 11 (1) 328 Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology. |
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