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Sumner KM, Yadav R, Noble EK, Sandford R, Joshi D, Tartof SY, Wernli KJ, Martin ET, Gaglani M, Zimmerman RK, Talbot HK, Grijalva CG, Belongia EA, Chung JR, Rogier E, Coughlin MM, Flannery B. Anti-SARS-CoV-2 Antibody Levels Associated with COVID-19 Protection in Outpatients Tested for SARS-CoV-2, US Flu VE Network, October 2021-June 2022. J Infect Dis 2024:jiae090. [PMID: 38390968 DOI: 10.1093/infdis/jiae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND We assessed associations between binding antibody (bAb) concentration <5 days of symptom onset and testing positive for COVID-19 among patients in a test-negative study. METHODS From October 2021─June 2022, study sites in seven states enrolled patients aged ≥6 months presenting with acute respiratory illness. Respiratory specimens were tested for SARS-CoV-2. In blood specimens, we measured concentrations of anti-SARS-CoV-2 antibodies against the ancestral strain spike protein receptor binding domain (RBD) and nucleocapsid (N) antigens in standardized binding antibody units (BAU/mL). Percent change in odds of COVID-19 by increasing anti-RBD bAb was estimated using logistic regression as (1-adjusted odds ratio of COVID-19)x100, adjusting for COVID-19 mRNA vaccine doses, age, site, and high-risk exposure. RESULTS Out of 2,018 symptomatic patients, 662 (33%) tested positive for acute SARS-CoV-2 infection. Geometric mean RBD bAb were lower among COVID-19 cases than SARS-CoV-2 test-negative patients during both the Delta-predominant (112 vs. 498 BAU/mL) and Omicron-predominant (823 vs. 1,189 BAU/mL) periods. Acute phase ancestral spike RBD bAb associated with 50% lower odds of COVID-19 were 1,968 BAU/mL against Delta and 3,375 BAU/mL against Omicron; thresholds may differ in other laboratories. CONCLUSION During acute illness, antibody concentrations against ancestral spike RBD were associated with protection against COVID-19.
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Affiliation(s)
- Kelsey M Sumner
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ruchi Yadav
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Emma K Noble
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Ryan Sandford
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Devyani Joshi
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sara Y Tartof
- Kaiser Permanente Southern California, Department of Research & Evaluation, Pasadena, CA, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA
| | - Karen J Wernli
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Manjusha Gaglani
- Baylor Scott & White Health, Temple, TX, USA
- Baylor College of Medicine - Temple, Temple, TX, USA
- Texas A&M University College of Medicine, Temple, TX, USA
| | | | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Jessie R Chung
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Rogier
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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Nguyen DT, Sumner KM, Nguyen TTM, Phan MQ, Hoang TM, Vo CD, Nguyen TD, Nguyen PT, Yang G, Jang Y, Jones J, Olsen SJ, Gould PL, Nguyen LV, Davis CT. Avian influenza A(H5) virus circulation in live bird markets in Vietnam, 2017-2022. Influenza Other Respir Viruses 2023; 17:e13245. [PMID: 38149927 PMCID: PMC10752245 DOI: 10.1111/irv.13245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND Highly pathogenic avian influenza A(H5) human infections are a global concern, with many A(H5) human cases detected in Vietnam, including a case in October 2022. Using avian influenza virus surveillance from March 2017-September 2022, we described the percent of pooled samples that were positive for avian influenza A, A(H5), A(H5N1), A(H5N6), and A(H5N8) viruses in live bird markets (LBMs) in Vietnam. METHODS Monthly at each LBM, 30 poultry oropharyngeal swab specimens and five environmental samples were collected. Samples were pooled in groups of five and tested for influenza A, A(H5), A(H5N1), A(H5N6), and A(H5N8) viruses by real-time reverse-transcription polymerase chain reaction. Trends in the percent of pooled samples that were positive for avian influenza were summarized by LBM characteristics and time and compared with the number of passively detected avian influenza outbreaks using Spearman's rank correlation. RESULTS A total of 25,774 pooled samples were collected through active surveillance at 167 LBMs in 24 provinces; 36.9% of pooled samples were positive for influenza A, 3.6% A(H5), 1.9% A(H5N1), 1.1% A(H5N6), and 0.2% A(H5N8). Influenza A(H5) viruses were identified January-December and at least once in 91.7% of sampled provinces. In 246 A(H5) outbreaks in poultry; 20.3% were influenza A(H5N1), 60.2% A(H5N6), and 19.5% A(H5N8); outbreaks did not correlate with active surveillance. CONCLUSIONS In Vietnam, influenza A(H5) viruses were detected by active surveillance in LBMs year-round and in most provinces sampled. In addition to outbreak reporting, active surveillance for A(H5) viruses in settings with high potential for animal-to-human spillover can provide situational awareness.
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Affiliation(s)
| | - Kelsey M. Sumner
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
- Epidemic Intelligence ServiceCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Thoa T. M. Nguyen
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | | | | | | | - Tho D. Nguyen
- National Center for Veterinary DiagnosisDepartment of Animal HealthHanoiVietnam
| | - Phuong T. Nguyen
- Regional Animal Health Officer Number 6Department of Animal HealthHo Chi Minh CityVietnam
| | - Genyan Yang
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Yunho Jang
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Joyce Jones
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Sonja J. Olsen
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Philip L. Gould
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | | | - Charles Todd Davis
- Influenza Division, National Center for Immunizations and Respiratory DiseaseCenters for Disease Control and PreventionAtlantaGeorgiaUSA
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Sumner KM, Masalovich S, O'Halloran A, Holstein R, Reingold A, Kirley PD, Alden NB, Herlihy RK, Meek J, Yousey-Hindes K, Anderson EJ, Openo KP, Monroe ML, Leegwater L, Henderson J, Lynfield R, McMahon M, McMullen C, Angeles KM, Spina NL, Engesser K, Bennett NM, Felsen CB, Lung K, Shiltz E, Thomas A, Talbot HK, Schaffner W, Swain A, George A, Rolfes MA, Reed C, Garg S. Severity of influenza-associated hospitalisations by influenza virus type and subtype in the USA, 2010-19: a repeated cross-sectional study. Lancet Microbe 2023; 4:e903-e912. [PMID: 37769676 PMCID: PMC10872935 DOI: 10.1016/s2666-5247(23)00187-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Influenza burden varies across seasons, partly due to differences in circulating influenza virus types or subtypes. Using data from the US population-based surveillance system, Influenza Hospitalization Surveillance Network (FluSurv-NET), we aimed to assess the severity of influenza-associated outcomes in individuals hospitalised with laboratory-confirmed influenza virus infections during the 2010-11 to 2018-19 influenza seasons. METHODS To evaluate the association between influenza virus type or subtype causing the infection (influenza A H3N2, A H1N1pdm09, and B viruses) and in-hospital severity outcomes (intensive care unit [ICU] admission, use of mechanical ventilation or extracorporeal membrane oxygenation [ECMO], and death), we used FluSurv-NET to capture data for laboratory-confirmed influenza-associated hospitalisations from the 2010-11 to 2018-19 influenza seasons for individuals of all ages living in select counties in 13 US states. All individuals had to have an influenza virus test within 14 days before or during their hospital stay and an admission date between Oct 1 and April 30 of an influenza season. Exclusion criteria were individuals who did not have a complete chart review; cases from sites that contributed data for three or fewer seasons; hospital-onset cases; cases with unidentified influenza type; cases of multiple influenza virus type or subtype co-infection; or individuals younger than 6 months and ineligible for the influenza vaccine. Logistic regression models adjusted for influenza season, influenza vaccination status, age, and FluSurv-NET site compared odds of in-hospital severity by virus type or subtype. When missing, influenza A subtypes were imputed using chained equations of known subtypes by season. FINDINGS Data for 122 941 individuals hospitalised with influenza were captured in FluSurv-NET from the 2010-11 to 2018-19 seasons; after exclusions were applied, 107 941 individuals remained and underwent influenza A virus imputation when missing A subtype (43·4%). After imputation, data for 104 969 remained and were included in the final analytic sample. Averaging across imputed datasets, 57·7% (weighted percentage) had influenza A H3N2, 24·6% had influenza A H1N1pdm09, and 17·7% had influenza B virus infections; 16·7% required ICU admission, 6·5% received mechanical ventilation or ECMO, and 3·0% died (95% CIs had a range of less than 0·1% and are not displayed). Individuals with A H1N1pdm09 had higher odds of in-hospital severe outcomes than those with A H3N2: adjusted odds ratios (ORs) for A H1N1pdm09 versus A H3N2 were 1·42 (95% CI 1·32-1·52) for ICU admission; 1·79 (1·60-2·00) for mechanical ventilation or ECMO use; and 1·25 (1·07-1·46) for death. The adjusted ORs for individuals infected with influenza B versus influenza A H3N2 were 1·06 (95% CI 1·01-1·12) for ICU admission, 1·14 (1·05-1·24) for mechanical ventilation or ECMO use, and 1·18 (1·07-1·31) for death. INTERPRETATION Despite a higher burden of hospitalisations with influenza A H3N2, we found an increased likelihood of in-hospital severe outcomes in individuals hospitalised with influenza A H1N1pdm09 or influenza B virus. Thus, it is important for individuals to receive an annual influenza vaccine and for health-care providers to provide early antiviral treatment for patients with suspected influenza who are at increased risk of severe outcomes, not only when there is high influenza A H3N2 virus circulation but also when influenza A H1N1pdm09 and influenza B viruses are circulating. FUNDING The US Centers for Disease Control and Prevention.
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Affiliation(s)
- Kelsey M Sumner
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA; Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Svetlana Masalovich
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Alissa O'Halloran
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rachel Holstein
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Arthur Reingold
- School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | | | - Nisha B Alden
- Colorado Department of Public Health and Environment, Denver, CA, USA
| | - Rachel K Herlihy
- Colorado Department of Public Health and Environment, Denver, CA, USA
| | - James Meek
- Connecticut Emerging Infections Program, Yale School of Public Health, New Haven, CT, USA
| | - Kimberly Yousey-Hindes
- Connecticut Emerging Infections Program, Yale School of Public Health, New Haven, CT, USA
| | - Evan J Anderson
- Department of Medicine and Depatment of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; Georgia Emerging Infections Program, Georgia Department of Public Health, Atlanta, GA, USA; Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Kyle P Openo
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA; Georgia Emerging Infections Program, Georgia Department of Public Health, Atlanta, GA, USA; Veterans Affairs Medical Center, Atlanta, GA, USA
| | | | - Lauren Leegwater
- Michigan Department of Health and Human Services, Lansing, MI, USA
| | - Justin Henderson
- Michigan Department of Health and Human Services, Lansing, MI, USA
| | | | | | | | - Kathy M Angeles
- New Mexico Emerging Infections Program, University of New Mexico, Albuquerque, NM, USA
| | - Nancy L Spina
- New York State Department of Health, Albany, NY, USA
| | | | - Nancy M Bennett
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Christina B Felsen
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Krista Lung
- Ohio Department of Health, Columbus, OH, USA
| | - Eli Shiltz
- Ohio Department of Health, Columbus, OH, USA
| | | | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Ashley Swain
- Salt Lake County Health Department, Salt Lake City, UT, USA
| | - Andrea George
- Salt Lake County Health Department, Salt Lake City, UT, USA
| | - Melissa A Rolfes
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carrie Reed
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shikha Garg
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
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Sumner KM, Yadav R, Noble EK, Sandford R, Joshi D, Tartof SY, Wernli KJ, Martin ET, Gaglani M, Zimmerman RK, Talbot HK, Grijalva CG, Chung JR, Rogier E, Coughlin MM, Flannery B. Anti-SARS-CoV-2 Antibody Levels Associated with COVID-19 Protection in Outpatients Tested for SARS-CoV-2, US Flu VE Network, October 2021-June 2022. medRxiv 2023:2023.09.21.23295919. [PMID: 37790578 PMCID: PMC10543239 DOI: 10.1101/2023.09.21.23295919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background We assessed the association between antibody concentration ≤5 days of symptom onset and COVID-19 illness among patients enrolled in a test-negative study. Methods From October 2021-June 2022, study sites in seven states enrolled and tested respiratory specimens from patients of all ages presenting with acute respiratory illness for SARS-CoV-2 infection using rRT-PCR. In blood specimens, we measured concentration of anti-SARS-CoV-2 antibodies against the ancestral strain spike protein receptor binding domain (RBD) and nucleocapsid (N) antigens in standardized binding antibody units (BAU/mL). Percent reduction in odds of symptomatic COVID-19 by anti-RBD antibody was estimated using logistic regression modeled as (1-adjusted odds ratio of COVID-19)×100, adjusting for COVID-19 vaccination status, age, site, and high-risk exposure. Results A total of 662 (33%) of 2,018 symptomatic patients tested positive for acute SARS-CoV-2 infection. During the Omicron-predominant period, geometric mean anti-RBD binding antibody concentrations measured 823 BAU/mL (95%CI:690-981) among COVID-19 case-patients versus 1,189 BAU/mL (95%CI:1,050-1,347) among SARS-CoV-2 test-negative patients. In the adjusted logistic regression, increasing levels of anti-RBD antibodies were associated with reduced odds of COVID-19 for both Delta and Omicron infections. Conclusion Higher anti-RBD antibodies in patients were associated with protection against symptomatic COVID-19 during emergence of SARS-CoV-2 Delta and Omicron variants.
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Affiliation(s)
- Kelsey M. Sumner
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ruchi Yadav
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Emma K. Noble
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Ryan Sandford
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Devyani Joshi
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sara Y. Tartof
- Kaiser Permanente Southern California, Department of Research & Evaluation
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA
| | - Karen J. Wernli
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Manjusha Gaglani
- Baylor Scott & White Health, Temple, TX, USA
- Texas A&M University College of Medicine, Temple, TX, USA
| | | | | | | | - Jessie R. Chung
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Rogier
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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Sumner KM, Duca LM, Arriola CS, Neyra J, Soto G, Romero C, Tinoco Y, Nogareda F, Matos E, Chavez V, Castillo M, Bravo E, Castro J, Thompson M, Azziz-Baumgartner E. Knowledge, attitudes, and practices associated with frequent influenza vaccination among healthcare personnel in Peru, 2016─2018. Vaccine X 2023; 14:100314. [PMID: 37234596 PMCID: PMC10205539 DOI: 10.1016/j.jvacx.2023.100314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction Despite a government-subsidized vaccination program, healthcare personnel (HCP) influenza vaccination uptake remains low in Peru. Using three years of cross-sectional surveys and an additional five years of prior vaccination history of HCP in Peru, we explored HCP knowledge, attitudes, and practices (KAP) of influenza illness and its impact on vaccination frequency. Methods In 2016, the Estudio Vacuna de Influenza Peru (VIP) cohort was initiated in Lima, Peru, which collected information about HCP KAP and influenza vaccination history from 2011─2018. HCP were classified by their 8-year influenza vaccination history as never (0 years), infrequently (1─4 years), or frequently (5─8 years) vaccinated. Logistic regression models were used to describe KAP associated with frequent compared to infrequent influenza vaccination, adjusted for each HCP's healthcare workplace, age, sex, preexisting medical conditions, occupation, and length of time providing direct patient care. Results From 2016─2018, 5131 HCP were recruited and 3120 fully enrolled in VIP; 2782 consistently reported influenza vaccination status and became our analytic sample. From 2011─2018, 14.3% of HCP never, 61.4% infrequently, and 24.4% frequently received influenza vaccines. Compared to HCP who were infrequently vaccinated, frequently vaccinated HCP were more likely to believe they were susceptible to influenza (adjusted odds ratio [aOR]:1.49, 95% confidence interval [CI]:1.22─1.82), perceived vaccination to be effective (aOR:1.92, 95%CI:1.59─2.32), were knowledgeable about influenza and vaccination (aOR:1.37, 95%CI:1.06─1.77), and believed vaccination had emotional benefits like reduced regret or anger if they became ill with influenza (aOR:1.96, 95%CI:1.60─2.42). HCP who reported vaccination barriers like not having time or a convenient place to receive vaccines had reduced odds of frequent vaccination (aOR:0.74, 95%CI:0.61─0.89) compared to those without reported barriers. Conclusion Few HCP frequently received influenza vaccines during an eight-year period. To increase HCP influenza vaccination in middle-income settings like Peru, campaigns could strengthen influenza risk perception, vaccine knowledge, and accessibility.
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Affiliation(s)
- Kelsey M. Sumner
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lindsey M. Duca
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carmen Sofia Arriola
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joan Neyra
- U.S. Naval Medical Research Unit No. 6, Bellavista, Peru
| | - Giselle Soto
- U.S. Naval Medical Research Unit No. 6, Bellavista, Peru
| | - Candice Romero
- U.S. Naval Medical Research Unit No. 6, Bellavista, Peru
| | - Yeny Tinoco
- U.S. Naval Medical Research Unit No. 6, Bellavista, Peru
| | - Francisco Nogareda
- Consultant to the Pan American Health Organization, 525 23rd Street NW, Washington, DC 20037, USA
| | | | | | - Maria Castillo
- Hospital Nacional de Salud del Niño, Lima, Peru
- Medical School, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduar Bravo
- Medical School, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Juan Castro
- Hospital Nacional Daniel Alcides Carrion, Lima, Peru
| | - Mark Thompson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Markwalter CF, Petersen JEV, Zeno EE, Sumner KM, Freedman E, Mangeni JN, Abel L, Obala AA, Prudhomme-O’Meara W, Taylor SM. Symptomatic malaria enhances protection from reinfection with homologous Plasmodium falciparum parasites. PLoS Pathog 2023; 19:e1011442. [PMID: 37307293 PMCID: PMC10289385 DOI: 10.1371/journal.ppat.1011442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/23/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
A signature remains elusive of naturally-acquired immunity against Plasmodium falciparum. We identified P. falciparum in a 14-month cohort of 239 people in Kenya, genotyped at immunogenic parasite targets expressed in the pre-erythrocytic (circumsporozoite protein, CSP) and blood (apical membrane antigen 1, AMA-1) stages, and classified into epitope type based on variants in the DV10, Th2R, and Th3R epitopes in CSP and the c1L region of AMA-1. Compared to asymptomatic index infections, symptomatic malaria was associated with reduced reinfection by parasites bearing homologous CSP-Th2R (adjusted hazard ratio [aHR]:0.63; 95% CI:0.45-0.89; p = 0.008) CSP-Th3R (aHR:0.71; 95% CI:0.52-0.97; p = 0.033), and AMA-1 c1L (aHR:0.63; 95% CI:0.43-0.94; p = 0.022) epitope types. The association of symptomatic malaria with reduced hazard of homologous reinfection was strongest for rare epitope types. Symptomatic malaria provides more durable protection against reinfection with parasites bearing homologous epitope types. The phenotype represents a legible molecular epidemiologic signature of naturally-acquired immunity by which to identify new antigen targets.
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Affiliation(s)
- Christine F. Markwalter
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - Jens E. V. Petersen
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Erica E. Zeno
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kelsey M. Sumner
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Elizabeth Freedman
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Judith N. Mangeni
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Andrew A. Obala
- School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Wendy Prudhomme-O’Meara
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, United States of America
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Steve M. Taylor
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, Duke University, Durham, North Carolina, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Lewis NM, Delahoy MJ, Sumner KM, Lauring AS, Bendall EE, Mortenson L, Edwards E, Stamper A, Flannery B, Martin ET. Risk factors for infection with influenza A(H3N2) virus on a US university campus, October-November 2021. Influenza Other Respir Viruses 2023; 17:e13151. [PMID: 37246148 DOI: 10.1111/irv.13151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Knowledge of the specific dynamics of influenza introduction and spread in university settings is limited. METHODS Persons with acute respiratory illness symptoms received influenza testing by molecular assay during October 6-November 23, 2022. Viral sequencing and phylogenetic analysis were conducted on nasal swab samples from case-patients. Case-control analysis of a voluntary survey of persons tested was used to identify factors associated with influenza; logistic regression was conducted to calculate odds ratios and 95% CIs. A subset of case-patients tested during the first month of the outbreak was interviewed to identify sources of introduction and early spread. RESULTS Among 3268 persons tested, 788 (24.1%) tested positive for influenza; 744 (22.8%) were included in the survey analysis. All 380 sequenced specimens were influenza A (H3N2) virus clade 3C.2a1b.2a.2, suggesting rapid transmission. Influenza (OR [95% CI]) was associated with indoor congregate dining (1.43 [1.002-2.03]), attending large gatherings indoors (1.83 [1.26-2.66]) or outdoors (2.33 [1.64-3.31]), and varied by residence type (apartment with ≥1 roommate: 2.93 [1.21-7.11], residence hall room alone: 4.18 [1.31-13.31], or with roommate: 6.09 [2.46-15.06], or fraternity/sorority house: 15.13 [4.30-53.21], all compared with single-dwelling apartment). Odds of influenza were lower among persons who left campus for ≥1 day during the week before their influenza test (0.49 [0.32-0.75]). Almost all early cases reported attending large events. CONCLUSIONS Congregate living and activity settings on university campuses can lead to rapid spread of influenza following introduction. Isolating following a positive influenza test or administering antiviral medications to exposed persons may help mitigate outbreaks.
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Affiliation(s)
- Nathaniel M Lewis
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
| | - Miranda J Delahoy
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
- Epidemic Intelligence Service, CDC, Atlanta, Georgia, USA
| | - Kelsey M Sumner
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
- Epidemic Intelligence Service, CDC, Atlanta, Georgia, USA
| | - Adam S Lauring
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Emily E Bendall
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Lindsey Mortenson
- University of Michigan University Health Service, Ann Arbor, Michigan, USA
| | - Elizabeth Edwards
- University of Michigan University Health Service, Ann Arbor, Michigan, USA
| | - Aleksandra Stamper
- University of Michigan University Health Service, Ann Arbor, Michigan, USA
| | - Brendan Flannery
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, USA
| | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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8
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Kniss K, Sumner KM, Tastad KJ, Lewis NM, Jansen L, Julian D, Reh M, Carlson E, Williams R, Koirala S, Buss B, Donahue M, Palm J, Kollmann L, Holzbauer S, Levine MZ, Davis T, Barnes JR, Flannery B, Brammer L, Fry A. Risk for Infection in Humans after Exposure to Birds Infected with Highly Pathogenic Avian Influenza A(H5N1) Virus, United States, 2022. Emerg Infect Dis 2023; 29:1215-1219. [PMID: 37095080 DOI: 10.3201/eid2906.230103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
During February 7─September 3, 2022, a total of 39 states experienced outbreaks of highly pathogenic avian influenza A(H5N1) virus in birds from commercial poultry farms and backyard flocks. Among persons exposed to infected birds, highly pathogenic avian influenza A(H5) viral RNA was detected in 1 respiratory specimen from 1 person.
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9
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Thomas CM, White EB, Kojima N, Fill MMA, Hanna S, Jones TF, Newhouse CN, Orejuela K, Roth E, Winders S, Chandler DR, Grijalva CG, Schaffner W, Schmitz JE, DaSilva J, Kirby MK, Mellis AM, Rolfes MA, Sumner KM, Flannery B, Talbot HK, Dunn JR. Early and Increased Influenza Activity Among Children - Tennessee, 2022-23 Influenza Season. MMWR Morb Mortal Wkly Rep 2023; 72:49-54. [PMID: 36656786 PMCID: PMC9869745 DOI: 10.15585/mmwr.mm7203a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Influenza seasons typically begin in October and peak between December and February (1); however, the 2022-23 influenza season in Tennessee began in late September and was characterized by high pediatric hospitalization rates during November. This report describes a field investigation conducted in Tennessee during November 2022, following reports of increasing influenza hospitalizations. Data from surveillance networks, patient surveys, and whole genome sequencing of influenza virus specimens were analyzed to assess influenza activity and secondary illness risk. Influenza activity increased earlier than usual among all age groups, and rates of influenza-associated hospitalization among children were high in November, reaching 12.6 per 100,000 in children aged <5 years, comparable to peak levels typically seen in high-severity seasons. Circulating influenza viruses were genetically similar to vaccine components. Among persons who received testing for influenza at outpatient clinics, children were twice as likely to receive a positive influenza test result as were adults. Among household contacts exposed to someone with influenza, children were more than twice as likely to become ill compared with adults. As the influenza season continues, it is important for all persons, especially those at higher risk for severe disease, to protect themselves from influenza. To prevent influenza and severe influenza complications, all persons aged ≥6 months should get vaccinated, avoid contact with ill persons, and take influenza antivirals if recommended and prescribed.
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10
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Markwalter CF, Petersen JEV, Zeno EE, Sumner KM, Freedman E, Mangeni JN, Abel L, Obala AA, Prudhomme-O’Meara W, Taylor SM. Symptomatic malaria enhances protection from reinfection with homologous Plasmodium falciparum parasites. medRxiv 2023:2023.01.04.23284198. [PMID: 36711685 PMCID: PMC9882554 DOI: 10.1101/2023.01.04.23284198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A signature remains elusive of naturally-acquired immunity against Plasmodium falciparum . We identified P. falciparum in a 14-month cohort of 239 people in Kenya, genotyped at immunogenic parasite targets expressed in the pre-erythrocytic (circumsporozoite protein, CSP) and blood (apical membrane antigen 1, AMA-1) stages, and classified into epitope type based on variants in the DV10, Th2R, and Th3R epitopes in CSP and the c1L region of AMA-1. Compared to asymptomatic index infections, symptomatic malaria was associated with a reduced reinfection by parasites bearing homologous CSP-Th2R (adjusted hazard ratio [aHR]:0.63; 95% CI:0.45-0.89; p=0.008) CSP-Th3R (aHR:0.71; 95% CI:0.52-0.97; p=0.033), and AMA-1 c1L (aHR:0.63; 95% CI:0.43-0.94; p=0.022) epitope types. The association of symptomatic malaria with reduced risk of homologous reinfection was strongest for rare epitope types. Symptomatic malaria more effectively promotes functional immune responses. The phenotype represents a legible molecular epidemiologic signature of naturally-acquired immunity by which to identify new antigen targets.
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Affiliation(s)
| | - Jens E. V. Petersen
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC USA
| | - Erica E. Zeno
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC USA,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC USA
| | - Kelsey M. Sumner
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC USA,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC USA
| | - Elizabeth Freedman
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC USA
| | - Judith N. Mangeni
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret Kenya
| | - Andrew A. Obala
- School of Medicine, College of Health Sciences, Moi University, Eldoret Kenya
| | - Wendy Prudhomme-O’Meara
- Duke Global Health Institute, Duke University, Durham NC USA,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC USA,School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Steve M. Taylor
- Duke Global Health Institute, Duke University, Durham NC USA,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC USA,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC USA,Corresponding author: Steve M Taylor ,
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11
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Sumner KM, Karron RA, Stockwell MS, Dawood FS, Stanford JB, Mellis A, Hacker E, Thind P, Castro MJE, Harris JP, Knoll MD, Schappell E, Hetrich MK, Duque J, Jeddy Z, Altunkaynak K, Poe B, Meece J, Stefanski E, Tong S, Lee JS, Dixon A, Veguilla V, Rolfes MA, Porucznik CA. Impact of age and symptom development on SARS-CoV-2 transmission in households with children—Maryland, New York, and Utah, August 2020–October 2021. Open Forum Infect Dis 2022; 9:ofac390. [PMID: 35991589 PMCID: PMC9384637 DOI: 10.1093/ofid/ofac390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
Background
Households are common places for spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We investigated factors associated with household transmission and acquisition of SARS-CoV-2.
Methods
Households with children ages <18 years were enrolled into prospective, longitudinal cohorts and followed August 2020─August 2021 in Utah, September 2020─August 2021 in New York City, and November 2020─October 2021 in Maryland. Participants self-collected nasal swabs weekly and with onset of acute illness. Swabs were tested for SARS-CoV-2 using reverse-transcription polymerase chain reaction. We assessed factors associated with SARS-CoV-2 acquisition using a multi-level logistic regression adjusted for household size and clustering and SARS-CoV-2 transmission using a logistic regression adjusted for household size.
Results
Among 2,053 people (513 households) enrolled, 180 people (8.8%; in 76 households) tested positive for SARS-CoV-2. Compared to children <12y, odds of acquiring infection were lower for adults ≥18y (adjusted odds ratio[aOR]:0.34, 95% confidence interval[CI]:0.14–0.87); however, this may reflect vaccination status, which protected against SARS-CoV-2 acquisition (aOR:0.17, 95%CI:0.03–0.91). Odds of onward transmission was similar between symptomatic and asymptomatic primary cases (aOR:1.00, 95%CI:0.35–2.93) and did not differ by age (12–17vs. < 12y aOR:1.08, 95%CI:0.20–5.62; ≥18vs. < 12y aOR:1.70, 95%CI:0.52–5.83).
Conclusions
Adults had lower odds of acquiring SARS-CoV-2 compared to children, but this association might be influenced by COVID-19 vaccination, which was primarily available for adults and protective against infection. In contrast, all ages, regardless of symptoms and COVID-19 vaccination, had similar odds of transmitting SARS-CoV-2. Findings underscore the importance of SARS-CoV-2 mitigation measures for persons of all ages.
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Affiliation(s)
- Kelsey M Sumner
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention , Atlanta, GA , USA
| | - Ruth A Karron
- Center for Immunization Research, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University , Baltimore, MD , USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center , New York, NY , USA
- Department of Population and Family Health, Mailman School of Public Health, Columbia University Irving Medical Center , New York, NY , USA
| | - Fatimah S Dawood
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
| | - Joseph B Stanford
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine , Salt Lake City, UT , USA
| | - Alexandra Mellis
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
| | - Emily Hacker
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine , Salt Lake City, UT , USA
| | - Priyam Thind
- Division of Child and Adolescent Health, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center , New York, NY , USA
| | - Maria Julia E Castro
- Division of Child and Adolescent Health, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center , New York, NY , USA
| | - John Paul Harris
- Division of Child and Adolescent Health, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center , New York, NY , USA
| | - Maria Deloria Knoll
- International Vaccine Access Center, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University , Baltimore, MD , USA
| | - Elizabeth Schappell
- Center for Immunization Research, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University , Baltimore, MD , USA
| | - Marissa K Hetrich
- International Vaccine Access Center, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University , Baltimore, MD , USA
| | | | | | | | | | - Jennifer Meece
- Marshfield Clinic Research Institute , Marshfield, WI , USA
| | | | - Suxiang Tong
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
| | - Justin S Lee
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
| | - Ashton Dixon
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
| | - Vic Veguilla
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
| | - Melissa A Rolfes
- Centers for Disease Control and Prevention COVID-19 Response , Atlanta, GA , USA
| | - Christina A Porucznik
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine , Salt Lake City, UT , USA
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12
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Masters NB, Mathis AD, Leung J, Raines K, Clemmons NS, Miele K, Balajee SA, Lanzieri TM, Marin M, Christensen DL, Clarke KR, Cruz MA, Gallagher K, Gearhart S, Gertz AM, Grady-Erickson O, Habrun CA, Kim G, Kinzer MH, Miko S, Oberste MS, Petras JK, Pieracci EG, Pray IW, Rosenblum HG, Ross JM, Rothney EE, Segaloff HE, Shepersky LV, Skrobarcek KA, Stadelman AM, Sumner KM, Waltenburg MA, Weinberg M, Worrell MC, Bessette NE, Peake LR, Vogt MP, Robinson M, Westergaard RP, Griesser RH, Icenogle JP, Crooke SN, Bankamp B, Stanley SE, Friedrichs PA, Fletcher LD, Zapata IA, Wolfe HO, Gandhi PH, Charles JY, Brown CM, Cetron MS, Pesik N, Knight NW, Alvarado-Ramy F, Bell M, Talley LE, Rotz LD, Rota PA, Sugerman DE, Gastañaduy PA, Ahluwalia IB, Akinkugbe OA, Aranas A, Arons M, Atherstone C, Bampoe V, Bessler P, Bligh L, Bonner K, Bowen VB, Broadwater K, Brunette GW, Brunkard JM, Burns DA, Cantrell M, Christensen BE, Cope JR, Cory J, Crawford NE, Daigle D, Daly SM, Dejonge P, Dualeh M, Dunn KH, Eidex RB, Elgethun K, Fajardo G, Fonseca-Ford M, Franc K, Gaines J, George N, Goodson J, Green C, Grober AJ, Hailu K, Hammond DR, Harcourt BH, Hess A, Hesse E, Hirst DV, Hornsby-Myers J, Humrighouse B, Ishaq M, Ishii K, James A, Jayapaul-Philip B, Jentes ES, Johnson L, Johnston M, Jolley CD, Kacha-Ochana A, Kaur H, Keaveney M, Kelly HC, Krishnasamy V, Kumar GS, Larkin M, Layde M, LeBouf RF, Lee D, Lira RC, Lopez R, Lozier MJ, Macler A, Mainzer H, Malden D, Malenfant J, Marano N, Marsh Z, Mayer O, McDonald R, Mehta N, Menon AN, Meyer E, Miles ST, Minhaj F, Mirza S, Moller KM, Morris SB, Neu DT, Oakley LP, Ocasio DV, Osborne T, Ou AC, Peck M, Person M, Posey D, Pullia A, Qi C, Raziano AJ, Richmond-Crum M, Roohi S, Saindon JM, Sami S, Sanchez-Gonzalez L, Schweitzer R, Schwitters AM, Shamout M, Shockey CE, Shragai T, Singler KB, Sison EJ, Smith D, Smith M, Sood NJ, Sunshine BJ, Trujillo A, Vallabhaneni S, Wickson A, Yoder JS, Zambuto LR, Cozzarelli T, Rice M, Ricks M, Birchfield JS, Nambiar A, Avrakatos A, Ballard TP, Dennis E, Gambino-Shirley K, Huston AE, Jennings MG, Oldham DM, Rabener MJ, Fandre MN, Jablonka RJ, Love A, Peduzzi OL, Snow K, Greer JA, Hughes CA, Humphreys MA, Korduba AB, Neamand-Cheney KA, Pritchard NL, Smith AM, Whelpley JL, Adekoya S, Alexander V, Davis M, Falk J, Kurkjian K, McCarty E, Moss J, Myrick-West A, Patel C, Pruitt R, Saady D, Sockwell D, Touma A, Wheawill S, Woolard D, Young A, Griffin-Thomas L, Kelly S, McLeod J, Lambert MC, Danz TL, Davis T, Guenther K, Hanson E. Public Health Actions to Control Measles Among Afghan Evacuees During Operation Allies Welcome - United States, September-November 2021. MMWR Morb Mortal Wkly Rep 2022; 71:592-596. [PMID: 35482557 PMCID: PMC9098237 DOI: 10.15585/mmwr.mm7117a2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
On August 29, 2021, the United States government oversaw the emergent establishment of Operation Allies Welcome (OAW), led by the U.S. Department of Homeland Security (DHS) and implemented by the U.S. Department of Defense (DoD) and U.S. Department of State (DoS), to safely resettle U.S. citizens and Afghan nationals from Afghanistan to the United States. Evacuees were temporarily housed at several overseas locations in Europe and Asia* before being transported via military and charter flights through two U.S. international airports, and onward to eight U.S. military bases,† with hotel A used for isolation and quarantine of persons with or exposed to certain infectious diseases.§ On August 30, CDC issued an Epi-X notice encouraging public health officials to maintain vigilance for measles among Afghan evacuees because of an ongoing measles outbreak in Afghanistan (25,988 clinical cases reported nationwide during January-November 2021) (1) and low routine measles vaccination coverage (66% and 43% for the first and second doses, respectively, in 2020) (2).
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13
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Mahamar A, Sumner KM, Levitt B, Freedman B, Traore A, Barry A, Issiaka D, Dembele AB, Kanoute MB, Attaher O, Diarra BN, Sagara I, Djimde A, Duffy PE, Fried M, Taylor SM, Dicko A. Effect of three years' seasonal malaria chemoprevention on molecular markers of resistance of Plasmodium falciparum to sulfadoxine-pyrimethamine and amodiaquine in Ouelessebougou, Mali. Malar J 2022; 21:39. [PMID: 35135546 PMCID: PMC8822718 DOI: 10.1186/s12936-022-04059-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/21/2022] [Indexed: 11/11/2022] Open
Abstract
Background In 2012, seasonal malaria chemoprevention (SMC) was recommended as policy for malaria control by the World Health Organization (WHO) in areas of highly seasonal malaria transmission across the Sahel sub-region in Africa along with monitoring of drug resistance. We assessed the long-term impact of SMC on Plasmodium falciparum resistance to sulfadoxine-pyrimethamine (SP) and amodiaquine (AQ) over a 3-year period of SMC implementation in the health district of Ouelessebougou, Mali. Methods In 8 randomly selected sub-districts of Ouelessebougou, Mali, children aged 0–5 years were randomly selected during cross-sectional surveys at baseline (August 2014) and 1, 2 and 3 years post-SMC, at the beginning and end of the malaria transmission season. Blood smears and blood spots on filter paper were obtained and frequencies of mutation in P. falciparum genes related to resistance to SP and AQ (Pfdhfr, Pfdhps, Pfmdr1, and Pfcrt) were assessed by PCR amplification on individual samples and PCR amplification followed by deep sequencing on pooled (by site and year) samples. Results At each survey, approximately 50–100 individual samples were analysed by PCR amplification and a total of 1,164 samples were analysed by deep sequencing with an average read depth of 18,018–36,918 after pooling by site and year. Most molecular markers of resistance did not increase in frequency over the period of study (2014–2016). After 3 years of SMC, the frequencies of Pfdhps 540E, Pfdhps 437G and Pfcrt K76T remained similar compared to baseline (4.0 vs 1.4%, p = 0.41; 74.5 vs 64.6%, p = 0.22; 71.3 vs 67.4%, p = 0.69). Nearly all samples tested carried Pfdhfr 59R, and this proportion remained similar 3 years after SMC implementation (98.8 vs 100%, p = 1). The frequency of Pfmdr1 N86Y increased significantly over time from 5.6% at baseline to 18.6% after 3 years of SMC (p = 0.016). Results of pooled analysis using deep sequencing were consistent with those by individual analysis with standard PCR, but also indicated for the first time the presence of mutations at the Pfdhps A581G allele at a frequency of 11.7% after 2 years of SMC, as well as the Pfdhps I431V allele at frequencies of 1.6–9.3% following 1 and 2 years of SMC, respectively. Conclusion Two and 3 years of SMC implementation were associated with increased frequency of the Pfmdr1 N86Y mutation but not Pfdhps 540E, Pfdhps 437G and Pfcrt K76T. The first-time detection of the Pfdhps haplotype bearing the I431V and A581G mutations in Mali, even at low frequency, warrants further long-term surveillance.
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Affiliation(s)
- Almahamoudou Mahamar
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali.
| | - Kelsey M Sumner
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.,Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Brandt Levitt
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Betsy Freedman
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Aliou Traore
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Amadou Barry
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Djibrilla Issiaka
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Adama B Dembele
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Moussa B Kanoute
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Oumar Attaher
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | | | - Issaka Sagara
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Abdoulaye Djimde
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology (LMIV), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology (LMIV), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Alassane Dicko
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
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14
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Markwalter CF, Menya D, Wesolowski A, Esimit D, Lokoel G, Kipkoech J, Freedman E, Sumner KM, Abel L, Ambani G, Meredith HR, Taylor SM, Obala AA, O'Meara WP. Plasmodium falciparum importation does not sustain malaria transmission in a semi-arid region of Kenya. PLOS Glob Public Health 2022; 2:e0000807. [PMID: 36962553 PMCID: PMC10021402 DOI: 10.1371/journal.pgph.0000807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022]
Abstract
Human movement impacts the spread and transmission of infectious diseases. Recently, a large reservoir of Plasmodium falciparum malaria was identified in a semi-arid region of northwestern Kenya historically considered unsuitable for malaria transmission. Understanding the sources and patterns of transmission attributable to human movement would aid in designing and targeting interventions to decrease the unexpectedly high malaria burden in the region. Toward this goal, polymorphic parasite genes (ama1, csp) in residents and passengers traveling to Central Turkana were genotyped by amplicon deep sequencing. Genotyping and epidemiological data were combined to assess parasite importation. The contribution of travel to malaria transmission was estimated by modelling case reproductive numbers inclusive and exclusive of travelers. P. falciparum was detected in 6.7% (127/1891) of inbound passengers, including new haplotypes which were later detected in locally-transmitted infections. Case reproductive numbers approximated 1 and did not change when travelers were removed from transmission networks, suggesting that transmission is not fueled by travel to the region but locally endemic. Thus, malaria is not only prevalent in Central Turkana but also sustained by local transmission. As such, interrupting importation is unlikely to be an effective malaria control strategy on its own, but targeting interventions locally has the potential to drive down transmission.
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Affiliation(s)
| | - Diana Menya
- School of Public Health, Moi University College of Health Sciences, Eldoret, Kenya
| | - Amy Wesolowski
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Daniel Esimit
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Gilchrist Lokoel
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Joseph Kipkoech
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Elizabeth Freedman
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Kelsey M Sumner
- Duke University School of Medicine, Durham, North Carolina, United States of America
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - George Ambani
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Hannah R Meredith
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Steve M Taylor
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Andrew A Obala
- School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Wendy P O'Meara
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
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15
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Sumner KM, Ehlinger A, Georgiou ME, Wurst KE. Development and evaluation of standardized pregnancy identification and trimester distribution algorithms in U.S. IBM MarketScan® Commercial and Medicaid data. Birth Defects Res 2021; 113:1357-1367. [PMID: 34523818 DOI: 10.1002/bdr2.1954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/07/2021] [Accepted: 09/01/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVES Creation of new algorithms to identify pregnancies in automated health care claims databases is of public health importance, as it allows us to learn more about medication use and safety in a vulnerable population. Previous algorithms were largely created using international classification of disease codes, but despite the U.S. code transition in 2015, few algorithms are available with the latest ICD-10-CM codes. METHODS Using U.S. IBM MarketScan® Commercial Claims and Encounters and Multi-State Medicaid databases for women aged 10-64 years during 2014 and 2016, two pregnancy algorithms (ICD-9-CM and ICD-10-CM) were created using expert clinical review. The algorithms were evaluated by assessing the distribution of pregnancy outcomes (live birth and pregnancy losses) within each time-based cohort and the ability of the algorithms to identify select medication use during pregnancy. Medication exposure, demographics, comorbidities, and pregnancy outcomes were compared to published literature estimates for the two time periods. RESULTS For the IBM MarketScan® Commercial database, the algorithms identified 687,228 pregnancies in 2014 and 444,293 in 2016. In the IBM MarketScan® Medicaid database, 389,132 pregnancies in 2014 and 406,418 in 2016 were identified. Percentages of most pregnancy outcomes identified using the algorithms were similar to national data sources; however, percentages of preterm births and pregnancy losses were not comparable. Most medication use estimates from the algorithms were similar to or higher than published estimates. CONCLUSIONS By incorporating the latest ICD-10-CM codes, the new algorithms provide more complete estimates of medication use during pregnancy than algorithms using the outdated codes.
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Affiliation(s)
- Kelsey M Sumner
- Value Evidence Outcomes Epidemiology, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Anna Ehlinger
- Access and Customer Engagement Strategy Pricing, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Mary E Georgiou
- Value Evidence Outcomes Epidemiology, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Keele E Wurst
- Value Evidence Outcomes Epidemiology, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
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16
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Sumner KM, Mangeni JN, Obala AA, Freedman E, Abel L, Meshnick SR, Edwards JK, Pence BW, Prudhomme-O'Meara W, Taylor SM. Impact of asymptomatic Plasmodium falciparum infection on the risk of subsequent symptomatic malaria in a longitudinal cohort in Kenya. eLife 2021; 10:e68812. [PMID: 34296998 PMCID: PMC8337072 DOI: 10.7554/elife.68812] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Asymptomatic Plasmodium falciparum infections are common in sub-Saharan Africa, but their effect on subsequent symptomaticity is incompletely understood. Methods In a 29-month cohort of 268 people in Western Kenya, we investigated the association between asymptomatic P. falciparum and subsequent symptomatic malaria with frailty Cox models. Results Compared to being uninfected, asymptomatic infections were associated with an increased 1 month likelihood of symptomatic malaria (adjusted hazard ratio [aHR]: 2.61, 95% CI: 2.05 to 3.33), and this association was modified by sex, with females (aHR: 3.71, 95% CI: 2.62 to 5.24) at higher risk for symptomaticity than males (aHR: 1.76, 95% CI: 1.24 to 2.50). This increased symptomatic malaria risk was observed for asymptomatic infections of all densities and in people of all ages. Long-term risk was attenuated but still present in children under age 5 (29-month aHR: 1.38, 95% CI: 1.05 to 1.81). Conclusions In this high-transmission setting, asymptomatic P. falciparum can be quickly followed by symptoms and may be targeted to reduce the incidence of symptomatic illness. Funding This work was supported by the National Institute of Allergy and Infectious Diseases (R21AI126024 to WPO, R01AI146849 to WPO and SMT).
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Affiliation(s)
- Kelsey M Sumner
- Department of Epidemiology, Gillings School of Global Public Health, University of North CarolinaChapel HillUnited States
- Division of Infectious Diseases, School of Medicine, Duke UniversityDurhamUnited States
| | - Judith N Mangeni
- School of Public Health, College of Health Sciences, Moi UniversityEldoretKenya
| | - Andrew A Obala
- School of Medicine, College of Health Sciences, Moi UniversityEldoretKenya
| | - Elizabeth Freedman
- Division of Infectious Diseases, School of Medicine, Duke UniversityDurhamUnited States
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral HospitalEldoretKenya
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North CarolinaChapel HillUnited States
| | - Jessie K Edwards
- Department of Epidemiology, Gillings School of Global Public Health, University of North CarolinaChapel HillUnited States
| | - Brian W Pence
- Department of Epidemiology, Gillings School of Global Public Health, University of North CarolinaChapel HillUnited States
| | - Wendy Prudhomme-O'Meara
- Division of Infectious Diseases, School of Medicine, Duke UniversityDurhamUnited States
- School of Public Health, College of Health Sciences, Moi UniversityEldoretKenya
- Duke Global Health Institute, Duke UniversityDurhamUnited States
| | - Steve M Taylor
- Department of Epidemiology, Gillings School of Global Public Health, University of North CarolinaChapel HillUnited States
- Division of Infectious Diseases, School of Medicine, Duke UniversityDurhamUnited States
- Duke Global Health Institute, Duke UniversityDurhamUnited States
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17
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Sumner KM, Freedman E, Mangeni JN, Obala AA, Abel L, Edwards JK, Emch M, Meshnick SR, Pence BW, Prudhomme-O'Meara W, Taylor SM. Exposure to diverse Plasmodium falciparum genotypes shapes the risk of symptomatic malaria in incident and persistent infections: A longitudinal molecular epidemiologic study in Kenya. Clin Infect Dis 2021; 73:1176-1184. [PMID: 33904907 DOI: 10.1093/cid/ciab357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Repeated exposure to malaria infections could protect against symptomatic progression, as people develop adaptive immunity to infections acquired over time. METHODS We investigated how new, recurrent, and persistent Plasmodium falciparum infections were associated with the odds of developing symptomatic compared to asymptomatic malaria. Using a 14-month longitudinal cohort in Western Kenya, we used amplicon deep sequencing of two polymorphic genes (pfama1 and pfcsp) to assess overlap of parasite genotypes (represented by haplotypes) acquired within an individual's successive infections. We hypothesized infections with novel haplotypes would increase the odds of symptomatic malaria. RESULTS After excluding initial infections, we observed 534 asymptomatic and 88 symptomatic infections across 186 people. We detected 109 pfcsp haplotypes, and each infection was classified as harboring novel, recurrent or persistent haplotypes. Incident infections with only new haplotypes had higher odds of symptomatic malaria when compared to infections with only recurrent haplotypes [odds ratio (OR): 3.24, 95% confidence interval (CI): 1.20 to 8.78], but infections with both new and recurrent haplotypes [OR: 0.64, 95% CI: 0.15 to 2.65] did not. Assessing persistent infections, those with mixed (persistent with new or recurrent) haplotypes [OR: 0.77, 95% CI: 0.21 to 2.75] had no association with symptomatic malaria compared to infections with only persistent haplotypes. Results were similar for pfama1. CONCLUSIONS These results confirm that incident infections with only novel haplotypes were associated with increased odds of symptomatic malaria compared to infections with only recurrent haplotypes but this relationship was not seen when haplotypes persisted over time in consecutive infections.
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Affiliation(s)
- Kelsey M Sumner
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA
| | - Elizabeth Freedman
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA
| | - Judith N Mangeni
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Andrew A Obala
- School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Jessie K Edwards
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Department of Geography, University of North Carolina, Chapel Hill NC, USA
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Brian W Pence
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Wendy Prudhomme-O'Meara
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA.,School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya.,Duke Global Health Institute, Duke University, Durham NC, USA
| | - Steve M Taylor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA.,Duke Global Health Institute, Duke University, Durham NC, USA
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18
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Wurst KE, Sumner KM, Stanislaus D, Powell M, Cunnington M. A model for human and animal data integration: Weight of evidence strategy. Birth Defects Res 2020; 112:1505-1512. [PMID: 32770662 DOI: 10.1002/bdr2.1775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Integration of animal and human data to assess potential risks of the use of medications in pregnancy is important. A qualitative weight of evidence process enables all available evidence to be considered in a consistent, systematic manner. METHODS We aim to describe the weight of evidence methodology utilized by the authors, a summary of which was presented at the 59th Annual Meeting of the Teratology Society entitled "Integration of Human and Animal Data to Inform Medication Use in Pregnant Women." The qualitative weight of evidence process evaluates data that inform on a potential relationship between an adverse pregnancy outcome and a medication exposure. An interdisciplinary panel evaluates all available human and animal data related to the question of interest. Study quality assessments of both human and animal data are incorporated. The evaluation assesses gaps in the data from the following areas: (a) strength, (b) specificity, (c) consistency, (d) dose response relationship, (e) methodological considerations, and (f) biological plausibility for the potential association of interest. RESULTS The panel integrates all the information to arrive at an assessment of the evidence and provides recommendations, which may include obtaining more specific information. We provide examples of how the authors apply this process at a pharmaceutical company for evaluation of potential postmarketing safety issues regarding medications and pregnancy outcomes. CONCLUSIONS This weight of evidence method improves the ability to integrate published literature and other data sources to assess the potential risks of medication use in pregnant women and inform future drug safety studies.
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Affiliation(s)
- Keele E Wurst
- Epidemiology, Value Evidence Outcomes, GlaxoSmithKline, Uxbridge UK, Research Triangle Park, North Carolina, USA
| | - Kelsey M Sumner
- Epidemiology, Value Evidence Outcomes, GlaxoSmithKline, Uxbridge UK, Research Triangle Park, North Carolina, USA.,Department of Epidemiology, University of North Carolina, Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Dinesh Stanislaus
- Reproductive Toxicology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Marcy Powell
- Safety and Medical Governance, GlaxoSmithKline, Research Triangle Park, North Carolina, USA
| | - Marianne Cunnington
- Epidemiology, Value Evidence Outcomes, GlaxoSmithKline, Uxbridge UK, Research Triangle Park, North Carolina, USA
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19
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Taylor SM, Sumner KM, Freedman B, Mangeni JN, Obala AA, Prudhomme O'Meara W. Direct Estimation of Sensitivity of Plasmodium falciparum Rapid Diagnostic Test for Active Case Detection in a High-Transmission Community Setting. Am J Trop Med Hyg 2020; 101:1416-1423. [PMID: 31674301 DOI: 10.4269/ajtmh.19-0558] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Community-based active case detection of malaria parasites with conventional rapid diagnostic tests (cRDTs) is a strategy used most commonly in low-transmission settings. We estimated the sensitivity of this approach in a high-transmission setting in Western Kenya. We tested 3,547 members of 912 households identified in 2013-2014 by index children with (case) and without (control) cRDT-positive malaria. All were tested for Plasmodium falciparum with both a cRDT targeting histidine-rich protein 2 and with an ultrasensitive real-time polymerase chain reaction (PCR). We computed cRDT sensitivity against PCR as the referent, compared prevalence between participant types, and estimated cRDT detectability as a function of PCR-estimated parasite density. Parasite prevalence was 22.9% by cRDTs and 61.5% by PCR. Compared with children aged < 5 years or adults aged > 15 years, geometric mean parasite densities (95% CI) were highest in school-age children aged 5-15 years (8.4 p/uL; 6.6-10.6). The overall sensitivity of cRDT was 36%; among asymptomatic household members, cRDT sensitivity was 25.5% and lowest in adults aged > 15 years (15.8%). When modeled as a function of parasite density, relative to school-age children, the probability of cRDT positivity was reduced in both children aged < 5 years (odds ratio [OR] 0.48; 95% CI: 0.34-0.69) and in adults aged > 15 years (OR: 0.35; 95% CI: 0.27-0.47). An HRP2-detecting cRDT had poor sensitivity for active P. falciparum case detection in asymptomatic community members, and sensitivity was lowest in highly prevalent low-density infections and in adults. Future studies can model the incremental effects of high-sensitivity rapid diagnostic tests and the impacts on transmission.
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Affiliation(s)
- Steve M Taylor
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina.,Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina.,Duke Global Health Institute, Durham, North Carolina
| | - Kelsey M Sumner
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina.,Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Betsy Freedman
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | | | - Andrew A Obala
- College of Health Sciences, Moi University, Eldoret, Kenya
| | - Wendy Prudhomme O'Meara
- College of Health Sciences, Moi University, Eldoret, Kenya.,Duke Global Health Institute, Durham, North Carolina.,Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
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20
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Nelson CS, Sumner KM, Freedman E, Saelens JW, Obala AA, Mangeni JN, Taylor SM, O'Meara WP. High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya. Nat Commun 2019; 10:5615. [PMID: 31819062 PMCID: PMC6901486 DOI: 10.1038/s41467-019-13578-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/14/2019] [Indexed: 01/03/2023] Open
Abstract
Novel interventions that leverage the heterogeneity of parasite transmission are needed to achieve malaria elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon next-generation sequencing of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From April 2013 to July 2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. Here, we evaluate genetic similarity between infected individuals using three indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly share haplotypes with their own household members. Furthermore, we observe robust temporal structuring of parasite genetic similarity and identify the unique molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures. Here, Nelson et al. use amplicon next-generation sequencing of two P. falciparum polymorphic gene regions to investigate the genetic similarity of parasite populations across time and space in a pediatric cohort in Kenya. They identify both micro- and macro-scale structuring of malaria parasites in this high-transmission setting, which could inform future intervention strategies.
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Affiliation(s)
- Cody S Nelson
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.
| | - Kelsey M Sumner
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Elizabeth Freedman
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Andrew A Obala
- School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Judith N Mangeni
- School of Nursing, Moi University College of Health Sciences, Eldoret, Kenya
| | - Steve M Taylor
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Wendy P O'Meara
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
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21
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Sumner KM, McCabe CM, Nunn CL. Network size, structure, and pathogen transmission: a simulation study comparing different community detection algorithms. BEHAVIOUR 2018. [DOI: 10.1163/1568539x-00003508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Social substructure can influence pathogen transmission. Modularity measures the degree of social contact within versus between “communities” in a network, with increasing modularity expected to reduce transmission opportunities. We investigated how social substructure scales with network size and disease transmission. Using small-scale primate social networks, we applied seven community detection algorithms to calculate modularity and subgroup cohesion, defined as individuals’ interactions within subgroups proportional to the network. We found larger networks were more modular with higher subgroup cohesion, but the association’s strength varied by community detection algorithm and substructure measure. These findings highlight the importance of choosing an appropriate community detection algorithm for the question of interest, and if not possible, using multiple algorithms. Disease transmission simulations revealed higher modularity and subgroup cohesion resulted in fewer infections, confirming that social substructure has epidemiological consequences. Increased subdivision in larger networks could reflect constrained time budgets or evolved defences against disease risk.
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Affiliation(s)
- Kelsey M. Sumner
- aDepartment of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- bDepartment of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Collin M. McCabe
- bDepartment of Evolutionary Anthropology, Duke University, Durham, NC, USA
- cDivision of Infectious Diseases, Department of Medicine, Duke University, Durham, NC, USA
- dDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Charles L. Nunn
- bDepartment of Evolutionary Anthropology, Duke University, Durham, NC, USA
- eDuke Global Health Institute, Duke University, Durham, NC, USA
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