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  1. Article ; Online: Web Exclusive. Annals for Hospitalists Inpatient Notes - Clinical Pearls-E-Cigarette, or Vaping, Product Use-Associated Lung Injury.

    Ghinai, Isaac / Layden, Jennifer E

    Annals of internal medicine

    2019  Volume 171, Issue 12, Page(s) HO2–HO3

    Language English
    Publishing date 2019-12-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 336-0
    ISSN 1539-3704 ; 0003-4819
    ISSN (online) 1539-3704
    ISSN 0003-4819
    DOI 10.7326/M19-3574
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Notes from the Field: Characteristics of Tetrahydrocannabinol-Containing E-cigarette, or Vaping, Products Used by Adults - Illinois, September-October 2019.

    Navon, Livia / Ghinai, Isaac / Layden, Jennifer

    MMWR. Morbidity and mortality weekly report

    2020  Volume 69, Issue 29, Page(s) 973–975

    MeSH term(s) Adolescent ; Adult ; Aged ; Dronabinol/adverse effects ; Dronabinol/analysis ; Electronic Nicotine Delivery Systems/statistics & numerical data ; Humans ; Illinois/epidemiology ; Lung Injury/epidemiology ; Middle Aged ; Surveys and Questionnaires ; Vaping/epidemiology ; Young Adult
    Chemical Substances Dronabinol (7J8897W37S)
    Language English
    Publishing date 2020-07-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 412775-4
    ISSN 1545-861X ; 0149-2195
    ISSN (online) 1545-861X
    ISSN 0149-2195
    DOI 10.15585/mmwr.mm6929a5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Selection of artemisinin partial resistance Kelch13 mutations in Uganda in 2016-22 was at a rate comparable to that seen previously in South-East Asia.

    Meier-Scherling, Cecile P G / Watson, Oliver J / Asua, Victor / Ghinai, Isaac / Katairo, Thomas / Garg, Shreeya / Conrad, Melissa / Rosenthal, Philip J / Okell, Lucy C / Bailey, Jeffrey A

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: Background: Artemisinin partial resistance, mediated by mutations in the : Methods: We investigated K13 mutation prevalence at 16 sites in Uganda (2016-2022, 6586 samples), and five sites in SEA (2003-2018, 5465 samples) by calculating selection ... ...

    Abstract Background: Artemisinin partial resistance, mediated by mutations in the
    Methods: We investigated K13 mutation prevalence at 16 sites in Uganda (2016-2022, 6586 samples), and five sites in SEA (2003-2018, 5465 samples) by calculating selection coefficients using Bayesian mixed-effect linear models. We then tested whether SEA K13 mutation prevalence could have been forecast accurately using up to the first five years of available data and forecast future K13 mutation prevalence in Uganda.
    Findings: The selection coefficient for the prevalence of relevant K13 mutations (441L, 469F/Y, 561H, 675V) was estimated at s=0·383 (95% CrI: 0·247 - 0·528) per year, a 38% relative prevalence increase. Selection coefficients across Uganda were s=0·968 (0·463 - 1·569) for 441L, s=0·153 (-0·445 - 0·727) for 469F, s=0·222 (-0·011 - 0·398) for 469Y, and s=0·152 (-0·023 - 0·312) for 675V. In SEA, the selection coefficient was s=-0·005 (-0·852 - 0·814) for 539T, s=0·574 (-0·092 - 1·201) for 580Y, and s=0·308 (0·089 - 0·536) for all validated K13 mutations. Forecast prevalences for Uganda assuming constant selection neared fixation (>95% prevalence) within a decade (2028-2033) for combined K13 mutations.
    Interpretation: The selection of K13 mutations in Uganda was at a comparable rate to that observed in SEA, suggesting K13 mutations may continue to increase quickly in Uganda.
    Funding: NIH R01AI156267, R01AI075045, and R01AI089674.
    Language English
    Publishing date 2024-02-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.03.24302209
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Health Belief Model to Assess Mpox Knowledge, Attitudes, and Practices among Residents and Staff, Cook County Jail, Illinois, USA, July-August 2022.

    Hassan, Rashida / Meehan, Ashley A / Hughes, Sarah / Beeson, Amy / Spencer, Hillary / Howard, Jourdan / Tietje, Lauren / Richardson, Morgan / Schultz, Anne / Zawitz, Chad / Ghinai, Isaac / Hagan, Liesl M

    Emerging infectious diseases

    2024  Volume 30, Issue 13, Page(s) S49–S55

    Abstract: In summer 2022, a case of mpox was confirmed in a resident at the Cook County Jail (CCJ) in Chicago, Illinois, USA. We conducted in-depth interviews with CCJ residents and staff to assess mpox knowledge, attitudes, and practices; hygiene and cleaning ... ...

    Abstract In summer 2022, a case of mpox was confirmed in a resident at the Cook County Jail (CCJ) in Chicago, Illinois, USA. We conducted in-depth interviews with CCJ residents and staff to assess mpox knowledge, attitudes, and practices; hygiene and cleaning practices; and risk behaviors. We characterized findings by using health belief model constructs. CCJ residents and staff perceived increased mpox susceptibility but were unsure about infection severity; they were motivated to protect themselves but reported limited mpox knowledge as a barrier and desired clear communication to inform preventive actions. Residents expressed low self-efficacy to protect themselves because of contextual factors, including perceived limited access to cleaning, disinfecting, and hygiene items. Our findings suggest correctional facilities can support disease prevention by providing actionable and tailored messages; educating residents and staff about risk and vaccination options; and ensuring access to and training for hygiene, cleaning, and disinfecting supplies.
    MeSH term(s) Humans ; Health Belief Model ; Health Knowledge, Attitudes, Practice ; Illinois ; Jails ; Mpox (monkeypox)
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1380686-5
    ISSN 1080-6059 ; 1080-6040
    ISSN (online) 1080-6059
    ISSN 1080-6040
    DOI 10.3201/eid3013.230643
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory.

    Barbian, Hannah J / Kittner, Alyse / Teran, Richard / Bobrovska, Sofiya / Qiu, Xueting / English, Kayla / Green, Stefan J / Ghinai, Isaac / Pacilli, Massimo / Hayden, Mary K

    BMC public health

    2024  Volume 24, Issue 1, Page(s) 59

    Abstract: Background: Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health ... ...

    Abstract Background: Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health Laboratory in Chicago developed and employed a genomic surveillance response playbook for the early detection and surveillance of emerging SARS-CoV-2 variants.
    Methods: The playbook outlines modifications to sampling strategies, laboratory workflows, and communication processes based on the emerging variant's predicted viral characteristics, observed public health impact in other jurisdictions and local community risk level. The playbook outlines procedures for implementing and reporting enhanced and accelerated genomic surveillance, including supplementing whole genome sequencing (WGS) with variant screening by quantitative PCR (qPCR).
    Results: The ability of the playbook to improve the response to an emerging variant was tested for SARS-CoV-2 Omicron BA.1. Increased submission of clinical remnant samples from local hospital laboratories enabled detection of a new variant at an average of 1.4% prevalence with 95% confidence rather than 3.5% at baseline. Genotyping qPCR concurred with WGS lineage assignments in 99.9% of 1541 samples with results by both methods, and was more sensitive, providing lineage results in 90.4% of 1833 samples rather than 85.1% for WGS, while significantly reducing the time to lineage result.
    Conclusions: The genomic surveillance response playbook provides a structured, stepwise, and data-driven approach to responding to emerging SARS-CoV-2 variants. These pre-defined processes can serve as a template for other genomic surveillance programs to streamline workflows and expedite the detection and public health response to emerging variants. Based on the processes piloted during the Omicron BA.1 response, this method has been applied to subsequent Omicron subvariants and can be readily applied to future SARS-CoV-2 emerging variants and other public health surveillance activities.
    MeSH term(s) Humans ; COVID-19/diagnosis ; COVID-19/epidemiology ; Laboratories, Hospital ; Public Health ; Public Health Surveillance ; SARS-CoV-2/genetics
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-023-17536-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Multistate Outbreak of Infection with SARS-CoV-2 Omicron Variant after Event in Chicago, Illinois, USA, 2021.

    Spencer, Hillary / Teran, Richard A / Barbian, Hannah J / Love, Sarah / Berg, Rachel / Black, Stephanie R / Ghinai, Isaac / Kerins, Janna L

    Emerging infectious diseases

    2022  Volume 28, Issue 6, Page(s) 1281–1283

    Abstract: Bars and restaurants are high-risk settings for SARS-CoV-2 transmission. A multistate outbreak after a bar gathering in Chicago, Illinois, USA, highlights Omicron variant transmissibility, the value of local genomic surveillance and interstate ... ...

    Abstract Bars and restaurants are high-risk settings for SARS-CoV-2 transmission. A multistate outbreak after a bar gathering in Chicago, Illinois, USA, highlights Omicron variant transmissibility, the value of local genomic surveillance and interstate coordination, vaccination value, and the potential for rapid transmission of a novel variant across multiple states after 1 event.
    MeSH term(s) COVID-19/epidemiology ; Chicago/epidemiology ; Disease Outbreaks ; Humans ; Illinois/epidemiology ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-05-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1380686-5
    ISSN 1080-6059 ; 1080-6040
    ISSN (online) 1080-6059
    ISSN 1080-6040
    DOI 10.3201/eid2806.220411
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory

    Hannah J. Barbian / Alyse Kittner / Richard Teran / Sofiya Bobrovska / Xueting Qiu / Kayla English / Stefan J. Green / Isaac Ghinai / Massimo Pacilli / Mary K. Hayden

    BMC Public Health, Vol 24, Iss 1, Pp 1-

    2024  Volume 10

    Abstract: Abstract Background Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public ... ...

    Abstract Abstract Background Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health Laboratory in Chicago developed and employed a genomic surveillance response playbook for the early detection and surveillance of emerging SARS-CoV-2 variants. Methods The playbook outlines modifications to sampling strategies, laboratory workflows, and communication processes based on the emerging variant’s predicted viral characteristics, observed public health impact in other jurisdictions and local community risk level. The playbook outlines procedures for implementing and reporting enhanced and accelerated genomic surveillance, including supplementing whole genome sequencing (WGS) with variant screening by quantitative PCR (qPCR). Results The ability of the playbook to improve the response to an emerging variant was tested for SARS-CoV-2 Omicron BA.1. Increased submission of clinical remnant samples from local hospital laboratories enabled detection of a new variant at an average of 1.4% prevalence with 95% confidence rather than 3.5% at baseline. Genotyping qPCR concurred with WGS lineage assignments in 99.9% of 1541 samples with results by both methods, and was more sensitive, providing lineage results in 90.4% of 1833 samples rather than 85.1% for WGS, while significantly reducing the time to lineage result. Conclusions The genomic surveillance response playbook provides a structured, stepwise, and data-driven approach to responding to emerging SARS-CoV-2 variants. These pre-defined processes can serve as a template for other genomic surveillance programs to streamline workflows and expedite the detection and public health response to emerging variants. Based on the processes piloted during the Omicron BA.1 response, this method has been applied to subsequent Omicron subvariants and can be readily applied to future SARS-CoV-2 emerging variants and ...
    Keywords SARS-CoV-2 ; Genomic surveillance ; Disease outbreaks ; Infectious disease ; Public health preparedness ; Public health systems ; Public aspects of medicine ; RA1-1270
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Multistate Outbreak of Infection with SARS-CoV-2 Omicron Variant after Event in Chicago, Illinois, USA, 2021

    Hillary Spencer / Richard A. Teran / Hannah J. Barbian / Sarah Love / Rachel Berg / Stephanie R. Black / Isaac Ghinai / Janna L. Kerins

    Emerging Infectious Diseases, Vol 28, Iss 6, Pp 1281-

    2022  Volume 1283

    Abstract: Bars and restaurants are high-risk settings for SARS-CoV-2 transmission. A multistate outbreak after a bar gathering in Chicago, Illinois, USA, highlights Omicron variant transmissibility, the value of local genomic surveillance and interstate ... ...

    Abstract Bars and restaurants are high-risk settings for SARS-CoV-2 transmission. A multistate outbreak after a bar gathering in Chicago, Illinois, USA, highlights Omicron variant transmissibility, the value of local genomic surveillance and interstate coordination, vaccination value, and the potential for rapid transmission of a novel variant across multiple states after 1 event.
    Keywords COVID-19 ; 2019 novel coronavirus disease ; coronavirus disease ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; viruses ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing.

    de Cesare, Mariateresa / Mwenda, Mulenga / Jeffreys, Anna E / Chirwa, Jacob / Drakeley, Chris / Schneider, Kammerle / Mambwe, Brenda / Glanz, Karolina / Ntalla, Christina / Carrasquilla, Manuela / Portugal, Silvia / Verity, Robert J / Bailey, Jeffrey A / Ghinai, Isaac / Busby, George B / Hamainza, Busiku / Hawela, Moonga / Bridges, Daniel J / Hendry, Jason A

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1413

    Abstract: Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum ... ...

    Abstract Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3-4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.
    MeSH term(s) Humans ; Plasmodium falciparum/genetics ; Nanopore Sequencing ; Cost-Benefit Analysis ; Malaria, Falciparum/diagnosis ; Malaria/epidemiology ; Genomics ; Vaccines
    Chemical Substances Vaccines
    Language English
    Publishing date 2024-02-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45688-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Assessment of a Hotel-Based Protective Housing Program for Incidence of SARS-CoV-2 Infection and Management of Chronic Illness Among Persons Experiencing Homelessness.

    Huggett, Thomas D / Tung, Elizabeth L / Cunningham, Megan / Ghinai, Isaac / Duncan, Heather L / McCauley, Maura E / Detmer, Wayne M

    JAMA network open

    2021  Volume 4, Issue 12, Page(s) e2138464

    Abstract: Importance: Persons experiencing homelessness (PEH) are at higher risk for SARS-CoV-2 infection and severe illness due to COVID-19 because of a limited ability to physically distance and a higher burden of underlying health conditions.: Objective: To ...

    Abstract Importance: Persons experiencing homelessness (PEH) are at higher risk for SARS-CoV-2 infection and severe illness due to COVID-19 because of a limited ability to physically distance and a higher burden of underlying health conditions.
    Objective: To describe and assess a hotel-based protective housing intervention to reduce incidence of SARS-CoV-2 infection among PEH in Chicago, Illinois, with increased risk of severe illness due to COVID-19.
    Design, setting, and participants: This retrospective cohort study analyzed PEH who were provided protective housing in individual hotel rooms in downtown Chicago during the COVID-19 pandemic from April 2 through September 3, 2020. Participants were PEH at increased risk for severe COVID-19, defined as (1) aged at least 60 years regardless of health conditions, (2) aged at least 55 years with any underlying health condition posing increased risk, or (3) aged less than 55 years with any underlying health condition posing substantially increased risk (eg, HIV/AIDS).
    Exposures: Participants were housed in individual hotel rooms to reduce the risk of SARS-CoV-2 infection; on-site health care workers provided daily symptom monitoring, regular SARS-CoV-2 testing, and care for chronic health conditions. Additional on-site services included treatment of mental health and substance use disorders and social services.
    Main outcomes and measures: The main outcome measured was SARS-CoV-2 incidence, with SARS-Cov2 infection defined as a positive upper respiratory specimen using any polymerase chain reaction diagnostic assay authorized for emergency use by the Food and Drug Administration. Secondary outcomes were blood pressure control, glycemic control as measured by hemoglobin A1c, and housing placements at departure.
    Results: Of 259 participants from 16 homeless shelters in Chicago, 104 (40.2%) were aged at least 65 years, 190 (73.4%) were male, 185 (71.4%) were non-Hispanic Black, and 49 (18.9%) were non-Hispanic White. There was an observed reduction in SARS-CoV-2 incidence during the study period among the protective housing cohort (54.7 per 1000 people [95% CI, 22.4-87.1 per 1000 people]) compared with citywide rates for PEH residing in shelters (137.1 per 1000 people [95% CI, 125.1-149.1 per 1000 people]; P = .001). There was also an adjusted change in systolic blood pressure at a rate of -5.7 mm Hg (95% CI, -9.3 to -2.1 mm Hg) and hemoglobin A1c at a rate of -1.4% (95% CI, -2.4% to -0.4%) compared with baseline. More than half of participants (51% [n = 132]) departed from the intervention to housing of some kind (eg, supportive housing).
    Conclusions and relevance: This cohort study found that protective housing was associated with a reduction in SARS-CoV-2 infection among high-risk PEH during the first wave of the COVID-19 pandemic in Chicago. These findings suggest that with appropriate wraparound supports (ie, multisector services to address complex needs), such housing interventions may reduce the risk of SARS-CoV-2 infection, improve noncommunicable disease control, and provide a pathway to permanent housing.
    MeSH term(s) Adult ; Aged ; Blood Pressure ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; COVID-19 Testing ; Chicago ; Chronic Disease ; Delivery of Health Care/methods ; Female ; Glycated Hemoglobin A/metabolism ; Health Status Disparities ; Homeless Persons ; Housing ; Humans ; Incidence ; Male ; Middle Aged ; Noncommunicable Diseases/epidemiology ; Noncommunicable Diseases/therapy ; Program Evaluation ; Retrospective Studies ; SARS-CoV-2 ; Social Problems
    Chemical Substances Glycated Hemoglobin A
    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Evaluation Study ; Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2574-3805
    ISSN (online) 2574-3805
    DOI 10.1001/jamanetworkopen.2021.38464
    Database MEDical Literature Analysis and Retrieval System OnLINE

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