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Hwang W, Wantuch PL, Bernshtein B, Zhiteneva J, Slater D, Vater KH, Sridhar S, Oliver E, Roach DJ, Rao S, Turbett SE, Knoot CJ, Harding CM, Amin MN, Cross AS, LaRocque RC, Rosen DA, Harris JB. Antibody responses in Klebsiella pneumoniae bloodstream infection: a cohort study. bioRxiv 2024:2024.05.01.591958. [PMID: 38746292 PMCID: PMC11092611 DOI: 10.1101/2024.05.01.591958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Klebsiella pneumonia (Kpn) is the fourth leading cause of infection-related deaths globally, yet little is known about human antibody responses to invasive Kpn. In this study, we sought to determine whether the O-specific polysaccharide (OPS) antigen, a vaccine candidate, is immunogenic in humans with Kpn bloodstream infection (BSI). We also sought to define the cross-reactivity of human antibody responses among structurally related Kpn OPS subtypes and to assess the impact of capsule production on OPS-targeted antibody binding and function. Methods We measured plasma antibody responses to OPS (and MrkA, a fimbrial protein) in a cohort of patients with Kpn BSI and compared these with controls, including a cohort of healthy individuals and a cohort of individuals with Enterococcus BSI. We performed flow cytometry to measure the impact of Kpn capsule production on whole cell antibody binding and complement deposition, utilizing patient isolates with variable levels of capsule production and isogenic capsule-deficient strains derived from these isolates. Findings We enrolled 69 patients with Kpn BSI. Common OPS serotypes accounted for 57/69 (83%) of infections. OPS was highly immunogenic in patients with Kpn BSI, and peak OPS-IgG antibody responses in patients were 10 to 30-fold higher than antibody levels detected in healthy controls, depending on the serotype. There was significant cross-reactivity among structurally similar OPS subtypes, including the O1v1/O1v2, O2v1/O2v2 and O3/O3b subtypes. Physiological amounts of capsule produced by both hyperencapsulated and non-hyperencapsulated Kpn significantly inhibited OPS-targeted antibody binding and function. Interpretation OPS was highly immunogenic in patients with Kpn BSI, supporting its potential as a candidate vaccine antigen. The strong cross-reactivity observed between similar OPS subtypes in humans with Kpn BSI suggests that it may not be necessary to include all subtypes in an OPS-based vaccine. However, these observations are tempered by the fact that capsule production, even in non-highly encapsulated strains, has the potential to interfere with OPS antibody binding. This may limit the effectiveness of vaccines that exclusively target OPS. Funding National Institute of Allergy and Infectious Diseases at the National Institutes of Health. Research in Context Evidence before this study: Despite the potential of O-specific polysaccharide (OPS) as a vaccine antigen against Klebsiella pneumoniae (Kpn), the immunogenicity of OPS in humans remains largely unstudied, creating a significant knowledge gap with regard to vaccine development. A search of PubMed for publications up to March 18, 2024, using the terms " Klebsiella pneumoniae " and "O-specific polysaccharide" or "O-antigen" or "lipopolysaccharide" revealed no prior studies addressing OPS antibody responses in humans with Kpn bloodstream infections (BSI). One prior study 1 evaluated antibody response to a single lipopolysaccharide (which contains one subtype of OPS) in humans with invasive Kpn infection; however, in this study OPS typing of the infecting strains and target antigen were not described. Added value of this study: Our investigation into OPS immunogenicity in a human cohort marks a significant advance. Analyzing plasma antibody responses in 69 patients with Kpn BSI, we found OPS to be broadly immunogenic across all the types and subtypes examined, and there was significant cross-reactivity among structurally related OPS antigens. We also demonstrated that Kpn capsule production inhibit OPS antibody binding and the activation of complement on the bacterial surface, even in classical Kpn strains expressing lower levels of capsule.Implications of all the available evidence: While the immunogenicity and broad cross-reactivity of OPS in humans with Kpn BSI suggests it is a promising vaccine candidate, the obstruction of OPS antibody binding and engagement by physiologic levels of Kpn capsule underscores the potential limitations of an exclusively OPS-antigen based vaccine for Kpn. Our study provides insights for the strategic development of vaccines aimed at combating Kpn infections, an important antimicrobial resistant pathogen.
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Phillips MC, LaRocque RC, Thompson GR. Infectious Diseases in a Changing Climate. JAMA 2024; 331:1318-1319. [PMID: 38506835 DOI: 10.1001/jama.2023.27724] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
This JAMA Insights in the Climate Change and Health series discusses the importance of clinicians having awareness of changes in the geographic range, seasonality, and intensity of transmission of infectious diseases to help them diagnose, treat, and prevent these diseases.
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Affiliation(s)
- Matthew C Phillips
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
| | - Regina C LaRocque
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
| | - George R Thompson
- Division of Infectious Diseases, Department of Medicine, University of California-Davis Medical Center, Sacramento
- Department of Medical Microbiology and Immunology, University of California-Davis
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3
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Dash P, Hakim A, Akter A, Banna HA, Kaisar MH, Aktar A, Jahan SR, Ferdous J, Basher SR, Kamruzzaman M, Chowdhury F, Akter A, Tauheed I, Weil AA, Charles RC, Calderwood SB, Ryan ET, LaRocque RC, Harris JB, Bhuiyan TR, Qadri F. Cholera toxin and O-specific polysaccharide immune responses after oral cholera vaccination with Dukoral in different age groups of Bangladeshi participants. mSphere 2024; 9:e0056523. [PMID: 38391226 PMCID: PMC10964428 DOI: 10.1128/msphere.00565-23] [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: 12/05/2023] [Accepted: 12/20/2023] [Indexed: 02/24/2024] Open
Abstract
Vaccination is important to prevent cholera. There are limited data comparing anti-O-specific polysaccharide (OSP) and anti-cholera toxin-specific immune responses following oral whole-cell with cholera toxin B-subunit (WC-rBS) vaccine (Dukoral, Valneva) administration in different age groups. An understanding of the differences is relevant because young children are less well protected by oral cholera vaccines than older children and adults. We compared responses in 50 adults and 49 children (ages 2 to <18) who were administered two doses of WC-rBS at a standard 14-day interval. All age groups had significant IgA and IgG plasma-blast responses to the OSP and cholera toxin B-subunit (CtxB) antigens that peaked 7 days after vaccination. However, in adults and older children (ages 5 to <18), antibody responses directed at the OSP antigen were largely IgA and IgG, with a minimal IgM response, while younger children (ages 2 to <5) mounted significant increases in IgM with minimal increases in IgA and IgG antibody responses 30 days after vaccination. In adults, anti-OSP and CtxB memory B-cell responses were detected after completion of the vaccination series, while children only mounted CtxB-specific IgG memory B-cell responses and no OSP-memory B-cell responses. In summary, children and adults living in a cholera endemic area mounted different responses to the WC-rBS vaccine, which may be a result of more prior exposure to Vibrio cholerae in older participants. The absence of class-switched antibody responses and memory B-cell responses to OSP may explain why protection wanes more rapidly after vaccination in young children compared to older vaccinees.IMPORTANCEVaccination is an important strategy to prevent cholera. Though immune responses targeting the OSP of V. cholerae are believed to mediate protection against cholera, there are limited data on anti-OSP responses after vaccination in different age groups, which is important as young children are not well protected by current oral cholera vaccines. In this study, we found that adults mounted memory B-cell responses to OSP, which were not seen in children. Adults and older children mounted class-switched (IgG and IgA) serum antibody responses to OSP, which were not seen in young children who had only IgM responses to OSP. The lack of class-switched antibody responses and memory B-cell responses to OSP in younger participants may be due to lack of prior exposure to V. cholerae and could explain why protection wanes more rapidly after vaccination in young children.
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Affiliation(s)
- Pinki Dash
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Al Hakim
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Aklima Akter
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Hasan Al Banna
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - M. Hasanul Kaisar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Amena Aktar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sultana Rownok Jahan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jannatul Ferdous
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Salima Raiyan Basher
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Kamruzzaman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Fahima Chowdhury
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Afroza Akter
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Imam Tauheed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ana A. Weil
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason B. Harris
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Division of Global Health, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Taufiqur Rahman Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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Lypaczewski P, Chac D, Dunmire CN, Tandoc KM, Chowdhury F, Khan AI, Bhuiyan T, Harris JB, LaRocque RC, Calderwood SB, Ryan ET, Qadri F, Shapiro BJ, Weil AA. Diversity of Vibrio cholerae O1 through the human gastrointestinal tract during cholera. bioRxiv 2024:2024.02.08.579476. [PMID: 38370713 PMCID: PMC10871328 DOI: 10.1101/2024.02.08.579476] [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: 02/20/2024]
Abstract
Vibrio cholerae O1 causes the diarrheal disease cholera, and the small intestine is the site of active infection. During cholera, cholera toxin is secreted from V. cholerae and induces a massive fluid influx into the small intestine, which causes vomiting and diarrhea. Typically, V. cholerae genomes are sequenced from bacteria passed in stool, but rarely from vomit, a fluid that may more closely represents the site of active infection. We hypothesized that the V. cholerae O1 population bottlenecks along the gastrointestinal tract would result in reduced genetic variation in stool compared to vomit. To test this, we sequenced V. cholerae genomes from ten cholera patients with paired vomit and stool samples. Genetic diversity was low in both vomit and stool, consistent with a single infecting population rather than co-infection with divergent V. cholerae O1 lineages. The number of single nucleotide variants decreased between vomit and stool in four patients, increased in two, and remained unchanged in four. The number of genes encoded in the V. cholerae genome decreased between vomit and stool in eight patients and increased in two. Pangenome analysis of assembled short-read sequencing demonstrated that the toxin-coregulated pilus operon more frequently contained deletions in genomes from vomit compared to stool. However, these deletions were not detected by PCR or long-read sequencing, indicating that interpreting gene presence or absence patterns from short-read data alone may be incomplete. Overall, we found that V. cholerae O1 isolated from stool is genetically similar to V. cholerae recovered from the upper intestinal tract.
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Affiliation(s)
- Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Denise Chac
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | | | - Fahima Chowdhury
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Ashraful I. Khan
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Taufiqur Bhuiyan
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Jason B. Harris
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, US
- Division of Global Health, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, US
- Harvard Medical School, Boston, MA, USA
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, US
- Harvard Medical School, Boston, MA, USA
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, US
- Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Ana A. Weil
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
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5
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Machoko MMP, Dong Y, Grozdani A, Hong H, Oliver E, Hyle EP, Ryan ET, Colubri A, LaRocque RC. Knowledge, attitudes and practices regarding the use of mobile travel health apps. J Travel Med 2024; 31:taad089. [PMID: 37410376 PMCID: PMC10823485 DOI: 10.1093/jtm/taad089] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
We performed a survey of US international travellers to evaluate their knowledge, attitudes and practices regarding mobile technologies related to health. We found that many international travellers carry smartphones and are interested in receiving health information from a mobile app when they travel abroad.
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Affiliation(s)
- Munashe M P Machoko
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, USA
| | - Yinan Dong
- University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Hung Hong
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Elizabeth Oliver
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
| | - Emily P Hyle
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Andrés Colubri
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Regina C LaRocque
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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6
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Roach DJ, Sridhar S, Oliver E, Rao SR, Slater DM, Hwang W, Hutt Vater K, Dinesh A, Qadri F, Chisti MJ, Pierce VM, Turbett SE, Bhattacharyya RP, Worby CJ, Earl AM, LaRocque RC, Harris JB. Clinical and Genomic Characterization of a Cohort of Patients With Klebsiella pneumoniae Bloodstream Infection. Clin Infect Dis 2024; 78:31-39. [PMID: 37633257 PMCID: PMC10810715 DOI: 10.1093/cid/ciad507] [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: 06/14/2023] [Revised: 08/09/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND The clinical and microbial factors associated with Klebsiella pneumoniae bloodstream infections (BSIs) are not well characterized. Prior studies have focused on highly resistant or hypervirulent isolates, limiting our understanding of K. pneumoniae strains that commonly cause BSI. We performed a record review and whole-genome sequencing to investigate the clinical characteristics, bacterial diversity, determinants of antimicrobial resistance, and risk factors for in-hospital death in a cohort of patients with K. pneumoniae BSI. METHODS We identified 562 patients at Massachusetts General Hospital with K. pneumoniae BSIs between 2016 and 2022. We collected data on comorbid conditions, infection source, clinical outcomes, and antibiotic resistance and performed whole-genome sequencing on 108 sequential BSI isolates from 2021 to 2022. RESULTS Intra-abdominal infection was the most common source of infection accounting for 34% of all BSIs. A respiratory tract source accounted for 6% of BSIs but was associated with a higher in-hospital mortality rate (adjusted odds ratio, 5.4 [95% confidence interval, 2.2-12.8]; P < .001 for comparison with other sources). Resistance to the first antibiotic prescribed was also associated with a higher risk of death (adjusted odds ratio, 5.2 [95% confidence interval, 2.2-12.4]; P < .001). BSI isolates were genetically diverse, and no clusters of epidemiologically and genetically linked cases were observed. Virulence factors associated with invasiveness were observed at a low prevalence, although an unexpected association between O-antigen type and the source of infection was found. CONCLUSIONS These observations demonstrate the versatility of K. pneumoniae as an opportunistic pathogen and highlight the need for new approaches for surveillance and the rapid identification of patients with invasive antimicrobial-resistant K. pneumoniae infection.
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Affiliation(s)
- David J Roach
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sushmita Sridhar
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sowmya R Rao
- Department of Global Health, Boston University, Boston, Massachusetts, USA
| | - Damien M Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Wontae Hwang
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kian Hutt Vater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Anupama Dinesh
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Firdausi Qadri
- Dhaka Hospital, International Centre for Diarrheal Disease Research, Bangladesh
| | - Mohammod J Chisti
- Dhaka Hospital, International Centre for Diarrheal Disease Research, Bangladesh
| | - Virginia M Pierce
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Roby P Bhattacharyya
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Colin J Worby
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Ashlee M Earl
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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7
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Akhtar M, Islam MR, Khaton F, Soltana UH, Jafrin SA, Rahman SIA, Tauheed I, Ahmed T, Khan II, Akter A, Khan ZH, Islam MT, Khanam F, Biswas PK, Ahmmed F, Ahmed S, Rashid MM, Hossain MZ, Alam AN, Alamgir ASM, Rahman M, Ryan ET, Harris JB, LaRocque RC, Flora MS, Chowdhury F, Khan AI, Banu S, Shirin T, Bhuiyan TR, Qadri F. Appearance of tolerance-induction and non-inflammatory SARS-CoV-2 spike-specific IgG4 antibodies after COVID-19 booster vaccinations. Front Immunol 2023; 14:1309997. [PMID: 38173725 PMCID: PMC10763240 DOI: 10.3389/fimmu.2023.1309997] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Background Understanding the characteristics of the humoral immune responses following COVID-19 vaccinations is crucial for refining vaccination strategies and predicting immune responses to emerging SARS-CoV-2 variants. Methods A longitudinal analysis of SARS-CoV-2 spike receptor binding domain (RBD) specific IgG antibody responses, encompassing IgG subclasses IgG1, IgG2, IgG3, and IgG4 was performed. Participants received four mRNA vaccine doses (group 1; n=10) or two ChAdOx1 nCoV-19 and two mRNA booster doses (group 2; n=19) in Bangladesh over two years. Results Findings demonstrate robust IgG responses after primary Covishield or mRNA doses; declining to baseline within six months. First mRNA booster restored and surpassed primary IgG responses but waned after six months. Surprisingly, a second mRNA booster did not increase IgG levels further. Comprehensive IgG subclass analysis showed primary Covishield/mRNA vaccination generated predominantly IgG1 responses with limited IgG2/IgG3, Remarkably, IgG4 responses exhibited a distinct pattern. IgG4 remained undetectable initially but increased extensively six months after the second mRNA dose, eventually replacing IgG1 after the 3rd/4th mRNA doses. Conversely, initial Covishield recipients lack IgG4, surged post-second mRNA booster. Notably, mRNA-vaccinated individuals displayed earlier, robust IgG4 levels post first mRNA booster versus Covishield counterparts. IgG1 to IgG4 ratios decreased with increasing doses, most pronounced with four mRNA doses. This study highlights IgG response kinetics, influenced by vaccine type and doses, impacting immunological tolerance and IgG4 induction, shaping future vaccination strategies. Conclusions This study highlights the dynamics of IgG responses dependent on vaccine type and number of doses, leading to immunological tolerance and IgG4 induction, and shaping future vaccination strategies.
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Affiliation(s)
- Marjahan Akhtar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md. Rashedul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Fatema Khaton
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Umma Hany Soltana
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Syeda Anoushka Jafrin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sadia Isfat Ara Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Imam Tauheed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tasnuva Ahmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ishtiakul Islam Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Afroza Akter
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zahid Hasan Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md. Taufiqul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Prasanta Kumar Biswas
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Faisal Ahmmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Shakeel Ahmed
- Bangladesh Institute of Tropical & Infectious Diseases, Chittagong, Bangladesh
| | - Md. Mamunur Rashid
- Bangladesh Institute of Tropical & Infectious Diseases, Chittagong, Bangladesh
| | - Md. Zakir Hossain
- Bangladesh Institute of Tropical & Infectious Diseases, Chittagong, Bangladesh
| | - Ahmed Nawsher Alam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - A. S. M. Alamgir
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Mahbubur Rahman
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | | | - Fahima Chowdhury
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful Islam Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Taufiqur Rahman Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
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Brown TS, Mohareb AM, LaRocque RC. Universal Masking in Health Care Settings. Ann Intern Med 2023; 176:eL230347. [PMID: 38109751 DOI: 10.7326/l23-0347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Affiliation(s)
- Tyler S Brown
- Section of Infectious Diseases, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Amir M Mohareb
- Division of Infectious Diseases, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts
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Brown DG, Worby CJ, Pender MA, Brintz BJ, Ryan ET, Sridhar S, Oliver E, Harris JB, Turbett SE, Rao SR, Earl AM, LaRocque RC, Leung DT. Development of a prediction model for the acquisition of extended spectrum beta-lactam-resistant organisms in U.S. international travellers. J Travel Med 2023; 30:taad028. [PMID: 36864572 PMCID: PMC10628771 DOI: 10.1093/jtm/taad028] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
BACKGROUND Extended spectrum beta-lactamase producing Enterobacterales (ESBL-PE) present a risk to public health by limiting the efficacy of multiple classes of beta-lactam antibiotics against infection. International travellers may acquire these organisms and identifying individuals at high risk of acquisition could help inform clinical treatment or prevention strategies. METHODS We used data collected from a cohort of 528 international travellers enrolled in a multicentre US-based study to derive a clinical prediction rule (CPR) to identify travellers who developed ESBL-PE colonization, defined as those with new ESBL positivity in stool upon return to the United States. To select candidate features, we used data collected from pre-travel and post-travel questionnaires, alongside destination-specific data from external sources. We utilized LASSO regression for feature selection, followed by random forest or logistic regression modelling, to derive a CPR for ESBL acquisition. RESULTS A CPR using machine learning and logistic regression on 10 features has an internally cross-validated area under the receiver operating characteristic curve (cvAUC) of 0.70 (95% confidence interval 0.69-0.71). We also demonstrate that a four-feature model performs similarly to the 10-feature model, with a cvAUC of 0.68 (95% confidence interval 0.67-0.69). This model uses traveller's diarrhoea, and antibiotics as treatment, destination country waste management rankings and destination regional probabilities as predictors. CONCLUSIONS We demonstrate that by integrating traveller characteristics with destination-specific data, we could derive a CPR to identify those at highest risk of acquiring ESBL-PE during international travel.
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Affiliation(s)
- David Garrett Brown
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melissa A Pender
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ben J Brintz
- Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Edward T Ryan
- Harvard Medical School, Boston, MA, USA
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sushmita Sridhar
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sarah E Turbett
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Sowmya R Rao
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Regina C LaRocque
- Harvard Medical School, Boston, MA, USA
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel T Leung
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
- Division of Microbiology & Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
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10
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Kaisar MH, Kelly M, Kamruzzaman M, Bhuiyan TR, Chowdhury F, Khan AI, LaRocque RC, Calderwood SB, Harris JB, Charles RC, Čížová A, Mečárová J, Korcová J, Bystrický S, Kováč P, Xu P, Qadri F, Ryan ET. Comparison of O-specific polysaccharide responses in patients following infection with Vibrio cholerae O139 versus vaccination with a bivalent (O1/O139) oral killed cholera vaccine in Bangladesh. mSphere 2023; 8:e0025523. [PMID: 37646517 PMCID: PMC10597347 DOI: 10.1128/msphere.00255-23] [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: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 09/01/2023] Open
Abstract
Cholera caused by Vibrio cholerae O139 emerged in the early 1990s and spread rapidly to 11 Asian countries before receding for unclear reasons. Protection against cholera is serogroup-specific, which is defined by the O-specific polysaccharide (OSP) component of lipopolysaccharide (LPS). V. cholerae O139 also expresses the OSP-capsule. We, therefore, assessed antibody responses targeting V. cholerae O139 OSP, LPS, capsule, and vibriocidal responses in patients in Bangladesh with cholera caused by V. cholerae O139. We compared these responses to those of age-gender-blood group-matched recipients of the bivalent oral cholera vaccine (OCV O1/O139). We found prominent OSP, LPS, and vibriocidal responses in patients, with a high correlation between these responses. OSP responses primarily targeted the terminal tetrasaccharide of OSP. Vaccinees developed OSP, LPS, and vibriocidal antibody responses, but of significantly lower magnitude and responder frequency (RF) than matched patients. We separately analyzed responses in pediatric vaccinees born after V. cholerae O139 had receded in Bangladesh. We found that OSP responses were boosted in children who had previously received a single dose of bivalent OCV 3 yr previously but not in vaccinated immunologically naïve children. Our results suggest that OSP-specific responses occur during cholera caused by V. cholerae O139 despite the presence of capsules, that vaccination with bivalent OCV is poorly immunogenic in the short term in immunologically naïve individuals, but that OSP-specific immune responses can be primed by previous exposure, although whether such responses can protect against O139 cholera is uncertain. IMPORTANCE Cholera is a severe dehydrating illness in humans caused by Vibrio cholerae serogroups O1 or O139. Protection against cholera is serogroup-specific, which is defined by the O-specific polysaccharide (OSP) of V. cholerae LPS. Yet, little is known about immunity to O139 OSP. In this study, we assessed immune responses targeting OSP in patients from an endemic region with cholera caused by V. cholerae O139. We compared these responses to those of the age-gender-blood group-matched recipients of the bivalent oral cholera vaccine. Our results suggest that OSP-specific responses occur during cholera caused by V. cholerae O139 and that the OSP responses primarily target the terminal tetrasaccharide of OSP. Our results further suggest that vaccination with the bivalent vaccine is poorly immunogenic in the short term for inducing O139-specific OSP responses in immunologically naïve individuals, but OSP-specific immune responses can be primed by previous exposure or vaccination.
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Affiliation(s)
- M. Hasanul Kaisar
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Meagan Kelly
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mohammad Kamruzzaman
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Taufiqur R. Bhuiyan
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Fahima Chowdhury
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful Islam Khan
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason B. Harris
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Division of Global Health, MassGeneral Hospital for Children, Boston, Massachusetts, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alžbeta Čížová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Mečárová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Korcová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Slavomír Bystrický
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Pavol Kováč
- Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA
| | - Peng Xu
- Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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11
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Worby CJ, Sridhar S, Turbett SE, Becker MV, Kogut L, Sanchez V, Bronson RA, Rao SR, Oliver E, Walker AT, Walters MS, Kelly P, Leung DT, Knouse MC, Hagmann SHF, Harris JB, Ryan ET, Earl AM, LaRocque RC. Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis. Lancet Microbe 2023; 4:e790-e799. [PMID: 37716364 PMCID: PMC10680401 DOI: 10.1016/s2666-5247(23)00147-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 09/18/2023]
Abstract
BACKGROUND Culture-based studies have shown that acquisition of extended-spectrum β-lactamase-producing Enterobacterales is common during international travel; however, little is known about the role of the gut microbiome before and during travel, nor about acquisition of other antimicrobial-resistant organisms. We aimed to identify (1) whether the gut microbiome provided colonisation resistance against antimicrobial-resistant organism acquisition, (2) the effect of travel and travel behaviours on the gut microbiome, and (3) the scale and global heterogeneity of antimicrobial-resistant organism acquisition. METHODS In this metagenomic analysis, participants were recruited at three US travel clinics (Boston, MA; New York, NY; and Salt Lake City, UT) before international travel. Participants had to travel internationally between Dec 8, 2017, and April 30, 2019, and have DNA extractions for stool samples both before and after travel for inclusion. Participants were excluded if they had at least one low coverage sample (<1 million read pairs). Stool samples were collected at home before and after travel, sent to a clinical microbiology laboratory to be screened for three target antimicrobial-resistant organisms (extended-spectrum β-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales), and underwent DNA extraction and shotgun metagenomic sequencing. We profiled metagenomes for taxonomic composition, antibiotic-resistant gene content, and characterised the Escherichia coli population at the strain level. We analysed pre-travel samples to identify the gut microbiome risk factors associated with acquisition of the three targeted antimicrobial resistant organisms. Pre-travel and post-travel samples were compared to identify microbiome and resistome perturbation and E coli strain acquisition associated with travel. FINDINGS A total of 368 individuals travelled between the required dates, and 296 had DNA extractions available for both before and after travel. 29 travellers were excluded as they had at least one low coverage sample, leaving a final group of 267 participants. We observed a perturbation of the gut microbiota, characterised by a significant depletion of microbial diversity and enrichment of the Enterobacteriaceae family. Metagenomic strain tracking confirmed that 67% of travellers acquired new strains of E coli during travel that were phylogenetically distinct from their pre-travel strains. We observed widespread enrichment of antibiotic-resistant genes in the gut, with a median 15% (95% CI 10-20, p<1 × 10-10) increase in burden (reads per kilobase per million reads). This increase included antibiotic-resistant genes previously classified as threats to public health, which were 56% (95% CI 36-91, p=2 × 10-11) higher in abundance after travel than before. Fluoroquinolone antibiotic-resistant genes were aquired by 97 (54%) of 181 travellers with no detected pre-travel carriage. Although we found that visiting friends or relatives, travel to south Asia, and eating uncooked vegetables were risk factors for acquisition of the three targeted antimicrobial resistant organisms, we did not observe an association between the pre-travel microbiome structure and travel-related antimicrobial-resistant organism acquisition. INTERPRETATION This work highlights a scale of E coli and antimicrobial-resistant organism acquisition by US travellers not apparent from previous culture-based studies, and suggests that strategies to control antimicrobial-resistant organisms addressing international traveller behaviour, rather than modulating the gut microbiome, could be worthwhile. FUNDING US Centers for Disease Control and Prevention and National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Colin J Worby
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sushmita Sridhar
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah E Turbett
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Margaret V Becker
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Lucyna Kogut
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Vanessa Sanchez
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan A Bronson
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sowmya R Rao
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Allison Taylor Walker
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maroya Spalding Walters
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul Kelly
- Division of Infectious Diseases, Bronx Care Center, Bronx, NY, USA
| | - Daniel T Leung
- Division of Infectious Diseases and Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, USA
| | - Mark C Knouse
- Department of Medicine, Lehigh Valley Health Network, Allentown, PA, USA
| | - Stefan H F Hagmann
- Division of Pediatric Infectious Diseases, Steven and Alexandra Cohen Children's Medical Center of New York/Northwell Health, New Hyde Park, NY, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Division of Pediatric Global Health, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Edward T Ryan
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Travellers' Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Regina C LaRocque
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Travellers' Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
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12
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Kakoullis L, Steffen R, Osterhaus A, Goeijenbier M, Rao SR, Koiso S, Hyle EP, Ryan ET, LaRocque RC, Chen LH. Influenza: seasonality and travel-related considerations. J Travel Med 2023; 30:taad102. [PMID: 37535890 DOI: 10.1093/jtm/taad102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/08/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
RATIONALE FOR REVIEW This review aims to summarize the transmission patterns of influenza, its seasonality in different parts of the globe, air travel- and cruise ship-related influenza infections and interventions to reduce transmission. KEY FINDINGS The seasonality of influenza varies globally, with peak periods occurring mainly between October and April in the northern hemisphere (NH) and between April and October in the southern hemisphere (SH) in temperate climate zones. However, influenza seasonality is significantly more variable in the tropics. Influenza is one of the most common travel-related, vaccine-preventable diseases and can be contracted during travel, such as during a cruise or through air travel. Additionally, travellers can come into contact with people from regions with ongoing influenza transmission. Current influenza immunization schedules in the NH and SH leave individuals susceptible during their respective spring and summer months if they travel to the other hemisphere during that time. CONCLUSIONS/RECOMMENDATIONS The differences in influenza seasonality between hemispheres have substantial implications for the effectiveness of influenza vaccination of travellers. Health care providers should be aware of influenza activity when patients report travel plans, and they should provide alerts and advise on prevention, diagnostic and treatment options. To mitigate the risk of travel-related influenza, interventions include antivirals for self-treatment (in combination with the use of rapid self-tests), extending the shelf life of influenza vaccines to enable immunization during the summer months for international travellers and allowing access to the influenza vaccine used in the opposite hemisphere as a travel-related vaccine. With the currently available vaccines, the most important preventive measure involves optimizing the seasonal influenza vaccination. It is also imperative that influenza is recognized as a travel-related illness among both travellers and health care professionals.
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Affiliation(s)
- Loukas Kakoullis
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Robert Steffen
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, 8001, Switzerland
- Division of Epidemiology, Human Genetics & Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Albert Osterhaus
- Research Center Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, 30559, Germany
| | - Marco Goeijenbier
- Department of Intensive Care, Spaarne Gasthuis, Haarlem, 2035, Netherlands
- Department of Intensive Care, Erasmus Medical Center, Rotterdam, 3015, Netherlands
| | - Sowmya R Rao
- Department of Global Health, Boston University, Boston, MA 02118, USA
| | - Satoshi Koiso
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily P Hyle
- Harvard Medical School, Boston, MA 02115, USA
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, 02114, USA
| | - Edward T Ryan
- Harvard Medical School, Boston, MA 02115, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, 02114, USA
| | - Regina C LaRocque
- Harvard Medical School, Boston, MA 02115, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, 02114, USA
| | - Lin H Chen
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Infectious Diseases and Travel Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA
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13
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Abstract
International travel can cause new illness or exacerbate existing conditions. Because primary care providers are frequent sources of health advice to travelers, they should be familiar with destination-specific disease risks, be knowledgeable about travel and routine vaccines, be prepared to prescribe chemoprophylaxis and self-treatment regimens, and be aware of travel medicine resources. Primary care providers should recognize travelers who would benefit from referral to a specialized travel clinic for evaluation. Those requiring yellow fever vaccination, immunocompromised hosts, pregnant persons, persons with multiple comorbid conditions, or travelers with complex itineraries may warrant specialty referral.
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Affiliation(s)
- Robert J Rolfe
- Duke University School of Medicine, Durham, North Carolina (R.J.R.)
| | - Edward T Ryan
- Harvard Medical School, Boston, Massachusetts (E.T.R., R.C.L.)
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14
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Turbett SE, Bronson RA, Worby CJ, McGrath GEG, Hodgkins E, Becker M, Belford B, Kogut L, Oliver E, Ryan ET, LaRocque RC, Earl AM, Pierce VM. Intrinsic Resistance to Colistin in the Genus Hafnia. J Clin Microbiol 2023; 61:e0132622. [PMID: 37022168 PMCID: PMC10204633 DOI: 10.1128/jcm.01326-22] [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: 09/07/2022] [Accepted: 02/20/2023] [Indexed: 04/07/2023] Open
Abstract
A bacterial species is considered to be intrinsically resistant to an antimicrobial when nearly all of the wild-type isolates (i.e., those without acquired resistance) exhibit minimum inhibitory concentration (MIC) values that are sufficiently high such that susceptibility testing is unnecessary, and that the antimicrobial should not be considered for therapy. Accordingly, knowledge of intrinsic resistance influences both the selection of treatment regimens and the approach to susceptibility testing in the clinical laboratory, where unexpected results also facilitate the recognition of microbial identification or susceptibility testing errors. Previously, limited data have suggested that Hafnia spp. may be intrinsically resistant to colistin. We evaluated the in vitro activity of colistin against 119 Hafniaceae that were isolated from human samples: 75 (63%) from routine clinical cultures and 44 (37%) from stool samples of travelers undergoing screening for antimicrobial resistant organisms. Broth microdilution colistin MICs were ≥4 μg/mL for 117 of 119 (98%) isolates. Whole-genome sequencing of 96 of the isolates demonstrated that the colistin-resistant phenotype was not lineage-specific. 2 of the 96 (2%) isolates harbored mobile colistin resistance genes. Compared to whole-genome sequencing, VITEK MS matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and VITEK 2 GN ID failed to consistently distinguish between Hafnia alvei, Hafnia paralvei, and Obesumbacterium proteus. In conclusion, using a reference antimicrobial susceptibility testing method and a genetically diverse collection of isolates, we found Hafnia spp. to be intrinsically resistant to colistin. The recognition of this phenotype will help inform rational approaches by which to perform antimicrobial susceptibility testing and therapy for patients with infections that are caused by Hafnia spp.
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Affiliation(s)
- Sarah E Turbett
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Department of Medicine, Boston, Massachusetts, USA
- Harvard Medical School, Department of Pathology, Boston, Massachusetts, USA
| | - Ryan A Bronson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Graham E G McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Emily Hodgkins
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Margaret Becker
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Barbara Belford
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lucyna Kogut
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Department of Medicine, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Department of Medicine, Boston, Massachusetts, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Virginia M Pierce
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Department of Pathology, Boston, Massachusetts, USA
- Pediatric Infectious Disease Unit, MassGeneral Hospital for Children, Boston, Massachusetts, USA
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15
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Wiens KE, Iyer AS, Bhuiyan TR, Lu LL, Cizmeci D, Gorman MJ, Yuan D, Becker RL, Ryan ET, Calderwood SB, LaRocque RC, Chowdhury F, Khan AI, Levine MM, Chen WH, Charles RC, Azman AS, Qadri F, Alter G, Harris JB. Predicting Vibrio cholerae infection and symptomatic disease: a systems serology study. Lancet Microbe 2023; 4:e228-e235. [PMID: 36907197 PMCID: PMC10186354 DOI: 10.1016/s2666-5247(22)00391-3] [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] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 03/11/2023]
Abstract
BACKGROUND Vibriocidal antibodies are currently the best characterised correlate of protection against cholera and are used to gauge immunogenicity in vaccine trials. Although other circulating antibody responses have been associated with a decreased risk of infection, the correlates of protection against cholera have not been comprehensively compared. We aimed to analyse antibody-mediated correlates of protection from both V cholerae infection and cholera-related diarrhoea. METHODS We conducted a systems serology study that analysed 58 serum antibody biomarkers as correlates of protection against V cholerae O1 infection or diarrhoea. We used serum samples from two cohorts: household contacts of people with confirmed cholera in Dhaka, Bangladesh, and cholera-naive volunteers who were recruited at three centres in the USA, vaccinated with a single dose of CVD 103-HgR live oral cholera vaccine, and then challenged with V cholerae O1 El Tor Inaba strain N16961. We measured antigen-specific immunoglobulin responses against antigens using a customised Luminex assay and used conditional random forest models to examine which baseline biomarkers were most important for classifying individuals who went on to develop infection versus those who remained uninfected or asymptomatic. V cholerae infection was defined as having a positive stool culture result on days 2-7 or day 30 after enrolment of the household's index cholera case and, in the vaccine challenge cohort, was the development of symptomatic diarrhoea (defined as two or more loose stools of ≥200 mL each, or a single loose stool of ≥300 mL over a 48-h period). FINDINGS In the household contact cohort (261 participants from 180 households), 20 (34%) of the 58 studied biomarkers were associated with protection against V cholerae infection. We identified serum antibody-dependent complement deposition targeting the O1 antigen as the most predictive correlate of protection from infection in the household contacts, whereas vibriocidal antibody titres ranked lower. A five-biomarker model predicted protection from V cholerae infection with a cross-validated area under the curve (cvAUC) of 79% (95% CI 73-85). This model also predicted protection against diarrhoea in unvaccinated volunteers challenged with V cholerae O1 after vaccination (n=67; area under the curve [AUC] 77%, 95% CI 64-90). Although a different five-biomarker model best predicted protection from the development of cholera diarrhoea in the challenged vaccinees (cvAUC 78%, 95% CI 66-91), this model did poorly at predicting protection against infection in the household contacts (AUC 60%, 52-67). INTERPRETATION Several biomarkers predict protection better than vibriocidal titres. A model based on protection against infection among household contacts was predictive of protection against both infection and diarrhoeal illness in challenged vaccinees, suggesting that models based on observed conditions in a cholera-endemic population might be more likely to identify broadly applicable correlates of protection than models trained on single experimental settings. FUNDING National Institute of Allergy and Infectious Diseases and National Institute of Child Health and Human Development, National Institutes of Health.
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Affiliation(s)
- Kirsten E Wiens
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology and Biostatistics, Temple University College of Public Health, Philadelphia, PA, USA
| | - Anita S Iyer
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Taufiqur R Bhuiyan
- Infectious Diseases Division, International Centre for Diarrheoal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Lenette L Lu
- Division of Infectious Diseases and Geographic Medicine, Department of Internal Medicine and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Parkland Health and Hospital System, Dallas, TX, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, Massachusetts Institute of Technology, and Harvard, Cambridge, MA, USA
| | - Matthew J Gorman
- Ragon Institute of MGH, Massachusetts Institute of Technology, and Harvard, Cambridge, MA, USA
| | - Dansu Yuan
- Ragon Institute of MGH, Massachusetts Institute of Technology, and Harvard, Cambridge, MA, USA
| | - Rachel L Becker
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Stephen B Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Fahima Chowdhury
- Infectious Diseases Division, International Centre for Diarrheoal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Ashraful I Khan
- Infectious Diseases Division, International Centre for Diarrheoal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Myron M Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wilbur H Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrheoal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Galit Alter
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, Massachusetts Institute of Technology, and Harvard, Cambridge, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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16
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Yorki S, Shea T, Cuomo CA, Walker BJ, LaRocque RC, Manson AL, Earl AM, Worby CJ. Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Brief Bioinform 2023; 24:bbad050. [PMID: 36804804 PMCID: PMC10025444 DOI: 10.1093/bib/bbad050] [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: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type's strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.
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Affiliation(s)
- Sosie Yorki
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruce J Walker
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Applied Invention, LLC, Cambridge, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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17
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Edelson PJ, Harold R, Ackelsberg J, Duchin JS, Lawrence SJ, Manabe YC, Zahn M, LaRocque RC. Climate Change and the Epidemiology of Infectious Diseases in the United States. Clin Infect Dis 2023; 76:950-956. [PMID: 36048507 DOI: 10.1093/cid/ciac697] [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: 05/23/2022] [Revised: 08/08/2022] [Accepted: 08/24/2022] [Indexed: 11/14/2022] Open
Abstract
The earth is rapidly warming, driven by increasing atmospheric carbon dioxide and other gases that result primarily from fossil fuel combustion. In addition to causing arctic ice melting and extreme weather events, climatologic factors are linked strongly to the transmission of many infectious diseases. Changes in the prevalence of infectious diseases not only reflect the impacts of temperature, humidity, and other weather-related phenomena on pathogens, vectors, and animal hosts but are also part of a complex of social and environmental factors that will be affected by climate change, including land use, migration, and vector control. Vector- and waterborne diseases and coccidioidomycosis are all likely to be affected by a warming planet; there is also potential for climate-driven impacts on emerging infectious diseases and antimicrobial resistance. Additional resources for surveillance and public health activities are urgently needed, as well as systematic education of clinicians on the health impacts of climate change.
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Affiliation(s)
- Paul J Edelson
- College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Rachel Harold
- Medical Society Consortium on Climate and Health, Center for Climate Change Communication, George Mason University, Fairfax, Virginia, USA
| | - Joel Ackelsberg
- New York City Department of Health and Mental Hygiene, Bureau of Communicable Disease, New York, New York, USA
| | - Jeffrey S Duchin
- Public Health-Seattle and King County, Seattle, Washington, USA.,Division of Infectious Diseases, University of Washington, Seattle, Washington, USA
| | | | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matt Zahn
- Orange County Health Care Agency, Santa Ana, California, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
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18
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Turbett SE, Tomkins-Tinch CH, Anahtar MN, Dugdale CM, Hyle EP, Shenoy ES, Shaw B, Egbuonu K, Bowman KA, Zachary KC, Adams GC, Hooper DC, Ryan ET, LaRocque RC, Bassett IV, Triant VA, Siddle KJ, Rosenberg E, Sabeti PC, Schaffner SF, MacInnis BL, Lemieux JE, Charles RC. Distinguishing Severe Acute Respiratory Syndrome Coronavirus 2 Persistence and Reinfection: A Retrospective Cohort Study. Clin Infect Dis 2023; 76:850-860. [PMID: 36268576 PMCID: PMC9619827 DOI: 10.1093/cid/ciac830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/21/2022] [Revised: 09/06/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection is poorly understood, partly because few studies have systematically applied genomic analysis to distinguish reinfection from persistent RNA detection related to initial infection. We aimed to evaluate the characteristics of SARS-CoV-2 reinfection and persistent RNA detection using independent genomic, clinical, and laboratory assessments. METHODS All individuals at a large academic medical center who underwent a SARS-CoV-2 nucleic acid amplification test (NAAT) ≥45 days after an initial positive test, with both tests between 14 March and 30 December 2020, were analyzed for potential reinfection. Inclusion criteria required having ≥2 positive NAATs collected ≥45 days apart with a cycle threshold (Ct) value <35 at repeat testing. For each included subject, likelihood of reinfection was assessed by viral genomic analysis of all available specimens with a Ct value <35, structured Ct trajectory criteria, and case-by-case review by infectious diseases physicians. RESULTS Among 1569 individuals with repeat SARS-CoV-2 testing ≥45 days after an initial positive NAAT, 65 (4%) met cohort inclusion criteria. Viral genomic analysis characterized mutations present and was successful for 14/65 (22%) subjects. Six subjects had genomically supported reinfection, and 8 subjects had genomically supported persistent RNA detection. Compared to viral genomic analysis, clinical and laboratory assessments correctly distinguished reinfection from persistent RNA detection in 12/14 (86%) subjects but missed 2/6 (33%) genomically supported reinfections. CONCLUSIONS Despite good overall concordance with viral genomic analysis, clinical and Ct value-based assessments failed to identify 33% of genomically supported reinfections. Scaling-up genomic analysis for clinical use would improve detection of SARS-CoV-2 reinfections.
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Affiliation(s)
- Sarah E Turbett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA
| | - Christopher H Tomkins-Tinch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Melis N Anahtar
- Department of Pathology, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Caitlin M Dugdale
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Emily P Hyle
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Erica S Shenoy
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bennett Shaw
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, USA
| | | | - Kathryn A Bowman
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Kimon C Zachary
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gordon C Adams
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - David C Hooper
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Ingrid V Bassett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Virginia A Triant
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Katherine J Siddle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital (MGH), Boston, Massachusetts, USA
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Harvard University, Boston, Massachusetts, USA
| | - Stephen F Schaffner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Jacob E Lemieux
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
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19
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Posen HJ, Wong W, Farrar DS, Campigotto A, Chan T, Barker KR, Hagmann SHF, Ryan ET, LaRocque RC, Earl AM, Worby CJ, Castelli F, Fumadó VP, Britton PN, Libman M, Hamer DH, Morris SK. Travel-associated extensively drug-resistant typhoid fever: a case series to inform management in non-endemic regions. J Travel Med 2023; 30:6651791. [PMID: 35904457 DOI: 10.1093/jtm/taac086] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/29/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Extensively drug-resistant (XDR) typhoid fever is a threat to travelers to Pakistan. We describe a multicontinental case series of travel-acquired XDR typhoid fever to demonstrate the global spread of the problem and encourage preventive interventions as well as appropriate empiric antimicrobial use. METHODS Cases were extracted from the GeoSentinel database, microbiologic laboratory records of two large hospitals in Toronto, Canada, and by invitation to TropNet sites. All isolates were confirmed XDR Salmonella enterica serovar Typhi (Salmonella typhi), with resistance to ampicillin, ceftriaxone, ciprofloxacin and trimethoprim-sulfamethoxazole. RESULTS Seventeen cases were identified in Canada (10), USA (2), Spain (2), Italy (1), Australia (1) and Norway (1). Patients under 18 years represented 71% (12/17) of cases, and all patients travelled to Pakistan to visit friends or relatives. Only one patient is known to have been vaccinated. Predominant symptoms were fever, abdominal pain, vomiting and diarrhoea. Antimicrobial therapy was started on Day 1 of presentation in 75% (12/16) of patients, and transition to a carbapenem or azithromycin occurred a median of 2 days after blood culture was drawn. Antimicrobial susceptibilities were consistent with the XDR S. typhi phenotype, and whole genome sequencing on three isolates confirmed their belonging to the XDR variant of the H58 clade. CONCLUSIONS XDR typhoid fever is a particular risk for travelers to Pakistan, and empiric use of a carbapenem or azithromycin should be considered. Pre-travel typhoid vaccination and counseling are necessary and urgent interventions, especially for visiting friends and relatives travelers. Ongoing sentinel surveillance of XDR typhoid fever is needed to understand changing epidemiology.
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Affiliation(s)
- H Joshua Posen
- Department of Paediatrics, Division of Infectious Diseases, Hospital for Sick Children, Toronto, ON, Canada
| | - Waison Wong
- Department of Paediatric Infectious Diseases and Immunology, Alder Hey Children's Hospital, Liverpool, UK
| | - Daniel S Farrar
- Centre for Global Child Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Aaron Campigotto
- Department of Paediatric Laboratory Medicine, Division of Microbiology, Hospital for Sick Children, Toronto, ON, Canada
| | - Tiffany Chan
- Division of Infectious Diseases, Trillium Health Partners, Mississauga, ON, Canada
| | - Kevin R Barker
- Division of Microbiology, Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON, Canada
- Institute for Better Health, Trillium Health Partners, Mississauga, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Stefan H F Hagmann
- Division of Pediatric Infectious Diseases, Steven and Alexandra Cohen Children's Medical Center/Northwell Health, New Hyde Park, NY, USA
- Department of Pediatrics, Donald and Barbara Zucker School of Medicine/Hofstra Northwell, New Hempstead, NY, USA
| | - Edward T Ryan
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Regina C LaRocque
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute (Cambridge Massachusetts), MA, USA
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute (Cambridge Massachusetts), MA, USA
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia, Brescia, Italy
- ASST Spedali Civili, Brescia, Italy
| | - Victoria Pérez Fumadó
- Infectious Diseases Department, Hospital Universitari Sant Joan de Déu, Barcelona, Spain
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, the Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Michael Libman
- J.D. MacLean Centre for Tropical Diseases, McGill University, Montreal, Quebec
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
- Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Center for Emerging Infectious Diseases Research and Policy, Boston University, Boston, MA, USA
| | - Shaun K Morris
- Department of Paediatrics, Division of Infectious Diseases, Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Child Health Evaluative Sciences, Hospital for Sick Children Research Institute, Toronto, ON, Canada
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20
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Jones FK, Bhuiyan TR, Muise RE, Khan AI, Slater DM, Hutt Vater KR, Chowdhury F, Kelly M, Xu P, Kováč P, Biswas R, Kamruzzaman M, Ryan ET, Calderwood SB, LaRocque RC, Lessler J, Charles RC, Leung DT, Qadri F, Harris JB, Azman AS. Identifying Recent Cholera Infections Using a Multiplex Bead Serological Assay. mBio 2022; 13:e0190022. [PMID: 36286520 PMCID: PMC9765614 DOI: 10.1128/mbio.01900-22] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/31/2022] [Indexed: 11/20/2022] Open
Abstract
Estimates of incidence based on medically attended cholera can be severely biased. Vibrio cholerae O1 leaves a lasting antibody signal and recent advances showed that these can be used to estimate infection incidence rates from cross-sectional serologic data. Current laboratory methods are resource intensive and challenging to standardize across laboratories. A multiplex bead assay (MBA) could efficiently expand the breadth of measured antibody responses and improve seroincidence accuracy. We tested 305 serum samples from confirmed cholera cases (4 to 1083 d postinfection) and uninfected contacts in Bangladesh using an MBA (IgG/IgA/IgM for 7 Vibrio cholerae O1-specific antigens) as well as traditional vibriocidal and enzyme-linked immunosorbent assays (2 antigens, IgG, and IgA). While postinfection vibriocidal responses were larger than other markers, several MBA-measured antibodies demonstrated robust responses with similar half-lives. Random forest models combining all MBA antibody measures allowed for accurate identification of recent cholera infections (e.g., past 200 days) including a cross-validated area under the curve (cvAUC200) of 92%, with simpler 3 IgG antibody models having similar accuracy. Across infection windows between 45 and 300 days, the accuracy of models trained on MBA measurements was non-inferior to models based on traditional assays. Our results illustrated a scalable cholera serosurveillance tool that can be incorporated into multipathogen serosurveillance platforms. IMPORTANCE Reliable estimates of cholera incidence are challenged by poor clinical surveillance and health-seeking behavior biases. We showed that cross-sectional serologic profiles measured with a high-throughput multiplex bead assay can lead to accurate identification of those infected with pandemic Vibrio cholerae O1, thus allowing for estimates of seroincidence. This provides a new avenue for understanding the epidemiology of cholera, identifying priority areas for cholera prevention/control investments, and tracking progress in the global fight against this ancient disease.
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Affiliation(s)
- Forrest K. Jones
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Taufiqur R. Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rachel E. Muise
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ashraful I. Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Damien M. Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kian Robert Hutt Vater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Fahima Chowdhury
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Meagan Kelly
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Peng Xu
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavol Kováč
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rajib Biswas
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Kamruzzaman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
- University of North Carolina Population Center, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Daniel T. Leung
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew S. Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Institute of Global Health, University of Geneva, Geneva, Switzerland
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21
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Akhtar M, Basher SR, Nizam NN, Kamruzzaman M, Khaton F, Banna HA, Kaisar MH, Karmakar PC, Hakim A, Akter A, Ahmed T, Tauheed I, Islam S, Ahmmed F, Mahamud S, Hasnat MA, Sumon MA, Rashed A, Ghosh S, Calderwood SB, Harris JB, Charles RC, LaRocque RC, Ryan ET, Banu S, Shirin T, Chowdhury F, Bhuiyan TR, Qadri F. Longevity of memory B cells and antibodies, as well as the polarization of effector memory helper T cells, are associated with disease severity in patients with COVID-19 in Bangladesh. Front Immunol 2022; 13:1052374. [PMID: 36578502 PMCID: PMC9791541 DOI: 10.3389/fimmu.2022.1052374] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
The longevity of immune responses induced by different degrees of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection provides information important to understanding protection against coronavirus disease 2019 (COVID-19). Here, we report the persistence of SARS-CoV-2 spike receptor-binding domain (RBD) specific antibodies and memory B cells recognizing this antigen in sequential samples from patients in Bangladesh with asymptomatic, mild, moderate and severe COVID-19 out to six months following infection. Since the development of long-lived memory B cells, as well as antibody production, is likely to be dependent on T helper (Th) cells, we also investigated the phenotypic changes of Th cells in COVID-19 patients over time following infection. Our results show that patients with moderate to severe COVID-19 mounted significant levels of IgG antibodies out to six months following infection, while patients with asymptomatic or mild disease had significant levels of IgG antibodies out to 3 months following infection, but these then fell more rapidly at 6 months than in patients with higher disease severity. Patients from all severity groups developed circulating memory B cells (MBCs) specific to SARS-CoV-2 spike RBD by 3 months following infection, and these persisted until the last timepoint measured at 6 months. A T helper cell response with an effector memory phenotype was observed following infection in all symptomatic patients, while patients with asymptomatic infection had no significant increases in effector Th1, Th2 and Th17 effector memory cell responses. Our results suggest that the strength and magnitude of antibody and memory B cells induced following SARS-CoV-2 infection depend on the severity of the disease. Polarization of the Th cell response, with an increase in Th effector memory cells, occurs in symptomatic patients by day 7 following infection, with increases seen in Th1, Th2, Th17 and follicular helper T cell subsets.
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Affiliation(s)
- Marjahan Akhtar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Salima Raiyan Basher
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Nuder Nower Nizam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Mohammad Kamruzzaman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Fatema Khaton
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Hasan Al Banna
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - M Hasanul Kaisar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Polash Chandra Karmakar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Al Hakim
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Afroza Akter
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Tasnuva Ahmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Imam Tauheed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Shaumik Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Faisal Ahmmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Shakil Mahamud
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Mohammad Abul Hasnat
- Department of Cardiology, Department of Oncology, Kurmitola General Hospital, Dhaka, Bangladesh
| | - Mostafa Aziz Sumon
- Department of Cardiology, Department of Oncology, Kurmitola General Hospital, Dhaka, Bangladesh
| | - Asif Rashed
- Department of Microbiology, Department of Medicine, Mugda Medical College and Hospital, Dhaka, Bangladesh
| | - Shuvro Ghosh
- Department of Microbiology, Department of Medicine, Mugda Medical College and Hospital, Dhaka, Bangladesh
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Sayera Banu
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Fahima Chowdhury
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Taufiqur Rahman Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (ICDDRB), Dhaka, Bangladesh
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22
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Gregory DJ, Vannier A, Duey AH, Roady TJ, Dzeng RK, Pavlovic MN, Chapin MH, Mukherjee S, Wilmot H, Chronos N, Charles RC, Ryan ET, LaRocque RC, Miller TE, Garcia-Beltran WF, Thierauf JC, Iafrate AJ, Mullenbrock S, Stump MD, Wetzel RK, Polakiewicz RD, Naranbhai V, Poznansky MC. Repertoires of SARS-CoV-2 epitopes targeted by antibodies vary according to severity of COVID-19. Virulence 2022; 13:890-902. [PMID: 35587156 PMCID: PMC9122311 DOI: 10.1080/21505594.2022.2073025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023] Open
Abstract
Antibodies to SARS-CoV-2 are central to recovery and immunity from COVID-19. However, the relationship between disease severity and the repertoire of antibodies against specific SARS-CoV-2 epitopes an individual develops following exposure remains incompletely understood. Here, we studied seroprevalence of antibodies to specific SARS-CoV-2 and other betacoronavirus antigens in a well-annotated, community sample of convalescent and never-infected individuals obtained in August 2020. One hundred and twenty-four participants were classified into five groups: previously exposed but without evidence of infection, having no known exposure or evidence of infection, seroconverted without symptoms, previously diagnosed with symptomatic COVID-19, and recovered after hospitalization with COVID-19. Prevalence of IgGs specific to the following antigens was compared between the five groups: recombinant SARS-CoV-2 and betacoronavirus spike and nucleocapsid protein domains, peptides from a tiled array of 22-mers corresponding to the entire spike and nucleocapsid proteins, and peptides corresponding to predicted immunogenic regions from other proteins of SARS-CoV-2. Antibody abundance generally correlated positively with severity of prior illness. A number of specific immunogenic peptides and some that may be associated with milder illness or protection from symptomatic infection were identified. No convincing association was observed between antibodies to Receptor Binding Domain(s) (RBDs) of less pathogenic betacoronaviruses HKU1 or OC43 and COVID-19 severity. However, apparent cross-reaction with SARS-CoV RBD was evident and some predominantly asymptomatic individuals had antibodies to both MERS-CoV and SARS-CoV RBDs. Findings from this pilot study may inform development of diagnostics, vaccines, and therapeutic antibodies, and provide insight into viral pathogenic mechanisms.
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Affiliation(s)
- David J. Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
- Pediatric Infectious Disease, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Augustin Vannier
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Akiro H. Duey
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Tyler J. Roady
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Richard K. Dzeng
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Maia N. Pavlovic
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H. Chapin
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Sonia Mukherjee
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Richelle C. Charles
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital Boston, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward T. Ryan
- Cardiology Care Clinics, Eatonton, GA, USA
- Division of Infectious Diseases, Massachusetts General Hospital Boston, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Regina C. LaRocque
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital Boston, Boston, MA, USA
| | - Tyler E. Miller
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Wilfredo F. Garcia-Beltran
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Julia C. Thierauf
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - A. John Iafrate
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | - Vivek Naranbhai
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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23
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Dunmire CN, Chac D, Chowdhury F, Khan AI, Bhuiyan TR, LaRocque RC, Akter A, Amin MA, Ryan ET, Qadri F, Weil AA. Vibrio cholerae Isolation from Frozen Vomitus and Stool Samples. J Clin Microbiol 2022; 60:e0108422. [PMID: 36169311 PMCID: PMC9580352 DOI: 10.1128/jcm.01084-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Chelsea N. Dunmire
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Denise Chac
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Fahima Chowdhury
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful I. Khan
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Taufiqur R. Bhuiyan
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | - Afroza Akter
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Ashraful Amin
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Edward T. Ryan
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ana A. Weil
- Department of Medicine, University of Washington, Seattle, Washington, USA
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24
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Kawser Z, Hossain M, Suliman S, Lockman S, Gitaka J, Bandawe G, Rahmat R, Hasan I, Siddik AB, Afrad MH, Rahman MZ, Miller G, Walt DR, Ivers LC, LaRocque RC, Harris JB, Qadri F. An Assessment of a Rapid SARS-CoV-2 Antigen Test in Bangladesh. Am J Trop Med Hyg 2022; 107:845-849. [PMID: 35970285 DOI: 10.4269/ajtmh.22-0068] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/21/2021] [Indexed: 11/07/2022] Open
Abstract
Early detection of SARS-CoV-2 infection is crucial to prevent its spread. This study aimed to document test sensitivity/specificity, correlation with cycle threshold value from polymerase chain reaction (PCR), fitness-for-use in different populations and settings, and user perspectives that could inform large-scale implementation. In this study, we evaluated the performance of a rapid antigen detection test, BD Veritor, and compared this (and another rapid test, Standard Q) against reverse transcription PCR (RT-PCR) in terms of sensitivity and specificity in 130 symptomatic and 130 asymptomatic adults. In addition, we evaluated the suitability and ease of use of the BD Veritor test in a subsample of study participants (n = 42) and implementers (n = 5). At 95% confidence interval, the sensitivity of the BD Veritor and Standard Q test were 70% and 63% in symptomatic and 87% and 73% in asymptomatic individuals, respectively, regarding positive SARS-CoV-2 RT-PCR results. Overall, the BD Veritor test was 78% sensitive and 99.5% specific compared with RT-PCR irrespective of the cycle threshold. This warrants large field evaluation as well as use of the rapid antigen test for quick assessment of SARS-CoV-2 for containment of epidemics in the country.
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Affiliation(s)
- Zannat Kawser
- Institute for Developing Science and Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Mohabbat Hossain
- Institute for Developing Science and Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Sara Suliman
- Division of Experimental Medicine, Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya.,Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Gama Bandawe
- Biological Sciences Department, Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo, Malawi
| | - Redwan Rahmat
- Institute for Developing Science and Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Imrul Hasan
- Institute for Developing Science and Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Abu Bakar Siddik
- Institute for Developing Science and Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Mokibul Hassan Afrad
- International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammed Ziaur Rahman
- International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Glenn Miller
- Mass General Brigham Center for COVID Innovation, Boston, Massachusetts
| | - David R Walt
- Mass General Brigham Center for COVID Innovation, Boston, Massachusetts.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Louise C Ivers
- Department of Global Health and Social Medicine, Harvard Medical School, Boston Massachusetts.,MGH Center for Global Health, Massachusetts General Hospital, Boston, Massachusetts
| | - Regina C LaRocque
- MGH Center for Global Health, Massachusetts General Hospital, Boston, Massachusetts
| | - Jason B Harris
- MGH Center for Global Health, Massachusetts General Hospital, Boston, Massachusetts
| | - Firdausi Qadri
- International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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25
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Hyle EP, Le MH, Rao SR, Mulroy NM, Walker AT, Ryan ET, LaRocque RC. High-risk US international travelers seeking pretravel consultation during the COVID-19 pandemic. Open Forum Infect Dis 2022; 9:ofac399. [PMID: 36000001 PMCID: PMC9384642 DOI: 10.1093/ofid/ofac399] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Background To assess the implications of coronavirus disease 2019 (COVID-19)–related travel disruptions, we compared demographics and travel-related circumstances of US travelers seeking pretravel consultation regarding international travel at US Global TravEpiNet (GTEN) sites before and after the initiation of COVID-19 travel warnings. Methods We analyzed data in the GTEN database regarding traveler demographics and travel-related circumstances with standard questionnaires in the pre-COVID-19 period (January–December 2019) and the COVID-19 period (April 2020–March 2021), excluding travelers from January to March 2020. We conducted descriptive analyses of differences in demographics, travel-related circumstances, routine and travel-related vaccinations, and medications. Results Compared with 16 903 consultations in the pre-COVID-19 period, only 1564 consultations were recorded at GTEN sites during the COVID-19 period (90% reduction), with a greater proportion of travelers visiting friends and relatives (501/1564 [32%] vs 1525/16 903 [9%]), individuals traveling for >28 days (824/1564 [53%] vs 2522/16 903 [15%]), young children (6 mo–<6 y: 168/1564 [11%] vs 500/16 903 [3%]), and individuals traveling to Africa (1084/1564 [69%] vs 8049/16 903 [48%]). A smaller percentage of vaccine-eligible travelers received vaccines at pretravel consultations during the COVID-19 period than before, except for yellow fever and Japanese encephalitis vaccinations. Conclusions Compared with the pre-COVID-19 period, a greater proportion of travelers during the COVID-19 period were young children, were planning to visit friends and relatives, were traveling for >28 days, or were traveling to Africa, which are circumstances that contribute to high risk for travel-related infections. Fewer vaccine-eligible travelers were administered travel-related vaccines at pretravel consultations. Counseling and vaccination focused on high-risk international travelers must be prioritized during the COVID-19 pandemic.
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Affiliation(s)
- Emily P Hyle
- Medical Practice Evaluation Center, Massachusetts General Hospital , Boston, MA , USA
- Harvard Medical School , Boston, MA , USA
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital , Boston, MA , USA
- Division of Infectious Diseases, Massachusetts General Hospital , Boston, MA , USA
- Department of Medicine, Massachusetts General Hospital , Boston, MA , USA
| | - Mylinh H Le
- Medical Practice Evaluation Center, Massachusetts General Hospital , Boston, MA , USA
| | - Sowmya R Rao
- Department of Global Health, Boston University School of Public Health , Boston, MA , USA
| | - Nora M Mulroy
- Medical Practice Evaluation Center, Massachusetts General Hospital , Boston, MA , USA
| | - Allison T Walker
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention , Atlanta, GA , USA
| | - Edward T Ryan
- Harvard Medical School , Boston, MA , USA
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital , Boston, MA , USA
- Division of Infectious Diseases, Massachusetts General Hospital , Boston, MA , USA
- Department of Medicine, Massachusetts General Hospital , Boston, MA , USA
- Harvard T.H. Chan School of Public Heath , Boston, MA , USA
| | - Regina C LaRocque
- Harvard Medical School , Boston, MA , USA
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital , Boston, MA , USA
- Division of Infectious Diseases, Massachusetts General Hospital , Boston, MA , USA
- Department of Medicine, Massachusetts General Hospital , Boston, MA , USA
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26
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Schroeder PH, Brenner LN, Kaur V, Cromer SJ, Armstrong K, LaRocque RC, Ryan ET, Meigs JB, Florez JC, Charles RC, Mercader JM, Leong A. Proteomic analysis of cardiometabolic biomarkers and predictive modeling of severe outcomes in patients hospitalized with COVID-19. Cardiovasc Diabetol 2022; 21:136. [PMID: 35864532 PMCID: PMC9301894 DOI: 10.1186/s12933-022-01569-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/08/2022] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The high heterogeneity in the symptoms and severity of COVID-19 makes it challenging to identify high-risk patients early in the disease. Cardiometabolic comorbidities have shown strong associations with COVID-19 severity in epidemiologic studies. Cardiometabolic protein biomarkers, therefore, may provide predictive insight regarding which patients are most susceptible to severe illness from COVID-19. METHODS In plasma samples collected from 343 patients hospitalized with COVID-19 during the first wave of the pandemic, we measured 92 circulating protein biomarkers previously implicated in cardiometabolic disease. We performed proteomic analysis and developed predictive models for severe outcomes. We then used these models to predict the outcomes of out-of-sample patients hospitalized with COVID-19 later in the surge (N = 194). RESULTS We identified a set of seven protein biomarkers predictive of admission to the intensive care unit and/or death (ICU/death) within 28 days of presentation to care. Two of the biomarkers, ADAMTS13 and VEGFD, were associated with a lower risk of ICU/death. The remaining biomarkers, ACE2, IL-1RA, IL6, KIM1, and CTSL1, were associated with higher risk. When used to predict the outcomes of the future, out-of-sample patients, the predictive models built with these protein biomarkers outperformed all models built from standard clinical data, including known COVID-19 risk factors. CONCLUSIONS These findings suggest that proteomic profiling can inform the early clinical impression of a patient's likelihood of developing severe COVID-19 outcomes and, ultimately, accelerate the recognition and treatment of high-risk patients.
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Affiliation(s)
- Philip H Schroeder
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura N Brenner
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Varinderpal Kaur
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara J Cromer
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Katrina Armstrong
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Regina C LaRocque
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Edward T Ryan
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James B Meigs
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, 100 Cambridge St 16th Floor, Boston, MA, 02114, USA
| | - Jose C Florez
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Josep M Mercader
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Aaron Leong
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, 100 Cambridge St 16th Floor, Boston, MA, 02114, USA.
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27
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Kruse GR, Pelton-Cairns L, Taveras EM, Dargon-Hart S, Gundersen DA, Lee RM, Bierer BE, Lawlor E, LaRocque RC, Marcus JL, Davies ME, Emmons KM. Implementing expanded COVID-19 testing in Massachusetts community health centers through community partnerships: Protocol for an interrupted time series and stepped wedge study design. Contemp Clin Trials 2022; 118:106783. [PMID: 35533978 PMCID: PMC9076025 DOI: 10.1016/j.cct.2022.106783] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/27/2022] [Revised: 04/15/2022] [Accepted: 05/01/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Community Health Centers (CHCs) are a critical source of care for low-income and non-privately insured populations. During the pandemic, CHCs have leveraged their infrastructure and role as a trusted source of care to engage the communities they serve in COVID-19 testing. METHODS To directly address the impact that COVID-19 has had on historically marginalized populations in Massachusetts, we designed a study of community-engaged COVID-19 testing expansion: (1) leveraging existing partnerships to accelerate COVID-19 testing and rapidly disseminate effective implementation strategies; (2) incorporating efforts to address key barriers to testing participation in communities at increased risk for COVID-19; (3) further developing partnerships between communities and CHCs to address testing access and disparities; (4) grounding the study in the development of a shared ethical framework for advancing equity in situations of scarcity; and (5) developing mechanisms for communication and science translation to support community outreach. We use a controlled interrupted time series design, comparing number of COVID-19 tests overall and among people identified as members of high-risk groups served by intervention CHCs compared with six matched control CHCs in Massachusetts, followed by a stepped wedge design to pilot test strategies for tailored outreach by CHCs. CONCLUSIONS Here, we describe a community-partnered strategy to accelerate COVID-19 testing in historically marginalized populations that provides ongoing resources to CHCs for addressing testing needs in their communities. The study aligns with principles of community-engaged research including shared leadership, adequate resources for community partners, and the flexibility to respond to changing needs over time.
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Affiliation(s)
- Gina R Kruse
- Massachusetts General Hospital, Division of General Internal Medicine, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02114, USA.
| | | | - Elsie M Taveras
- Harvard Medical School, Boston, MA 02114, USA; Massachusetts General Hospital, Kraft Center for Community Health, Boston, MA 02114, USA; Massachusetts General Hospital, Division of Academic Pediatrics, Boston, MA 02114, USA
| | - Susan Dargon-Hart
- Massachusetts League of Community Health Centers, Boston, MA 02114, USA
| | - Daniel A Gundersen
- Dana Farber Cancer Institute, Division of Population Sciences, Boston, MA, USA
| | - Rebekka M Lee
- Harvard T.H. Chan School of Public Health, Department of Social and Behavioral Sciences, Boston, MA, USA; Harvard Catalyst | The Harvard Clinical and Translational Science Center, Boston, MA, USA
| | - Barbara E Bierer
- Harvard Medical School, Boston, MA 02114, USA; Harvard Catalyst | The Harvard Clinical and Translational Science Center, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Erica Lawlor
- Harvard Medical School, Boston, MA 02114, USA; Harvard Catalyst | The Harvard Clinical and Translational Science Center, Boston, MA, USA
| | - Regina C LaRocque
- Harvard Medical School, Boston, MA 02114, USA; Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA 02114, USA
| | - Julia L Marcus
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Madeline E Davies
- Massachusetts General Hospital, Kraft Center for Community Health, Boston, MA 02114, USA
| | - Karen M Emmons
- Harvard T.H. Chan School of Public Health, Department of Social and Behavioral Sciences, Boston, MA, USA; Harvard Catalyst | The Harvard Clinical and Translational Science Center, Boston, MA, USA
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28
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Bhuiyan TR, Akhtar M, Khaton F, Rahman SIA, Ferdous J, Alamgir A, Rahman M, Kawser Z, Hasan I, Calderwood SB, Harris JB, Charles RC, LaRocque RC, Ryan ET, Banu S, Shirin T, Qadri F. Covishield vaccine induces robust immune responses in Bangladeshi adults. IJID Regions 2022; 3:211-217. [PMID: 35720155 PMCID: PMC9050186 DOI: 10.1016/j.ijregi.2022.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
All participants became seropositive 2 months after receipt of the second dose of vaccine. Comparable antibody responses were observed in both males and females. Participants with previous severe acute respiratory syndrome coronavirus-2 infection showed a robust antibody response. Similar antibody responses were observed in participants with and without comorbidities.
Objective To evaluate severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific antibody responses after Covishield vaccination for 6 months after vaccination. Design SARS-CoV-2-specific antibody responses were assessed by enzyme-linked immunosorbent assay of the recombinant receptor-binding domain of SARS-CoV-2 in 381 adults given the Covishield vaccine at baseline (n=119), 1 month (n=126) and 2 months (n=75) after the first dose, 1 month after the second dose (n=161), and monthly for 3 additional months. Results Over 51% of participants were seropositive at baseline (before vaccination with Covishield), and almost all participants (159/161) became seropositive 1 month after the second dose. Antibody levels peaked 1 month after receipt of the second dose of vaccine, and decreased by 4 months after the first dose; the lowest responses were found 6 months after the first dose, although antibody responses and responder frequencies remained significantly higher compared with baseline (P<0.0001). Compared with younger participants, older participants had lower antibody responses 6 months after the first dose of vaccine (P<0.05). Participants who had previous SARS-CoV-2 infection showed robust higher antibody responses after vaccination. Conclusions These findings help to elucidate the longevity of vaccine-specific antibody responses following vaccination with Covishield, and provide information relevant to the planning of booster doses after the initial two doses of vaccine.
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Affiliation(s)
| | - Marjahan Akhtar
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Fatema Khaton
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | | | - Jannatul Ferdous
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - A.S.M. Alamgir
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Mahbubur Rahman
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Zannat Kawser
- Institute of Developing Sciences and Health Initiatives, Dhaka, Bangladesh
| | - Imrul Hasan
- Institute of Developing Sciences and Health Initiatives, Dhaka, Bangladesh
| | - Stephen Beaven Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edward Thomas Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sayera Banu
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
- Corresponding author: Address: Mucosal Immunology and Vaccinology Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh. Tel.: +880 (0)2 2222 77001 10, Ext. 2431.
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29
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Tolan NV, Sherman AC, Zhou G, Nabel KG, Desjardins M, Melanson S, Kanjilal S, Moheed S, Kupelian J, Kaufman RM, Ryan ET, LaRocque RC, Branda JA, Dighe AS, Abraham J, Baden LR, Charles RC, Turbett SE. The Effect of Vaccine Type and SARS-CoV-2 Lineage on Commercial SARS-CoV-2 Serologic and Pseudotype Neutralization Assays in mRNA Vaccine Recipients. Microbiol Spectr 2022; 10:e0021122. [PMID: 35311584 PMCID: PMC9045317 DOI: 10.1128/spectrum.00211-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 01/21/2022] [Accepted: 02/20/2022] [Indexed: 12/24/2022] Open
Abstract
The use of anti-spike (S) serologic assays as surrogate measurements of SARS-CoV-2 vaccine induced immunity will be an important clinical and epidemiological tool. The characteristics of a commercially available anti-S antibody assay (Roche Elecsys anti-SARS-CoV-2 S) were evaluated in a cohort of vaccine recipients. Levels were correlated with pseudotype neutralizing antibodies (NAb) across SARS-CoV-2 variants. We recruited adults receiving a two-dose series of mRNA-1273 or BNT162b2 and collected serum at scheduled intervals up to 8 months post-first vaccination. Anti-S and NAb levels were measured, and correlation was evaluated by (i) vaccine type and (ii) SARS-CoV-2 variant (wild-type, Alpha, Beta, Gamma, and three constructs Day 146*, Day 152*, and RBM-2). Forty-six mRNA vaccine recipients were enrolled. mRNA-1273 vaccine recipients had higher peak anti-S and NAb levels compared with BNT162b2 (P < 0.001 for anti-S levels; P < 0.05 for NAb levels). When anti-S and NAb levels were compared, there was good correlation (all r values ≥ 0.85) in both BNT162b2 and mRNA-1273 vaccine recipients across all evaluated variants; however, these correlations were nonlinear in nature. Lower correlation was identified between anti-S and NAb for the Beta variant (r = 0.88) compared with the wild-type (WT) strain (r = 0.94). Finally, the degree of neutralizing activity at any given anti-S level was lower for each variant compared with that of the WT strain, (P < 0.001). Although the Roche anti-S assay correlates well with NAb levels, this association is affected by vaccine type and SARS-CoV-2 variant. These variables must be considered when interpreting anti-S levels. IMPORTANCE We evaluated anti-spike antibody concentrations in healthy mRNA vaccinated individuals and compared these concentrations to values obtained from pseudotype neutralization assays targeting SARS-CoV-2 variants of concern to determine how well anti-spike antibodies correlate with neutralizing titers, which have been used as a marker of immunity from COVID-19 infection. We found high peak anti-spike concentrations in these individuals, with significantly higher levels seen in mRNA-1273 vaccine recipients. When we compared anti-spike and pseudotype neuralization titers, we identified good correlation; however, this correlation was affected by both vaccine type and variant, illustrating the difficulty of applying a "one size fits all" approach to anti-spike result interpretation. Our results support CDC recommendations to discourage anti-spike antibody testing to assess for immunity after vaccination and cautions providers in their interpretations of these results as a surrogate of protection in COVID-vaccinated individuals.
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Affiliation(s)
- Nicole V. Tolan
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amy C. Sherman
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Guohai Zhou
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Michaël Desjardins
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Stacy Melanson
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sanjat Kanjilal
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Serina Moheed
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John Kupelian
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Richard M. Kaufman
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Edward T. Ryan
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Regina C. LaRocque
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Anand S. Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Abraham
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Lindsey R. Baden
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Richelle C. Charles
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah E. Turbett
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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30
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Bangs AC, Gastañaduy P, Neilan AM, Fiebelkorn AP, Walker AT, Rao SR, Ryan ET, LaRocque RC, Walensky RP, Hyle EP. The Clinical and Economic Impact of Measles-Mumps-Rubella Vaccinations to Prevent Measles Importations From US Pediatric Travelers Returning From Abroad. J Pediatric Infect Dis Soc 2022; 11:257-266. [PMID: 35333347 PMCID: PMC9214784 DOI: 10.1093/jpids/piac011] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/01/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Pediatric international travelers account for nearly half of measles importations in the United States. Over one third of pediatric international travelers depart the United States without the recommended measles-mumps-rubella (MMR) vaccinations: 2 doses for travelers ≥12 months and 1 dose for travelers 6 to <12 months. METHODS We developed a model to compare 2 strategies among a simulated cohort of international travelers (6 months to <6 years): (1) No pretravel health encounter (PHE): travelers depart with baseline MMR vaccination status; (2) PHE: MMR-eligible travelers are offered vaccination. All pediatric travelers experience a destination-specific risk of measles exposure (mean, 30 exposures/million travelers). If exposed to measles, travelers' age and MMR vaccination status determine the risk of infection (range, 3%-90%). We included costs of medical care, contact tracing, and lost wages from the societal perspective. We varied inputs in sensitivity analyses. Model outcomes included projected measles cases, costs, and incremental cost-effectiveness ratios ($/quality-adjusted life year [QALY], cost-effectiveness threshold ≤$100 000/QALY). RESULTS Compared with no PHE, PHE would avert 57 measles cases at $9.2 million/QALY among infant travelers and 7 measles cases at $15.0 million/QALY among preschool-aged travelers. Clinical benefits of PHE would be greatest for infants but cost-effective only for travelers to destinations with higher risk for measles exposure (ie, ≥160 exposures/million travelers) or if more US-acquired cases resulted from an infected traveler, such as in communities with limited MMR coverage. CONCLUSIONS Pretravel MMR vaccination provides the greatest clinical benefit for infant travelers and can be cost-effective before travel to destinations with high risk for measles exposure or from communities with low MMR vaccination coverage.
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Affiliation(s)
- Audrey C Bangs
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paul Gastañaduy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anne M Neilan
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, USA,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Division of General Academic Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Parker Fiebelkorn
- Immunization Services Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Allison Taylor Walker
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sowmya R Rao
- MGH Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Travelers' Advice and Immunization Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Travelers' Advice and Immunization Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rochelle P Walensky
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, USA,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily P Hyle
- Corresponding Author: Emily P. Hyle, MD, MSc, Division of Infectious Diseases, Massachusetts General Hospital, 100 Cambridge Street, 16th Floor, Boston, MA 02114, USA. E-mail:
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31
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Bhuiyan TR, Akhtar M, Akter A, Khaton F, Rahman SIA, Ferdous J, Nazneen A, Sumon SA, Banik KC, Bablu AR, Alamgir A, Rahman M, Tony SR, Hossain K, Calderwood SB, Charles RC, Ryan ET, LaRocque RC, Harris JB, Rahman M, Chakraborty N, Rahman M, Arifeen SE, Flora MS, Shirin T, Banu S, Qadri F. Seroprevalence of SARS-CoV-2 antibodies in Bangladesh related to novel coronavirus infection. IJID Regions 2022; 2:198-203. [PMID: 35721426 PMCID: PMC8809641 DOI: 10.1016/j.ijregi.2022.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 01/11/2023]
Abstract
30% of the Bangladeshi population were found to be seropositive for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) immunoglobulin G antibodies. The highest seroprevalence rate (64%) was found in slum areas in Bangladesh. Thirty-eight percent and 29% of participants from urban and rural areas were SARS-CoV-2 seropositive. The highest seroprevalence rate for coronavirus disease 2019 was observed in August 2020.
Design A cross-sectional study was conducted amongst household members in 32 districts of Bangladesh to build knowledge about disease epidemiology and seroepidemiology of coronavirus disease 2019 (COVID-19). Objective Antibody responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) were assessed in people between April and October 2020. Results The national seroprevalence rates of immunoglobulin G (IgG) and IgM were estimated to be 30.4% and 39.7%, respectively. In Dhaka, the seroprevalence of IgG was 35.4% in non-slum areas and 63.5% in slum areas. In areas outside of Dhaka, the seroprevalence of IgG was 37.5% in urban areas and 28.7% in rural areas. Between April and October 2020, the highest seroprevalence rate (57% for IgG and 64% for IgM) was observed in August. IgM antibody was more prevalent in younger participants, while older participants had more frequent IgG seropositivity. Follow-up specimens from patients with COVID-19 and their household members suggested that both IgG and IgM seropositivity increased significantly at day 14 and day 28 compared with day 1 after enrolment. Conclusions: SARS-CoV-2 had spread extensively in Bangladesh by October 2020. This highlights the importance of monitoring seroprevalence data, particularly with the emergence of new SARS-CoV-2 variants over time.
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Affiliation(s)
| | - Marjahan Akhtar
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Aklima Akter
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Fatema Khaton
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Jannatul Ferdous
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Arifa Nazneen
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shariful Amin Sumon
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Kajal C. Banik
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Arifur Rahman Bablu
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - A.S.M. Alamgir
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Mahbubur Rahman
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Selim Reza Tony
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Khaled Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Mahmudur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shams El Arifeen
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Sayera Banu
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
- Corresponding author. Mucosal Immunology and Vaccinology Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh. Tel.: +880 (0)2 2222 77001 10, Ext 2431.
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32
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Nabel KG, Clark SA, Shankar S, Pan J, Clark LE, Yang P, Coscia A, McKay LGA, Varnum HH, Brusic V, Tolan NV, Zhou G, Desjardins M, Turbett SE, Kanjilal S, Sherman AC, Dighe A, LaRocque RC, Ryan ET, Tylek C, Cohen-Solal JF, Darcy AT, Tavella D, Clabbers A, Fan Y, Griffiths A, Correia IR, Seagal J, Baden LR, Charles RC, Abraham J. Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science 2022; 375:eabl6251. [PMID: 34855508 PMCID: PMC9127715 DOI: 10.1126/science.abl6251] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- BNT162 Vaccine/immunology
- Betacoronavirus/immunology
- COVID-19/immunology
- COVID-19/virology
- Cross Reactions
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Epitopes
- Evolution, Molecular
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Polysaccharides/analysis
- Protein Binding
- Protein Domains
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Viral Pseudotyping
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Affiliation(s)
- Katherine G. Nabel
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A. Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sundaresh Shankar
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Junhua Pan
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lars E. Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Pan Yang
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Adrian Coscia
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G. A. McKay
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Haley H. Varnum
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Vesna Brusic
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole V. Tolan
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Guohai Zhou
- Center for Clinical Investigation, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Michaël Desjardins
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Centre Hospitalier de l’Université de Montréal, Montreal QC H2X 0C1, Canada
| | - Sarah E. Turbett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Amy C. Sherman
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anand Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Edward T. Ryan
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Casey Tylek
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | | | | | | | | | - Yao Fan
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Jane Seagal
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | - Lindsey R. Baden
- Center for Clinical Investigation, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Akter A, Ahmed T, Tauheed I, Akhtar M, Rahman SIA, Khaton F, Ahmmed F, Ferdous J, Afrad MH, Kawser Z, Hossain M, Khondaker R, Hasnat MA, Sumon MA, Rashed A, Ghosh S, Calderwood SB, Charles RC, Ryan ET, Khatri P, Maecker HT, Obermoser G, Pulendran B, Clemens JD, Banu S, Shirin T, LaRocque RC, Harris JB, Bhuiyan TR, Chowdhury F, Qadri F. Disease characteristics and serological responses in patients with differing severity of COVID-19 infection: A longitudinal cohort study in Dhaka, Bangladesh. PLoS Negl Trop Dis 2022; 16:e0010102. [PMID: 34982773 PMCID: PMC8759637 DOI: 10.1371/journal.pntd.0010102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/14/2022] [Accepted: 12/17/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND COVID-19 caused by SARS-CoV-2 ranges from asymptomatic to severe disease and can cause fatal and devastating outcome in many cases. In this study, we have compared the clinical, biochemical and immunological parameters across the different disease spectrum of COVID-19 in Bangladeshi patients. METHODOLOGY/PRINCIPAL FINDINGS This longitudinal study was conducted in two COVID-19 hospitals and also around the community in Dhaka city in Bangladesh between November 2020 to March 2021. A total of 100 patients with COVID-19 infection were enrolled and classified into asymptomatic, mild, moderate and severe cases (n = 25/group). In addition, thirty age and sex matched healthy participants were enrolled and 21 were analyzed as controls based on exclusion criteria. After enrollment (study day1), follow-up visits were conducted on day 7, 14 and 28 for the cases. Older age, male gender and co-morbid conditions were the risk factors for severe COVID-19 disease. Those with moderate and severe cases of infection had low lymphocyte counts, high neutrophil counts along with a higher neutrophil-lymphocyte ratio (NLR) at enrollment; this decreased to normal range within 42 days after the onset of symptom. At enrollment, D-dimer, CRP and ferritin levels were elevated among moderate and severe cases. The mild, moderate, and severe cases were seropositive for IgG antibody by day 14 after enrollment. Moderate and severe cases showed significantly higher IgM and IgG levels of antibodies to SARS-CoV-2 compared to mild and asymptomatic cases. CONCLUSION/SIGNIFICANCE We report on the clinical, biochemical, and hematological parameters associated with the different severity of COVID-19 infection. We also show different profile of antibody response against SARS-CoV-2 in relation to disease severity, especially in those with moderate and severe disease manifestations compared to the mild and asymptomatic infection.
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Affiliation(s)
- Afroza Akter
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Tasnuva Ahmed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Imam Tauheed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Marjahan Akhtar
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Sadia Isfat Ara Rahman
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Fatema Khaton
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Faisal Ahmmed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Jannatul Ferdous
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Mokibul Hassan Afrad
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Zannat Kawser
- Institute for Developing Science & Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Mohabbat Hossain
- Institute for Developing Science & Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Rabeya Khondaker
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | | | | | - Asif Rashed
- Mugda Medical College & Hospital, Dhaka, Bangladesh
| | - Shuvro Ghosh
- Mugda Medical College & Hospital, Dhaka, Bangladesh
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Purvesh Khatri
- Stanford University, Stanford, California, United States of America
| | | | | | - Bali Pulendran
- Stanford University, Stanford, California, United States of America
| | - John D. Clemens
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
- UCLA Fielding School of Public Health, Los Angeles, California, United States of America (JD Clemens MD)
- Korea University School of Medicine, Seoul, South Korea (JD Clemens MD)
| | - Sayera Banu
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Taufiqur Rahman Bhuiyan
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Fahima Chowdhury
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh)
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Le MH, Rao SR, Walker AT, Ryan ET, LaRocque RC, Hyle EP. 738. Comparison of Characteristics of US International Travelers Seeking Pretravel Health Consultations at US Global TravEpiNet Sites Before and During the COVID-19 Pandemic. Open Forum Infect Dis 2021. [PMCID: PMC8644841 DOI: 10.1093/ofid/ofab466.935] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background In January–March 2020, the Centers for Disease Control and Prevention (CDC) issued multiple warnings regarding COVID-19 travel-associated risks. We sought to describe US travelers seeking pretravel consultation regarding international travel at US Global TravEpiNet (GTEN) sites before and after the initial COVID-19 travel warnings. Methods We prospectively collected data at 22 GTEN sites pre-COVID-19 (January–December 2019) and 18 GTEN sites during the COVID-19 pandemic (April 2020–March 2021). We excluded travelers evaluated during January–March 2020, when CDC travel guidance was evolving rapidly. Travelers used standardized questionnaires to self-report data regarding demographics and travel-related characteristics. Providers confirmed these data and documented their recommendations during pretravel consultation, which could be performed virtually. We conducted descriptive analyses of differences in demographics, travel-related characteristics, vaccinations, and medications (SAS v9.4; Cary, NC). Results Compared with 16,903 pre-COVID-19 consultations, only 1,564 consultations occurred during the COVID-19 pandemic, a 90% reduction (Table). During COVID-19, a greater proportion of travelers were children aged 1–5 years, visiting friends and relatives (VFR), with itineraries ≥ 30 days, and going to Africa; a smaller proportion of travelers were aged > 55 years, or traveling to Southeast Asia or the Western Pacific. During COVID-19, fewer vaccine-eligible travelers received vaccines at the pretravel consultation except for yellow fever, and a greater proportion were referred to another provider for vaccination (Figure). Table. Demographics and travel-related characteristics of international travelers seeking pretravel consultation at Global TravEpiNet sites before and during the COVID-19 pandemic ![]()
Table continued. Demographics and travel-related characteristics of international travelers seeking pretravel consultation at Global TravEpiNet sites before and during the COVID-19 pandemic ![]()
Figure. Vaccinations and reasons for nonvaccination among vaccine-eligible international travelers at pretravel consultations at Global TravEpiNet (GTEN) sites before and during the COVID-19 pandemic. ![]()
Among vaccine-eligible travelers, we summarized those who were vaccinated at the visit (blue) and not vaccinated (orange). We then categorized reasons for nonvaccination into: provider decision (solid), referral to another provider (dots), traveler refusal (striped), or other (hatched). COVID-19 vaccination was not available at GTEN sites during the analysis period; although COVID-19 vaccinations outside of GTEN sites might have affected vaccination recommendations, they were unlikely to have had a large effect given their limited availability in January-March 2021. Conclusion Compared with pre-COVID-19, US travelers seeking pretravel consultations at GTEN sites during the pandemic might be at higher risk for travel-related infections given VFR status, traveling for ≥ 30 days, and going to Africa. Fewer vaccine-eligible travelers were vaccinated at pretravel consultations, which could reflect more virtual pretravel consultations. Counseling and vaccination for international travelers continue to be priorities during the COVID-19 pandemic. Disclosures All Authors: No reported disclosures
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Affiliation(s)
- Mylinh H Le
- Medical Practice Evaluation Center, Boston, MA
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Sridhar S, Worby C, Bronson R, Turbett S, Harris J, Ryan ET, Earl A, LaRocque RC. 180. Alterations to the Gut Microbiomes and Acquisition of Bacteria Resistance Elements among US International Travelers. Open Forum Infect Dis 2021. [PMCID: PMC8644942 DOI: 10.1093/ofid/ofab466.180] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background This study investigated the impact of international travel on the acquisition and carriage of antimicrobial resistance (AMR). We prospectively assessed U.S. international travelers for the acquisition of resistant Enterobacterales species and evaluated changes in travelers’ gut microbiomes. Methods Metagenomic sequencing was performed on DNA extracted from pre- and post-travel stool samples of 273 U.S. international travelers. We used Kraken2 to assess microbial gut composition and analyzed antibiotic resistance gene (ARG) content using the Resistance Gene Identifier (RGI) and ResFinder, and read mapping to ARG databases. We assessed the change in gut profile and resistome associated with (i) all international travel; (ii) travel to specific geographic regions; and (iii) traveler’s diarrhea. Results International travel resulted in a perturbation of the gut microbiome, which was greater in travelers receiving treatment for diarrhea during travel (p = 4E-5). There was an overall loss in microbial diversity following travel, regardless of health outcome (p = 0.011); this was most consistently observed in travelers to South East Asia (SEA) (loss of gut diversity in 81% of SEA travelers). 78% of all travelers had a higher relative abundance of E. coli after travel, including 85% of travelers who acquired AMR bacteria during travel. Travel to South Asia was also associated with a significantly greater increase of E. coli relative to other destinations (p = 0.04). Additionally, the relative abundance of Pasteurellales was higher in the pre-travel samples of those who subsequently acquired AMR bacteria (FDR = 0.08). Furthermore, there was a significant increase in ARG content among the post-travel samples, with regional differences in the magnitude of acquisition (Figure 1). 72% of all travelers had a greater resistance burden post-travel. SEA was associated with the greatest increase in resistome diversity, while South America was associated with the greatest increase in overall ARG content. Resistance genes present in the gut microbiome. ![]()
Genes mapping to the Comprehensive Antibiotic Resistance Database were measured pre- (x-axis) and post-travel (y-axis) to assess the acquisition of resistance genes in association with travel, distinguished by geographic region. Colors indicate geographic regions visited by travelers: South America (red), South East Asia (blue), South Asia (green), Eastern Africa (purple), Southern Africa (orange), Other (grey). Conclusion International travel is associated with a perturbation in the gut microbial community, with the acquisition of AMR bacteria and genes, and an increase in the relative abundance of E. coli. These perturbations following travel may be important factors in the global spread of AMR. Disclosures All Authors: No reported disclosures
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Affiliation(s)
| | - Colin Worby
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ryan Bronson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | - Ashlee Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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Ryan ET, Leung DT, Jensen O, Weil AA, Bhuiyan TR, Khan AI, Chowdhury F, LaRocque RC, Harris JB, Calderwood SB, Qadri F, Charles RC. Systemic, Mucosal, and Memory Immune Responses following Cholera. Trop Med Infect Dis 2021; 6:192. [PMID: 34842841 PMCID: PMC8628923 DOI: 10.3390/tropicalmed6040192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 01/13/2023] Open
Abstract
Vibrio cholerae O1, the major causative agent of cholera, remains a significant public health threat. Although there are available vaccines for cholera, the protection provided by killed whole-cell cholera vaccines in young children is poor. An obstacle to the development of improved cholera vaccines is the need for a better understanding of the primary mechanisms of cholera immunity and identification of improved correlates of protection. Considerable progress has been made over the last decade in understanding the adaptive and innate immune responses to cholera disease as well as V. cholerae infection. This review will assess what is currently known about the systemic, mucosal, memory, and innate immune responses to clinical cholera, as well as recent advances in our understanding of the mechanisms and correlates of protection against V. cholerae O1 infection.
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Affiliation(s)
- Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (E.T.R.); (R.C.L.); (J.B.H.); (S.B.C.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Daniel T. Leung
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; (D.T.L.); (O.J.)
| | - Owen Jensen
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; (D.T.L.); (O.J.)
| | - Ana A. Weil
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98109, USA;
| | - Taufiqur Rahman Bhuiyan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (T.R.B.); (A.I.K.); (F.C.); (F.Q.)
| | - Ashraful Islam Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (T.R.B.); (A.I.K.); (F.C.); (F.Q.)
| | - Fahima Chowdhury
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (T.R.B.); (A.I.K.); (F.C.); (F.Q.)
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (E.T.R.); (R.C.L.); (J.B.H.); (S.B.C.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (E.T.R.); (R.C.L.); (J.B.H.); (S.B.C.)
- Department of Pediatrics, MassGeneral Hospital for Children, Boston, MA 02114, USA
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA 02115, USA
- Division of Pediatric Global Health, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (E.T.R.); (R.C.L.); (J.B.H.); (S.B.C.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (T.R.B.); (A.I.K.); (F.C.); (F.Q.)
| | - Richelle C. Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (E.T.R.); (R.C.L.); (J.B.H.); (S.B.C.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Abstract
PURPOSE OF REVIEW Antimicrobial resistance (AMR) in bacteria poses a major risk to global public health, with many factors contributing to the observed increase in AMR. International travel is one recognized contributor. The purpose of this review is to summarize current knowledge regarding the acquisition, carriage and spread of AMR bacteria by international travelers. RECENT FINDINGS Recent studies have highlighted that travel is an important risk factor for the acquisition of AMR bacteria, with approximately 30% of studied travelers returning with an acquired AMR bacterium. Epidemiological studies have shown there are three major risk factors for acquisition: travel destination, antimicrobial usage and travelers' diarrhea (TD). Analyses have begun to illustrate the AMR genes that are acquired and spread by travelers, risk factors for acquisition and carriage of AMR bacteria, and local transmission of imported AMR organisms. SUMMARY International travel is a contributor to the acquisition and dissemination of AMR organisms globally. Efforts to reduce the burden of AMR organisms should include a focus on international travelers. Routine genomic surveillance would further elucidate the role of international travel in the global spread of AMR bacteria.
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Affiliation(s)
- Sushmita Sridhar
- Division of Infectious Diseases, Massachusetts General Hospital
- Department of Medicine, Harvard Medical School
| | - Sarah E. Turbett
- Division of Infectious Diseases, Massachusetts General Hospital
- Department of Medicine, Harvard Medical School
- Department of Pathology
| | - Jason B. Harris
- Division of Pediatric Global Health, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital
- Department of Medicine, Harvard Medical School
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38
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Zabaleta N, Dai W, Bhatt U, Hérate C, Maisonnasse P, Chichester JA, Sanmiguel J, Estelien R, Michalson KT, Diop C, Maciorowski D, Dereuddre-Bosquet N, Cavarelli M, Gallouët AS, Naninck T, Kahlaoui N, Lemaitre J, Qi W, Hudspeth E, Cucalon A, Dyer CD, Pampena MB, Knox JJ, LaRocque RC, Charles RC, Li D, Kim M, Sheridan A, Storm N, Johnson RI, Feldman J, Hauser BM, Contreras V, Marlin R, Tsong Fang RH, Chapon C, van der Werf S, Zinn E, Ryan A, Kobayashi DT, Chauhan R, McGlynn M, Ryan ET, Schmidt AG, Price B, Honko A, Griffiths A, Yaghmour S, Hodge R, Betts MR, Freeman MW, Wilson JM, Le Grand R, Vandenberghe LH. An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates. Cell Host Microbe 2021; 29:1437-1453.e8. [PMID: 34428428 PMCID: PMC8346325 DOI: 10.1016/j.chom.2021.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 06/14/2021] [Revised: 07/12/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 pandemic has affected more than 185 million people worldwide resulting in over 4 million deaths. To contain the pandemic, there is a continued need for safe vaccines that provide durable protection at low and scalable doses and can be deployed easily. Here, AAVCOVID-1, an adeno-associated viral (AAV), spike-gene-based vaccine candidate demonstrates potent immunogenicity in mouse and non-human primates following a single injection and confers complete protection from SARS-CoV-2 challenge in macaques. Peak neutralizing antibody titers are sustained at 1 year and complemented by functional memory T cell responses. The AAVCOVID vector has no relevant pre-existing immunity in humans and does not elicit cross-reactivity to common AAVs used in gene therapy. Vector genome persistence and expression wanes following injection. The single low-dose requirement, high-yield manufacturability, and 1-month stability for storage at room temperature may make this technology well suited to support effective immunization campaigns for emerging pathogens on a global scale.
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Affiliation(s)
- Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Wenlong Dai
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Urja Bhatt
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Cécile Hérate
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Jessica A Chichester
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julio Sanmiguel
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Reynette Estelien
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Kristofer T Michalson
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cheikh Diop
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Dawid Maciorowski
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mariangela Cavarelli
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Anne-Sophie Gallouët
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Julien Lemaitre
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Wenbin Qi
- Novartis Gene Therapies, San Diego, CA, USA
| | | | - Allison Cucalon
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Cecilia D Dyer
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Betina Pampena
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James J Knox
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Dan Li
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Maya Kim
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Abigail Sheridan
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Nadia Storm
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rebecca I Johnson
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Vanessa Contreras
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Raphaël Ho Tsong Fang
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Catherine Chapon
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France; National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Eric Zinn
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Aisling Ryan
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Dione T Kobayashi
- Translational Innovation Fund, Mass General Brigham Innovation, Cambridge, MA, USA
| | - Ruchi Chauhan
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Marion McGlynn
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | - Anna Honko
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | - Michael R Betts
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mason W Freeman
- Center for Computational & Integrative Biology, Department of Medicine, and Translational Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James M Wilson
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France.
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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Aktar A, Rahman MA, Afrin S, Akter A, Uddin T, Yasmin T, Sami MIN, Dash P, Jahan SR, Chowdhury F, Khan AI, LaRocque RC, Charles RC, Bhuiyan TR, Mandlik A, Kelly M, Kováč P, Xu P, Calderwood SB, Harris JB, Qadri F, Ryan ET. Correction: Plasma and memory B cell responses targeting O-specific polysaccharide (OSP) are associated with protection against Vibrio cholerae O1 infection among household contacts of cholera patients in Bangladesh. PLoS Negl Trop Dis 2021; 15:e0009616. [PMID: 34280200 PMCID: PMC8289001 DOI: 10.1371/journal.pntd.0009616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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40
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Anahtar MN, Shaw BM, Slater D, Byrne EH, Botti-Lodovico Y, Adams G, Schaffner SF, Eversley J, McGrath GEG, Gogakos T, Lennerz J, Marble HD, Ritterhouse LL, Batten JM, Georgantas NZ, Pellerin R, Signorelli S, Thierauf J, Kemball M, Happi C, Grant DS, Ndiaye D, Siddle KJ, Mehta SB, Harris JB, Ryan ET, Pierce VM, LaRocque RC, Lemieux JE, Sabeti PC, Rosenberg ES, Branda JA, Turbett SE. Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay. J Clin Pathol 2021; 74:496-503. [PMID: 34049977 PMCID: PMC8311084 DOI: 10.1136/jclinpath-2020-207128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/21/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 12/31/2022]
Abstract
Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.
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Affiliation(s)
- Melis N Anahtar
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bennett M Shaw
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Damien Slater
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elizabeth H Byrne
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Yolanda Botti-Lodovico
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Gordon Adams
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stephen F Schaffner
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jacqueline Eversley
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Graham E G McGrath
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tasos Gogakos
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jochen Lennerz
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hetal Desai Marble
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lauren L Ritterhouse
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julie M Batten
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - N Zeke Georgantas
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rebecca Pellerin
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sylvia Signorelli
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julia Thierauf
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Otorhinolaryngology, University Hospital Heidelberg, Heidelberg, Baden-Württemberg, Germany
| | - Molly Kemball
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Christian Happi
- Department of Biological Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun, Nigeria
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Daouda Ndiaye
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun, Nigeria.,Department of Mycology and Pharmacology, Universite Cheikh Anta Diop, Dakar, Senegal
| | - Katherine J Siddle
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Samar B Mehta
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Jason B Harris
- Department of Pediatrics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Edward T Ryan
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Virginia M Pierce
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob E Lemieux
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA .,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pardis C Sabeti
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA .,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Eric S Rosenberg
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John A Branda
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sarah E Turbett
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA .,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
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41
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Uddin MI, Hossain M, Islam S, Akter A, Nishat NS, Nila TA, Rafique TA, Leung DT, Calderwood SB, Ryan ET, Harris JB, LaRocque RC, Bhuiyan TR, Qadri F. An assessment of potential biomarkers of environment enteropathy and its association with age and microbial infections among children in Bangladesh. PLoS One 2021; 16:e0250446. [PMID: 33886672 PMCID: PMC8061931 DOI: 10.1371/journal.pone.0250446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 04/06/2021] [Indexed: 01/13/2023] Open
Abstract
Interventional studies targeting environment enteropathy (EE) are impeded by the lack of appropriate, validated, non-invasive biomarkers of EE. Thus, we aimed to validate the association of potential biomarkers for EE with enteric infections and nutritional status in a longitudinal birth cohort study. We measured endotoxin core antibody (EndoCab) and soluble CD14 (sCD14) in serum, and myeloperoxidase (MPO) in feces using commercially available enzyme-linked immunosorbent assay (ELISA) kits. We found that levels of serum EndoCab and sCD14 increase with the cumulative incidence of enteric infections. We observed a significant correlation between the fecal MPO level in the children at 24 months of age with the total number of bacterial and viral infections, the total number of parasitic infections, and the total number of diarrheal episodes and diarrheal duration. We observed that the levels of serum EndoCab, sCD14, and fecal MPO at 3 months of age were significantly associated with whether children were malnourished at 18 months of age or not. Biomarkers such as fecal MPO, serum EndoCab and sCD14 in children at an early age may be useful as a measure of cumulative burden of preceding enteric infections, which are predictive of subsequent malnutrition status and may be useful non-invasive biomarkers for EE.
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Affiliation(s)
| | | | - Shahidul Islam
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Aklima Akter
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | | | | | | | - Daniel T. Leung
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Stephen B. Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jason B. Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Firdausi Qadri
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
- * E-mail: (FQ); (TRB)
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42
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Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball ME, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda JA, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown CM, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, MacInnis BL. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science 2021; 371:eabe3261. [PMID: 33303686 PMCID: PMC7857412 DOI: 10.1126/science.abe3261] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
Analysis of 772 complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from early in the Boston-area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, whereas other introductions into the facility had little effect. The second, at an international business conference, produced sustained community transmission and was exported, resulting in extensive regional, national, and international spread. The two events also differed substantially in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help to understand the link between individual clusters and wider community spread.
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Affiliation(s)
- Jacob E Lemieux
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bennett M Shaw
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christine Loreth
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Gordon Adams
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Christopher H Tomkins-Tinch
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lydia A Krasilnikova
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katherine C DeRuff
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Melissa Rudy
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Matthew R Bauer
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Kim A Lagerborg
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Erica Normandin
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sinéad B Chapman
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Steven K Reilly
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Melis N Anahtar
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amber Carter
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Cameron Myhrvold
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Molly E Kemball
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sushma Chaluvadi
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Caroline Cusick
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Katelyn Flowers
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Anna Neumann
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Felecia Cerrato
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Damien Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - David Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jessie M Gaeta
- Institute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA
- Section of General Internal Medicine, Boston University Medical Center, Boston, MA, USA
| | - Travis P Baggett
- Institute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James O'Connell
- Institute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andreas Gnirke
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Tami D Lieberman
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony Philippakis
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Meagan Burns
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Jeremy Luban
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Lawrence C Madoff
- Massachusetts Department of Public Health, Boston, MA, USA
- University of Massachusetts Medical School, Infectious Diseases and Immunology, Worcester, MA 01655, USA
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Virginia M Pierce
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Pediatric Infectious Disease Unit, Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Bronwyn L MacInnis
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
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Zabaleta N, Dai W, Bhatt U, Chichester JA, Sanmiguel J, Estelien R, Michalson KT, Diop C, Maciorowski D, Qi W, Hudspeth E, Cucalon A, Dyer CD, Pampena MB, Knox JJ, LaRocque RC, Charles RC, Li D, Kim M, Sheridan A, Storm N, Johnson RI, Feldman J, Hauser BM, Zinn E, Ryan A, Kobayashi DT, Chauhan R, McGlynn M, Ryan ET, Schmidt AG, Price B, Honko A, Griffiths A, Yaghmour S, Hodge R, Betts MR, Freeman MW, Wilson JM, Vandenberghe LH. Immunogenicity of an AAV-based, room-temperature stable, single dose COVID-19 vaccine in mice and non-human primates. bioRxiv 2021. [PMID: 33442684 DOI: 10.1101/2021.01.05.422952] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 pandemic has affected more than 70 million people worldwide and resulted in over 1.5 million deaths. A broad deployment of effective immunization campaigns to achieve population immunity at global scale will depend on the biological and logistical attributes of the vaccine. Here, two adeno-associated viral (AAV)-based vaccine candidates demonstrate potent immunogenicity in mouse and nonhuman primates following a single injection. Peak neutralizing antibody titers remain sustained at 5 months and are complemented by functional memory T-cells responses. The AAVrh32.33 capsid of the AAVCOVID vaccine is an engineered AAV to which no relevant pre-existing immunity exists in humans. Moreover, the vaccine is stable at room temperature for at least one month and is produced at high yields using established commercial manufacturing processes in the gene therapy industry. Thus, this methodology holds as a very promising single dose, thermostable vaccine platform well-suited to address emerging pathogens on a global scale.
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Walker AT, Gershman MD, Rao SR, LaRocque RC, Ryan ET. Yellow Fever Vaccine Administration at Global TravEpiNet (GTEN) Clinics during a Period of Limited Vaccine Availability in the United States, 2017-2018. Am J Trop Med Hyg 2021; 104:1079-1084. [PMID: 33534766 DOI: 10.4269/ajtmh.19-0859] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 11/20/2020] [Indexed: 11/07/2022] Open
Abstract
In 2016, Sanofi Pasteur (S-P) experienced a manufacturing disruption of yellow fever vaccine (YF-Vax), the only U.S.-licensed YF-Vax, depleting the U.S. supply by mid-2017. Sanofi Pasteur received approval to import Stamaril, S-P's French-manufactured YF-Vax, for use in 260 U.S. civilian clinics under an expanded access investigational new drug program (EAP). The CDC also broadened its YF-Vax indication in early 2018. Our objective was to assess usage at participating Global TravEpiNet (GTEN) clinics, a U.S. CDC-supported national consortium of clinical sites that administer vaccines, during this period of limited availability and changing recommendations. We analyzed 2012-2018 GTEN data for YF-Vax usage, unavailability, and reasons for refusal. We also performed a brief voluntary survey of GTEN sites to better understand their experience during the shortage. Yellow fever vaccine unavailability at certain GTEN clinics was intermittent and recurrent, starting months before total depletion. Unavailability at GTEN clinics peaked weeks before the total depletion. Compared with historic norms, YF-Vax usage following initial vaccine availability limitations did not change until vaccine recommendations were broadened. Refusal of recommended YF-Vax also decreased during this period. Queried sites participating in the EAP felt their supply of vaccine was adequate. Our analysis suggests that in response to depletion of a travel vaccine, an EAP can make an unlicensed product available, patients will participate in such a program, and the program can respond to expanding recommendations for vaccine usage.
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Affiliation(s)
- Allison Taylor Walker
- 1Travelers' Health Branch, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mark D Gershman
- 1Travelers' Health Branch, Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sowmya R Rao
- 2Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts.,3Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
| | - Regina C LaRocque
- 4Travelers' Advice and Immunization Center, Massachusetts General Hospital, Boston, Massachusetts.,5Harvard Medical School, Boston, Massachusetts
| | - Edward T Ryan
- 4Travelers' Advice and Immunization Center, Massachusetts General Hospital, Boston, Massachusetts.,5Harvard Medical School, Boston, Massachusetts.,6Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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45
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Worby CJ, Earl AM, Turbett SE, Becker M, Rao SR, Oliver E, Taylor Walker A, Walters M, Kelly P, Leung DT, Knouse M, Hagmann SHF, Ryan ET, LaRocque RC. Acquisition and Long-term Carriage of Multidrug-Resistant Organisms in US International Travelers. Open Forum Infect Dis 2020; 7:ofaa543. [PMID: 33409326 PMCID: PMC7759211 DOI: 10.1093/ofid/ofaa543] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 08/21/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022] Open
Abstract
We performed prospective screening of stool for multidrug-resistant organisms from 608 US international travelers and identified an acquisition rate of 38% following travel. Carriage rates remained significantly elevated for at least 6 months post-travel. Travel-related diarrhea was a risk factor for acquisition, as well as for long-term carriage upon return.
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Affiliation(s)
- Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Margaret Becker
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sowmya R Rao
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Allison Taylor Walker
- Division of Global Migration and Quarantine, Travelers' Health Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maroya Walters
- Division of Healthcare Quality Promotion, Prevention and Response Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul Kelly
- Bronx Care Center, New York, New York, USA
| | | | - Mark Knouse
- Lehigh Valley Medical Center, Allentown, Pennsylvania, USA
| | | | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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46
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Iyer AS, Jones FK, Nodoushani A, Kelly M, Becker M, Slater D, Mills R, Teng E, Kamruzzaman M, Garcia-Beltran WF, Astudillo M, Yang D, Miller TE, Oliver E, Fischinger S, Atyeo C, Iafrate AJ, Calderwood SB, Lauer SA, Yu J, Li Z, Feldman J, Hauser BM, Caradonna TM, Branda JA, Turbett SE, LaRocque RC, Mellon G, Barouch DH, Schmidt AG, Azman AS, Alter G, Ryan ET, Harris JB, Charles RC. Persistence and decay of human antibody responses to the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 patients. Sci Immunol 2020; 5:eabe0367. [PMID: 33033172 PMCID: PMC7857394 DOI: 10.1126/sciimmunol.abe0367] [Citation(s) in RCA: 442] [Impact Index Per Article: 110.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
We measured plasma and/or serum antibody responses to the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2 in 343 North American patients infected with SARS-CoV-2 (of which 93% required hospitalization) up to 122 days after symptom onset and compared them to responses in 1548 individuals whose blood samples were obtained prior to the pandemic. After setting seropositivity thresholds for perfect specificity (100%), we estimated sensitivities of 95% for IgG, 90% for IgA, and 81% for IgM for detecting infected individuals between 15 and 28 days after symptom onset. While the median time to seroconversion was nearly 12 days across all three isotypes tested, IgA and IgM antibodies against RBD were short-lived with median times to seroreversion of 71 and 49 days after symptom onset. In contrast, anti-RBD IgG responses decayed slowly through 90 days with only 3 seropositive individuals seroreverting within this time period. IgG antibodies to SARS-CoV-2 RBD were strongly correlated with anti-S neutralizing antibody titers, which demonstrated little to no decrease over 75 days since symptom onset. We observed no cross-reactivity of the SARS-CoV-2 RBD-targeted antibodies with other widely circulating coronaviruses (HKU1, 229 E, OC43, NL63). These data suggest that RBD-targeted antibodies are excellent markers of previous and recent infection, that differential isotype measurements can help distinguish between recent and older infections, and that IgG responses persist over the first few months after infection and are highly correlated with neutralizing antibodies.
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Affiliation(s)
- Anita S Iyer
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Forrest K Jones
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ariana Nodoushani
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Meagan Kelly
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Margaret Becker
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Damien Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Mills
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Erica Teng
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Mohammad Kamruzzaman
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | | | - Michael Astudillo
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Diane Yang
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen B Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Stephen A Lauer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Zhenfeng Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - John A Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guillaume Mellon
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Dan H Barouch
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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47
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Shirin T, Bhuiyan TR, Charles RC, Amin S, Bhuiyan I, Kawser Z, Rahat A, Alam AN, Sultana S, Aleem MA, Khan MH, Khan SR, LaRocque RC, Calderwood SB, Ryan ET, Slater DM, Banu S, Clemens J, Harris JB, Flora MS, Qadri F. Antibody responses after COVID-19 infection in patients who are mildly symptomatic or asymptomatic in Bangladesh. Int J Infect Dis 2020; 101:220-225. [PMID: 33031941 PMCID: PMC7534791 DOI: 10.1016/j.ijid.2020.09.1484] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Studies on serological responses following coronavirus disease-2019 (COVID-19) have been published primarily in individuals who are moderately or severely symptomatic, but there are few data from individuals who are mildly symptomatic or asymptomatic. METHODS We measured IgG, IgM, and IgA to the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by using enzyme-linked immunosorbent assay in mildly symptomatic (n = 108) and asymptomatic (n = 63) on days 1, 7, 14, and 30 following RT-PCR confirmation in Bangladesh and when compared with pre-pandemic samples, including healthy controls (n = 73) and individuals infected with other viruses (n = 79). RESULTS Mildly symptomatic individuals developed IgM and IgA responses by day 14 in 72% and 83% of individuals, respectively, while 95% of individuals developed IgG response, and rose to 100% by day 30. In contrast, individuals infected with SARS-CoV-2 but who remained asymptomatic developed antibody responses significantly less frequently, with only 20% positive for IgA and 22% positive for IgM by day 14, and 45% positive for IgG by day 30 after infection. CONCLUSIONS These results confirm immune responses are generated following COVID-19 who develop mildly symptomatic illness. However, those with asymptomatic infection do not respond or have lower antibody levels. These results will impact modeling needed for determining herd immunity generated by natural infection or vaccination.
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Affiliation(s)
- Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | | | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Shaheena Amin
- Infectious Diseases Division, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - Imran Bhuiyan
- Institute for Developing Science & Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Zannat Kawser
- Institute for Developing Science & Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Asifuzaman Rahat
- Institute for Developing Science & Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Ahmed Nawsher Alam
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Sharmin Sultana
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Md Abdul Aleem
- Infectious Diseases Division, icddr,b, Mohakhali, Dhaka, Bangladesh
| | | | | | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Stephen B Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Damien M Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Sayera Banu
- Infectious Diseases Division, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - John Clemens
- Infectious Diseases Division, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | - Firdausi Qadri
- Infectious Diseases Division, icddr,b, Mohakhali, Dhaka, Bangladesh.
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48
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Gandhi AR, Rao SR, Chen LH, Nelson MD, Ryan ET, LaRocque RC, Hyle EP. Prescribing Patterns of Antibiotics for the Self-Treatment of Travelers' Diarrhea in Global TravEpiNet, 2009-2018. Open Forum Infect Dis 2020; 7:ofaa376. [PMID: 33072808 PMCID: PMC7545114 DOI: 10.1093/ofid/ofaa376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 06/08/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Background International travelers are often prescribed antibiotics for self-treatment of travelers' diarrhea (TD), but the benefits and risks of antibiotics are debated. We assessed the prescribing patterns of empiric antibiotics for TD in international travelers evaluated at Global TravEpiNet (GTEN) sites (2009-2018). Methods We performed a prospective, multisite cross-sectional study regarding antibiotic prescriptions for the self-treatment of TD at 31 GTEN sites providing pretravel consultations to adult international travelers. We described traveler demographics, itineraries, and antibiotic(s) prescribed. We used multivariable logistic regressions to assess the association of year of consultation with antibiotic prescribing (yes/no) and class (fluoroquinolones vs azithromycin). We performed interrupted time-series analyses to examine differences in prescribing before and after the Food and Drug Administration (FDA) warning on fluoroquinolones (July 2016). Results Antibiotics were not prescribed in 23 096 (22.2%) of 103 843 eligible pretravel GTEN consultations; azithromycin and fluoroquinolones were most frequently prescribed. Antibiotic prescribing declined significantly each year between 2009 and 2018 (odds ratio [OR], 0.84; 95% CI, 0.79-0.89), as did fluoroquinolone prescribing, relative to azithromycin (OR, 0.77; 95% CI, 0.73-0.82). The rate of decline in fluoroquinolone prescribing was significantly greater after the FDA fluoroquinolone warning (15.3%/year) than before (1.1%/year; P < .001). Conclusions Empiric antibiotics for TD were prescribed in >75% of pretravel GTEN consultations, but antibiotic prescribing declined steadily between 2009 and 2018. Fluoroquinolones were less frequently prescribed than azithromycin, especially after the 2016 FDA fluoroquinolone warning. Emphasis on the risks of antibiotics may influence antibiotic prescribing by providers for empiric treatment of TD.
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Affiliation(s)
- Aditya R Gandhi
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sowmya R Rao
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Lin H Chen
- Travel Medicine Center, Mount Auburn Hospital, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Nelson
- Travel Medicine Center, Mount Auburn Hospital, Cambridge, Massachusetts, USA
| | - Edward T Ryan
- Harvard Medical School, Boston, Massachusetts, USA.,Travelers' Advice and Immunization Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Harvard Medical School, Boston, Massachusetts, USA.,Travelers' Advice and Immunization Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Emily P Hyle
- Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Travelers' Advice and Immunization Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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49
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Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball ME, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda J, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown CM, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, Maclnnis BL. Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. medRxiv 2020:2020.08.23.20178236. [PMID: 32869040 PMCID: PMC7457619 DOI: 10.1101/2020.08.23.20178236] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.
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Affiliation(s)
- Jacob E Lemieux
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bennett M Shaw
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christine Loreth
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Gordon Adams
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Christopher H Tomkins-Tinch
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lydia A Krasilnikova
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katherine C DeRuff
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Melissa Rudy
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Matthew R Bauer
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Kim A Lagerborg
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Erica Normandin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sinead B Chapman
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Steven K Reilly
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Melis N Anahtar
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amber Carter
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Cameron Myhrvold
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Molly E Kemball
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sushma Chaluvadi
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Caroline Cusick
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Katelyn Flowers
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Anna Neumann
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Felecia Cerrato
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Damien Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - John Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - David Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jessie M Gaeta
- lnstitute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA
- Section of General Internal Medicine, Boston University Medical Center, Boston
| | - Travis P Baggett
- lnstitute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James O'Connell
- lnstitute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andreas Gnirke
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Tami D Lieberman
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- lnstitute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony Philippakis
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Meagan Burns
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Jeremy Luban
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Lawrence C Madoff
- Massachusetts Department of Public Health, Boston, MA, USA
- University of Massachusetts Medical School, Infectious Diseases and Immunology, Worcester, MA 01655
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Virginia M Pierce
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Pediatric Infectious Disease Unit, MassGeneral Hospital for Children, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815
| | - Daniel J Park
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Bronwyn L Maclnnis
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA
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Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball ME, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda J, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown CM, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, Maclnnis BL. Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. medRxiv 2020. [PMID: 32869040 DOI: 10.1101/2020.04.12.20059618v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.
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Affiliation(s)
- Jacob E Lemieux
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bennett M Shaw
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christine Loreth
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Gordon Adams
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Christopher H Tomkins-Tinch
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lydia A Krasilnikova
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katherine C DeRuff
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Melissa Rudy
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Matthew R Bauer
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Kim A Lagerborg
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Erica Normandin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sinead B Chapman
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Steven K Reilly
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Melis N Anahtar
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amber Carter
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Cameron Myhrvold
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Molly E Kemball
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sushma Chaluvadi
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Caroline Cusick
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Katelyn Flowers
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Anna Neumann
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Felecia Cerrato
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Damien Slater
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - John Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - David Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jessie M Gaeta
- lnstitute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA.,Section of General Internal Medicine, Boston University Medical Center, Boston
| | - Travis P Baggett
- lnstitute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA.,Division of General Internal Medicine, Massachusetts General Hospital, Boston.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James O'Connell
- lnstitute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA.,Division of General Internal Medicine, Massachusetts General Hospital, Boston.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andreas Gnirke
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Tami D Lieberman
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,lnstitute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony Philippakis
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Meagan Burns
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Jeremy Luban
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Lawrence C Madoff
- Massachusetts Department of Public Health, Boston, MA, USA.,University of Massachusetts Medical School, Infectious Diseases and Immunology, Worcester, MA 01655
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Virginia M Pierce
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Pediatric Infectious Disease Unit, MassGeneral Hospital for Children, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815
| | - Daniel J Park
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Bronwyn L Maclnnis
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA
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