1
|
Mostafa HH, Fall A, Norton JM, Sachithanandham J, Yunker M, Abdullah O, Hanlon A, Gluck L, Morris CP, Pekosz A, Klein EY. Respiratory virus disease and outcomes at a large academic medical center in the United States: a retrospective observational study of the early 2023/2024 respiratory viral season. Microbiol Spectr 2024; 12:e0111624. [PMID: 39162510 PMCID: PMC11448398 DOI: 10.1128/spectrum.01116-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/22/2024] [Indexed: 08/21/2024] Open
Abstract
Respiratory disease, attributed to influenza, respiratory syncytial virus (RSV), and SARS-CoV-2, was reported nationally during the 2023/2024 respiratory viral season. The emergence of novel SARS-CoV-2 variants was considered a significant factor contributing to the rise in COVID-19 cases. Data from the Johns Hopkins Hospital System (JHHS) showed that enterovirus/rhinovirus had also been circulating at high rates. Analyzing clinical outcomes of the most prevalent respiratory viruses is crucial for understanding the role of circulating viral genotypes. A retrospective cohort of patients who tested positive for SARS-CoV-2, influenza, RSV, or enterovirus/rhinovirus between 1 June and 31 December 2023 was included in the study. Remnant clinical samples were utilized for targeted viral whole-genome sequencing and genotyping. Patients' metadata and outcomes following infection were studied, stratified by viral variants and genotypes. The increase of SARS-CoV-2 positivity in December was associated with the predominance of JN.1. Admissions for patients under 18 years old were primarily associated with enterovirus/rhinovirus and RSV, while older age groups were mainly linked to SARS-CoV-2 and influenza infections. SARS-CoV-2-related admissions increased with the predominance of the JN.1 variant in December. No significant difference in admissions for influenza subtypes, rhinovirus species, or SARS-CoV-2 variants was observed. RSV A was associated with slightly higher odds of admission compared with RSV B. Our data highlight the importance of systematically analyzing respiratory viral infections to inform public health strategies and clinical management, especially as SARS-CoV-2 becomes endemic. The findings highlight the value of expanded genomic surveillance in elucidating the clinical significance of viral evolution.IMPORTANCEThe analysis of the epidemiology and clinical outcomes of multiple co-circulating respiratory viruses in the early 2023/2024 respiratory virus season highlights the emergence of the SARS-CoV-2 JN.1 variant as well as underscores the importance of enterovirus/rhinovirus in respiratory infections. Understanding these dynamics is essential for refining public health strategies and clinical management, especially as SARS-CoV-2 transitions to an endemic status. This work emphasizes the need for ongoing surveillance, robust diagnostic algorithms, and detailed genomic analyses to anticipate and mitigate the burden of respiratory viral infections, ultimately contributing to more informed decision-making in healthcare settings and better patient outcomes.
Collapse
Affiliation(s)
- Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Amary Fall
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Julie M Norton
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Madeline Yunker
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Omar Abdullah
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Ann Hanlon
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Linda Gluck
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - C Paul Morris
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| |
Collapse
|
2
|
Yunker M, Villafuerte DA, Fall A, Norton JM, Abdullah O, Rothman RE, Fenstermacher KZJ, Morris CP, Pekosz A, Klein E, Mostafa HH. Genomic evolution of influenza during the 2023-2024 season, the johns hopkins health system. J Clin Virol 2024; 174:105718. [PMID: 39079210 PMCID: PMC11384212 DOI: 10.1016/j.jcv.2024.105718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 09/11/2024]
Abstract
Influenza, a human disease caused by viruses in the Orthomyxoviridae family, is estimated to infect 5% -10 % of adults and 20% -30 % of children annually. Influenza A (IAV) and Influenza B (IBV) viruses accumulate amino acid substitutions (AAS) in the hemagglutinin (HA) and neuraminidase (NA) proteins seasonally. These changes, as well as the dominating viral subtypes, vary depending on geographical location, which may impact disease prevalence and the severity of the season. Genomic surveillance is crucial for capturing circulation patterns and characterizing AAS that may affect disease outcomes, vaccine efficacy, or antiviral drug activities. In this study, whole-genome sequencing of IAV and IBV was attempted on positive remnant clinical samples (587) collected from 580 patients between June 2023 and February 2024 in the Johns Hopkins Health System (JHHS). Full-length HA segments were obtained from 424 (72.2 %) samples. H1N1pdm09 (71.7 %) was the predominant IAV subtype, followed by H3N2 (16.7 %) and IBV-Victoria clade V1A.3a.2 (11.6 %). Within H1N1pdm09 HA sequences, the 6B1A.5a.2a.1 (60.5 %) clade was the most represented. Full-length NA segments were obtained from 421 (71.7 %) samples. Within H1N1pdm09 and IBV, AAS previously proposed to change susceptibility to NA inhibitors were infrequently detected. Phylogeny of HA and NA demonstrated heterogeneous HA and NA H1N1pdm09 and IBV subclades. No significant differences were observed in admission rates or use of supplemental oxygen between different subtypes or clades. Influenza virus genomic surveillance is essential for understanding the seasonal evolution of influenza viruses and their association with disease prevalence and outcomes.
Collapse
MESH Headings
- Humans
- Influenza, Human/virology
- Influenza, Human/epidemiology
- Phylogeny
- Adult
- Whole Genome Sequencing
- Influenza B virus/genetics
- Influenza B virus/classification
- Influenza A virus/genetics
- Influenza A virus/classification
- Neuraminidase/genetics
- Evolution, Molecular
- Seasons
- Genome, Viral
- Middle Aged
- Male
- Young Adult
- Female
- Adolescent
- Child
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Child, Preschool
- Aged
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/drug effects
- Infant
- Amino Acid Substitution
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Aged, 80 and over
Collapse
Affiliation(s)
- Madeline Yunker
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology USA
| | - David A Villafuerte
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology USA
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology USA
| | - Julie M Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology USA
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology USA
| | - Richard E Rothman
- Department of Emergency Medicine, Johns Hopkins School of Medicine USA
| | | | - C Paul Morris
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Andrew Pekosz
- Department of Emergency Medicine, Johns Hopkins School of Medicine USA; W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health USA
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine USA; Center for Disease Dynamics, Economics, and Policy, Washington DC USA
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology USA.
| |
Collapse
|
3
|
Dong C, Li F, Sun Y, Long D, Chen C, Li M, Wei T, Martins RP, Chen T, Mak PI. A syndromic diagnostic assay on a macrochannel-to-digital microfluidic platform for automatic identification of multiple respiratory pathogens. LAB ON A CHIP 2024; 24:3850-3862. [PMID: 37961846 DOI: 10.1039/d3lc00728f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The worldwide COVID-19 pandemic has changed people's lives and the diagnostic landscape. The nucleic acid amplification test (NAT) as the gold standard for SARS-CoV-2 detection has been applied in containing its transmission. However, there remains a lack of an affordable on-site detection system at resource-limited areas. In this study, a low cost "sample-in-answer-out" system incorporating nucleic acid extraction, purification, and amplification was developed on a single macrochannel-to-digital microfluidic chip. The macrochannel fluidic subsystem worked as a world-to-chip interface receiving 500-1000 μL raw samples, which then underwent bead-based extraction and purification processes before being delivered to DMF. Electrodes actuate an eluent dispensed to eight independent droplets for reverse transcription quantitative polymerase chain reaction (RT-qPCR). By reading with 4 florescence channels, the system can accommodate a maximum of 32 detection targets. To evaluate the proposed platform, a comprehensive assessment was conducted on the microfluidic chip as well as its functional components (i.e., extraction and amplification). The platform demonstrated a superior performance. In particular, using clinical specimens, the chip targeting SARS-CoV-2 and Flu A/B exhibited 100% agreement with off-chip diagnoses. Furthermore, the fabrication of chips is ready for scaled-up manufacturing and they are cost-effective for disposable use since they are assembled using a printed circuit board (PCB) and prefabricated blocks. Overall, the macrochannel-to-digital microfluidic platform coincides with the requirements of point-of-care testing (POCT) because of its advantages: low-cost, ease of use, comparable sensitivity and specificity, and availability for mass production.
Collapse
Affiliation(s)
- Cheng Dong
- School of Intelligent Systems Science and Engineering/JNU-Industry School of Artificial Intelligence, Jinan University, Zhuhai 519000, China
| | - Fei Li
- Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Yun Sun
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Dongling Long
- Zhuhai Center for Disease Control and Prevention, Zhuhai 519087, China
| | - Chunzhao Chen
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhu Hai 519087, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, 07102, USA
| | - Tao Wei
- Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, 510640, China
- Pan Asia (Jiangmen) Institute of Biological Engineering and Health, Jiangmen, 529080, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
| | | | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
- Faculty of Science and Technology, University of Macau, Taipa, Macau SAR, 999078, China
| |
Collapse
|
4
|
Tang HT, Nörz D, Grunwald M, Giersch K, Pfefferle S, Fischer N, Aepfelbacher M, Rohde H, Lütgehetmann M. Analytical and clinical validation of a novel, laboratory-developed, modular multiplex-PCR panel for fully automated high-throughput detection of 16 respiratory viruses. J Clin Virol 2024; 173:105693. [PMID: 38820916 DOI: 10.1016/j.jcv.2024.105693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Viral respiratory Infections pose a health risk, especially to vulnerable patient populations. Effective testing programs can detect and differentiate these infections at an early stage, which is particularly important for high-risk clinical departments. The objective of this study was to develop and validate a multiplex PCR-panel for 16 different respiratory viruses on a fully-automated high-throughput platform. METHODS Three multiplex-PCR assays were designed to run on the cobas5800/6800/8800 systems, consolidating 16 viral targets: RESP1: SARS-CoV-2, influenza-A/B, RSV; RESP2: hMPV, hBoV, hAdV, rhino-/ENV; RESP3: HPIV-1-4, hCoV-229E, hCoV-NL63, hCoV-OC43, hCoV-HKU1. Analytic performance was evaluated using digital-PCR based standards and international reference material. Clinical performance was determined by comparing results from clinical samples with reference assays. RESULTS Analytical sensitivity (i.e. lower limit of detection (LoD), 95 % probability of detection) was determined as follows: SARS-CoV-2: 29.3 IU/ml, influenza-A: 179.9 cp/ml, influenza-B: 333.9 cp/ml and RSV: 283.1 cp/ml. LoDs of other pathogens ranged between 9.4 cp/ml (hCoV-NL63) and 21,419 cp/ml (HPIV-2). Linearity was verified over 4-7 log-steps with pooled standard differentials (SD) ranging between 0.18-0.70ct. Inter-/intra-run variability (precision) was assessed for all targets over 3 days. SDs ranged between 0.13-0.74ct. Positive agreement in clinical samples was 99.4 % and 95 % for SARS-CoV-2 and influenza-A respectively. Other targets were in the 80-100 % range. Negative agreement varied between 96.3-100 %. DISCUSSION Lab-developed tests are a key factor for effective clinical diagnostics. The multiplex panel presented in this study demonstrated high performance and provides an easily scalable high-throughput solution for respiratory virus testing, e.g. for testing in high-risk patient populations.
Collapse
Affiliation(s)
- Hui Ting Tang
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Dominik Nörz
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Moritz Grunwald
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Katja Giersch
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Susanne Pfefferle
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Martin Aepfelbacher
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Holger Rohde
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Marc Lütgehetmann
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany.
| |
Collapse
|
5
|
Buonsenso D, Camporesi A, Viozzi F, Lazzareschi I, Manca L, Caci A, Menna D, Santangelo R, Sanguinetti M, Raffaelli F, Fiori B, Zampino G, Valentini P. Determinants of antibiotic prescription in children with adenovirus respiratory tract infections. Eur J Pediatr 2024; 183:3489-3497. [PMID: 38780652 PMCID: PMC11263461 DOI: 10.1007/s00431-024-05615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
We performed this study to evaluate factors associated with antibiotic prescriptions in children with adenovirus infection, since no studies have attempted to address this aspect in the pediatric population. Retrospective study of children younger than 18 years of age tested positive for adenovirus on a syndromic nasopharyngeal test from 2018 to 2023. We compared the need of pediatric intensive care unit (PICU), invasive ventilation, and other respiratory support, viral etiologies, clinical presentations, imaging, and laboratory results in the precovid (2018-2019) and covid (2020-2022) period. The use of antibiotics was studied with multivariable logistic regression including demographic as well as clinical data as covariates. Two hundred fifty-eight patients were enrolled. One hundred fifty-eight patients received an antibiotic (mean duration 6.2 (±2.7) days (median 4; IQR: 4-7)). Presence of seizures and C-reactive protein values as predictors for antibiotic prescription (OR for seizures: 12.17; 95% CI: 1.42-103.91; p = 0.022; OR for CrP: 1.03; 95% CI: 1.01-1.04; p = 0.001). Seventy-four patients received intravenous antibiotics (74/156, 47.4%). Risk factors for intravenous antibiotic were the presence of decay (OR: 3.74; 95% CI: 1.25-11.71; p = 0.018), CrP values (OR: 1.02; 95% CI: 1.00-1.03; p = 0.001), and presence of seizures (OR: 16.34; 95% CI: 2.65-100.83; p = 0.003). Duration of intravenous antibiotics correlated with the presence of seizures (Coeff: 1.6; 95% CI: 0.41-2.89; p = 0.009) even when adjusted for CrP values. Conclusion: The clinical presentation of adenovirus infection in children is non-specific, leading to frequent antibiotic prescription despite bacterial co-infections was rare. Higher CrP values and presenting with seizures are significantly associated with a higher risk of receiving antibiotics. Rapid microbiological tests and newer biomarkers can help clinicians to improve antibiotic prescription in this cohort of children. What is Known: • Adenovirus infection is a common cause of fever and respiratory tract infections in children. • Children with adenovirus infections frequently receive antibiotics, but determinants of this practice are poorly established. What is New: • Higher C-reactive protein values and presenting with seizures are significantly associated with antibiotic prescription. • Since the beginning of COVID-19 and implementation of rapid diagnostics, less children with adenovirus infection received antibiotics.
Collapse
Affiliation(s)
- Danilo Buonsenso
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy.
- Centro di Salute Globale, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Anna Camporesi
- Anesthesia and Intensive Care Unit, 'Vittore Buzzi' Children's Hospital, Milan, Italy
| | - Francesca Viozzi
- Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ilaria Lazzareschi
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Lavinia Manca
- Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Annamaria Caci
- Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Daniele Menna
- Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rosaria Santangelo
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie-Sezione di Microbiologia, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie-Sezione di Microbiologia, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Francesca Raffaelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Barbara Fiori
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Giuseppe Zampino
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Piero Valentini
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| |
Collapse
|
6
|
Yunker M, Fall A, Norton JM, Abdullah O, Villafuerte DA, Pekosz A, Klein E, Mostafa HH. Genomic Evolution and Surveillance of Respiratory Syncytial Virus during the 2023-2024 Season. Viruses 2024; 16:1122. [PMID: 39066284 PMCID: PMC11281595 DOI: 10.3390/v16071122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a significant cause of morbidity, particularly in infants. This study describes RSV genomic diversity and disease outcomes during the 2023-2024 season in the Johns Hopkins Hospital System (JHHS). Between August and December 2023, 406 patient samples were sequenced, showing that RSV-B GB5.0.5a was the dominant genotype detected. RSV-A genotype GA2.3.5 was detected less frequently. Metadata analysis of patient data revealed that, although RSV-B was more commonly detected, patients with RSV-A infections were more frequently hospitalized. Analysis of both the G- and F-genes revealed multiple amino acid substitutions in both RSV-A and RSV-B, with some positions within the F-protein that could be associated with evasion of antibody responses. Phylogenetic analysis revealed the genetic diversity of circulating GB5.0.5a and GA2.3.5 genotypes. This study serves as an important baseline for genomic surveillance of RSV within the JHHS and will assist in characterizing the impact of the newly approved RSV vaccines on RSV genomic evolution and the emergence of escape mutations.
Collapse
Affiliation(s)
- Madeline Yunker
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Meyer B-121F, 600 N. Wolfe St., Baltimore, MD 21287, USA; (M.Y.); (A.F.); (J.M.N.); (O.A.); (D.A.V.)
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Meyer B-121F, 600 N. Wolfe St., Baltimore, MD 21287, USA; (M.Y.); (A.F.); (J.M.N.); (O.A.); (D.A.V.)
| | - Julie M. Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Meyer B-121F, 600 N. Wolfe St., Baltimore, MD 21287, USA; (M.Y.); (A.F.); (J.M.N.); (O.A.); (D.A.V.)
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Meyer B-121F, 600 N. Wolfe St., Baltimore, MD 21287, USA; (M.Y.); (A.F.); (J.M.N.); (O.A.); (D.A.V.)
| | - David A. Villafuerte
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Meyer B-121F, 600 N. Wolfe St., Baltimore, MD 21287, USA; (M.Y.); (A.F.); (J.M.N.); (O.A.); (D.A.V.)
| | - Andrew Pekosz
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (A.P.); (E.K.)
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (A.P.); (E.K.)
- Center for Disease Dynamics, Economics, and Policy, Washington, DC 20005, USA
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Meyer B-121F, 600 N. Wolfe St., Baltimore, MD 21287, USA; (M.Y.); (A.F.); (J.M.N.); (O.A.); (D.A.V.)
| |
Collapse
|
7
|
Khan S, Rathod P, Gupta VK, Khedekar PB, Chikhale RV. Evolution and Impact of Nucleic Acid Amplification Test (NAAT) for Diagnosis of Coronavirus Disease. Anal Chem 2024; 96:8124-8146. [PMID: 38687959 PMCID: PMC11112543 DOI: 10.1021/acs.analchem.3c05225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Sumbul
Fatma Khan
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Priyanka Rathod
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Vivek K. Gupta
- Department
of Biochemistry, National JALMA Institute
for Leprosy & Other Mycobacterial Diseases (ICMR), Agra -282004, India
| | - Pramod B. Khedekar
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Rupesh V. Chikhale
- UCL
School of Pharmacy, Department of Pharmaceutical and Biological Chemistry, University College London, London WC1N 1AX, United Kingdom
| |
Collapse
|
8
|
Jose Lucar, Rebecca Yee. Diagnostic Stewardship for Multiplex Respiratory Testing: What We Know and What Needs to Be Done. Clin Lab Med 2024; 44:45-61. [PMID: 38280797 DOI: 10.1016/j.cll.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Syndromic respiratory panels are now widely available in clinical microbiology laboratories and health care institutions. These panels can rapidly diagnose infections and detect antimicrobial resistance genes allowing for more rapid therapeutic optimization compared to standard microbiology approaches. However, given reimbursement concerns and limitations of multiplex molecular testing and results interpretation, maximum clinical utility and positive clinical outcomes depend on active diagnostic stewardship. Here, the authors review clinical outcomes of both upper and lower respiratory panels and present diagnostic stewardship strategies for optimal use of respiratory panels.
Collapse
Affiliation(s)
- Jose Lucar
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue Northeast, Washington, DC 20037, USA
| | - Rebecca Yee
- Department of Pathology, George Washington University School of Medicine and Health Sciences, 900 23rd Street Northwest, Washington, DC 20037, USA.
| |
Collapse
|
9
|
Buonsenso D, Ferro V, Viozzi F, Morello R, Proli F, Bersani G, Lazzareschi I, Santangelo R, Sanguinetti M, Fiori B, Zampino G, Valentini P. Changes in clinical, demographic, and outcome patterns of children hospitalized with non-SARS-CoV-2 viral low respiratory tract infections before and during the COVID pandemic in Rome, Italy. Pediatr Pulmonol 2024; 59:362-370. [PMID: 37937896 DOI: 10.1002/ppul.26755] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
INTRODUCTION We performed this study aiming to evaluate changes in epidemiology, clinical presentation and outcomes of children hospitalized for viral lower respiratory tract infections (LRTI). METHODS We performed a retrospective study of children younger than 18 years of age hospitalized for LRTIs with a positive respiratory viral testing from 2018 to 2022. We compared need of pediatric intensive care unit (PICU), invasive ventilation, and other respiratory support, viral etiologies, clinical presentations, imaging, and laboratory results in the precovid (2018-2019) and covid (2020-2022) period. RESULTS A total of 523 were included in the analysis. In the pandemic period, the detection of influenza was 95% less likely to occur (odds ratio [OR]: 0.05; 95% confidence interval [95% CI]: 0.02-0.12; p < .001), likewise the detection of adenovirus was 77% less likely to occur (OR: 0.23; 95% CI: 0.10-0.51; p < .001). In the pandemic period, the number of codetections increased from 15.52% in 2018 to 57.25% in 2022, resulting in a significantly increasing trend (p < .001). The odds of transfer to PICU was more than five times greater during the pandemic period (OR: 5.31; 95% CI: 1.78-15.86; p = .003). CONCLUSIONS We found that the pattern of LRTI in children during COVID-19 pandemic significantly changed in terms of etiologies and increased severity.
Collapse
Affiliation(s)
- Danilo Buonsenso
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Centro di Salute Globale, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Valentina Ferro
- Department of Emergency, Acceptance and General Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Viozzi
- Medicine and Surgery, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Rosa Morello
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Francesco Proli
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia Bersani
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Ilaria Lazzareschi
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie-Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Barbara Fiori
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Piero Valentini
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| |
Collapse
|
10
|
Abdullah O, Fall A, Klein E, Mostafa HH. Increased circulation of human adenovirus in 2023: an investigation of the circulating genotypes, upper respiratory viral loads, and hospital admissions in a large academic medical center. J Clin Microbiol 2024; 62:e0123723. [PMID: 38112530 PMCID: PMC10793258 DOI: 10.1128/jcm.01237-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE The circulation of human adenoviruses (HAdV) increased in 2023. In this manuscript, we show that HAdV-B3 was predominant in 2023 in a cohort characterized by the Johns Hopkins Hospital System. We also show that HAdV-B3 was associated with an increase in viral loads in respiratory samples and provide a correlation with the clinical presentations and outcomes.
Collapse
Affiliation(s)
- Omar Abdullah
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Amary Fall
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| | - Heba H. Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
11
|
Abdullah O, Fall A, Forman M, Howard C, Klein E, Mostafa HH. Respiratory Adenovirus Quantification with a Droplet Digital Polymerase Chain Reaction (ddPCR) Assay. Microbiol Spectr 2023; 11:e0026923. [PMID: 37070988 PMCID: PMC10269445 DOI: 10.1128/spectrum.00269-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
Human adenoviruses (HAdVs) are double-stranded DNA viruses that can cause a wide spectrum of disease, including respiratory infections. Little is known about the value of respiratory HAdV quantification and its correlation with disease severity. In this study, we developed a quantitative HAdV droplet digital PCR (ddPCR) assay to study the association between viral loads, circulating types, and clinical outcomes. Remnant respiratory specimens positive for HAdV after the standard of care testing were collected from December 2020 to April 2022. A total of 129 samples were tested by a ddPCR method. Typing was performed using Nanopore sequencing of the hexon gene hypervariable region. Clinical chart reviews were performed to correlate the viral loads with the disease severity. The ddPCR assay showed an analytical sensitivity and a lower limit of quantification below 100 copies/mL. Of 129 positive clinical samples, 100 were quantified by ddPCR, 7 were too concentrated to be quantified, and 22 were negative. Of the 22 false negatives, only 3 were successfully typed; however, 99 of the 107 positive samples had a characterized genotype. The main HAdV types identified in this cohort were C1 (49.5%) followed by C2 (34.3%). No significant difference in HAdV loads was noted between patients who were admitted, those who required supplemental oxygen, and outpatients or between different HAdV types. HAdV ddPCR is a reliable absolute quantification approach for HAdV from respiratory samples. HAdV loads at initial presentation does not appear to differ between patients who require hospitalization versus outpatients. IMPORTANCE Measuring viral load using droplet digital PCR (ddPCR) is an absolute quantification approach that can facilitate comparability between different laboratories. This approach could prove valuable in studies that focus on the clinical utility of quantification. In this study, we evaluate a human adenovirus (HAdV) ddPCR assay and study the relationship between viral loads and outcomes after HAdV respiratory infections.
Collapse
Affiliation(s)
- Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Michael Forman
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Craig Howard
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| |
Collapse
|
12
|
Morris CP, Eldesouki RE, Sachithanandham J, Fall A, Norton JM, Abdullah O, Gallagher N, Li M, Pekosz A, Klein EY, Mostafa HH. Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization. Clin Infect Dis 2023; 76:1276-1284. [PMID: 36366857 PMCID: PMC10069846 DOI: 10.1093/cid/ciac885] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The variant of concern Omicron has become the sole circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant for the past several months. Omicron subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 evolved over the time, with BA.1 causing the largest wave of infections globally in December 2021-January 2022. This study compared the clinical outcomes in patients infected with different Omicron subvariants and the relative viral loads and recovery of infectious virus from upper respiratory specimens. METHODS SARS-CoV-2-positive remnant clinical specimens, diagnosed at the Johns Hopkins Microbiology Laboratory between December 2021 and July 2022, were used for whole-genome sequencing. The clinical outcomes of infections with Omicron subvariants were compared with infections with BA.1. Cycle threshold (Ct) values and the recovery of infectious virus on the VeroTMPRSS2 cell line from clinical specimens were compared. RESULTS BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and coronavirus disease 2019 (COVID-19)-related hospitalizations at the Johns Hopkins system. After a peak in January, cases decreased in the spring, but the emergence of BA.2.12.1 followed by BA.5 in May 2022 led to an increase in case positivity and admissions. BA.1 infections had a lower mean Ct value when compared with other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values <20. CONCLUSIONS Omicron subvariants continue to be associated with a relatively high rate of polymerase chain reaction (PCR) positivity and hospital admissions. The BA.5 infections are more while BA.2 infections are less likely to have infectious virus, suggesting potential differences in infectibility during the Omicron waves.
Collapse
Affiliation(s)
- C Paul Morris
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, Maryland, USA
| | - Raghda E Eldesouki
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Histology, Genetics Unit, School of Medicine, Suez Canal University, Ismailia, Egypt
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amary Fall
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Julie M Norton
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Omar Abdullah
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
13
|
St Clair LA, Eldesouki RE, Sachithanandham J, Yin A, Fall A, Morris CP, Norton JM, Forman M, Abdullah O, Dhakal S, Barranta C, Golding H, Bersoff-Matcha SJ, Pilgrim-Grayson C, Berhane L, Cox AL, Burd I, Pekosz A, Mostafa HH, Klein EY, Klein SL. Reduced control of SARS-CoV-2 infection is associated with lower mucosal antibody responses in pregnant women. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.19.23287456. [PMID: 36993216 PMCID: PMC10055594 DOI: 10.1101/2023.03.19.23287456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Importance Pregnant women are at increased risk of severe COVID-19, but the contribution of viral RNA load, the presence of infectious virus, and mucosal antibody responses remain understudied. Objective To evaluate the association of COVID-19 outcomes following confirmed infection with vaccination status, mucosal antibody responses, infectious virus recovery and viral RNA levels in pregnant compared with non-pregnant women. Design A retrospective observational cohort study of remnant clinical specimens from SARS-CoV-2 infected patients between October 2020-May 2022. Setting Five acute care hospitals within the Johns Hopkins Health System (JHHS) in the Baltimore, MD-Washington, DC area. Participants Participants included confirmed SARS-CoV-2 infected pregnant women and matched non-pregnant women (matching criteria included age, race/ethnicity, and vaccination status). Exposure SARS-CoV-2 infection, with documentation of SARS-CoV-2 mRNA vaccination. Main Outcomes The primary dependent measures were clinical COVID-19 outcomes, infectious virus recovery, viral RNA levels, and mucosal anti-spike (S) IgG titers from upper respiratory tract samples. Clinical outcomes were compared using odds ratios (OR), and measures of virus and antibody were compared using either Fisher's exact test, two-way ANOVA, or regression analyses. Results were stratified according to pregnancy, vaccination status, maternal age, trimester of pregnancy, and infecting SARS-CoV-2 variant. Resultss A total of 452 individuals (117 pregnant and 335 non-pregnant) were included in the study, with both vaccinated and unvaccinated individuals represented. Pregnant women were at increased risk of hospitalization (OR = 4.2; CI = 2.0-8.6), ICU admittance, (OR = 4.5; CI = 1.2-14.2), and of being placed on supplemental oxygen therapy (OR = 3.1; CI =13-6.9). An age-associated decrease in anti-S IgG titer and corresponding increase in viral RNA levels (P< 0.001) was observed in vaccinated pregnant, but not non-pregnant, women. Individuals in their 3rd trimester had higher anti-S IgG titers and lower viral RNA levels (P< 0.05) than those in their 1st or 2nd trimesters. Pregnant individuals experiencing breakthrough infections due to the omicron variant had reduced anti-S IgG compared to non-pregnant women (P< 0.05). Conclusions and Relevance In this cohort study, vaccination status, maternal age, trimester of pregnancy, and infecting SARS-CoV-2 variant were each identified as drivers of differences in mucosal anti-S IgG responses in pregnant compared with non-pregnant women. Observed increased severity of COVID-19 and reduced mucosal antibody responses particularly among pregnant participants infected with the Omicron variant suggest that maintaining high levels of SARS-CoV-2 immunity may be important for protection of this at-risk population.
Collapse
Affiliation(s)
- Laura A St Clair
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Raghda E Eldesouki
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Medical Genetics Unit, Histology Department, School of Medicine, Suez Canal University, Egypt
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Yin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amary Fall
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - C Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Julie M Norton
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Forman
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Omar Abdullah
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Santosh Dhakal
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Caelan Barranta
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hana Golding
- Division of Viral Products, Center of Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | | | - Catherine Pilgrim-Grayson
- Division of Urology, Obstetrics, and Gynecology; Office of Rare Diseases, Pediatrics, Urologic and Reproductive Medicine; Office of New Drugs; Center for Drug Evaluation and Research; U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Leah Berhane
- Division of Urology, Obstetrics, and Gynecology; Office of Rare Diseases, Pediatrics, Urologic and Reproductive Medicine; Office of New Drugs; Center for Drug Evaluation and Research; U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Andrea L Cox
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Irina Burd
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Disease Dynamics, Economics, and Policy, Washington DC, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
14
|
Fall A, Han L, Abdullah O, Norton JM, Eldesouki RE, Forman M, Morris CP, Klein E, Mostafa HH. An increase in enterovirus D68 circulation and viral evolution during a period of increased influenza like illness, The Johns Hopkins Health System, USA, 2022. J Clin Virol 2023; 160:105379. [PMID: 36652754 DOI: 10.1016/j.jcv.2023.105379] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/30/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023]
Abstract
BACKGROUND An increase in influenza like illness in children and adolescents at the Johns Hopkins Health system during summer 2022 was associated with increased positivity for enterovirus/ rhinovirus. We sought to characterize the epidemiology and viral evolution of enterovirus D68 (EV-D68). METHODS A cohort of remnant respiratory samples tested at the Johns Hopkins Microbiology Laboratory was screened for EV-D68. EV-D68 positives were characterized by whole genome sequencing and viral loads were assessed by droplet digital PCR (ddPCR). Genomic changes and viral loads were analyzed along with patients' clinical presentations. RESULTS Of 566 screened samples, 126 were EV-D68 (22.3%). The median age of EV-D68 infected patients was four years, a total of 52 required supplemental oxygen (41.3%), and 35 (27.8%) were admitted. Lung disease was the most frequent comorbidity that was associated with hospitalization. A total of 75 complete and 32 partial genomes were characterized that made a new cluster within the B3 subclade that was closest to US genomes from 2018. Amino acid changes within the BC and DE loops were identified from 31 genomes (29%) which correlated with an increase in average viral load in respiratory specimens and the need for supplemental oxygen. CONCLUSIONS EV-D68 outbreaks continue to cause influenza like illness that could be overwhelming for the health system due to a significant demand for high flow oxygen. Viral evolution and an increase in the susceptible population are likely driving the trends of the increased EV-D68 infections.
Collapse
Affiliation(s)
- Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States
| | - Lijie Han
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States
| | - Julie M Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States
| | - Raghda E Eldesouki
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States
| | - Michael Forman
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States
| | - C Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States; National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, United States; Center for Disease Dynamics, Economics, and Policy, Washington DC, United States
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, United States.
| |
Collapse
|
15
|
Kreitmann L, Miglietta L, Xu K, Malpartida-Cardenas K, D’Souza G, Kaforou M, Brengel-Pesce K, Drazek L, Holmes A, Rodriguez-Manzano J. Next-generation molecular diagnostics: Leveraging digital technologies to enhance multiplexing in real-time PCR. Trends Analyt Chem 2023; 160:116963. [PMID: 36968318 PMCID: PMC7614363 DOI: 10.1016/j.trac.2023.116963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Real-time polymerase chain reaction (qPCR) enables accurate detection and quantification of nucleic acids and has become a fundamental tool in biological sciences, bioengineering and medicine. By combining multiple primer sets in one reaction, it is possible to detect several DNA or RNA targets simultaneously, a process called multiplex PCR (mPCR) which is key to attaining optimal throughput, cost-effectiveness and efficiency in molecular diagnostics, particularly in infectious diseases. Multiple solutions have been devised to increase multiplexing in qPCR, including single-well techniques, using target-specific fluorescent oligonucleotide probes, and spatial multiplexing, where segregation of the sample enables parallel amplification of multiple targets. However, these solutions are mostly limited to three or four targets, or highly sophisticated and expensive instrumentation. There is a need for innovations that will push forward the multiplexing field in qPCR, enabling for a next generation of diagnostic tools which could accommodate high throughput in an affordable manner. To this end, the use of machine learning (ML) algorithms (data-driven solutions) has recently emerged to leverage information contained in amplification and melting curves (AC and MC, respectively) - two of the most standard bio-signals emitted during qPCR - for accurate classification of multiple nucleic acid targets in a single reaction. Therefore, this review aims to demonstrate and illustrate that data-driven solutions can be successfully coupled with state-of-the-art and common qPCR platforms using a variety of amplification chemistries to enhance multiplexing in qPCR. Further, because both ACs and MCs can be predicted from sequence data using thermodynamic databases, it has also become possible to use computer simulation to rationalize and optimize the design of mPCR assays where target detection is supported by data-driven technologies. Thus, this review also discusses recent work converging towards the development of an end-to-end framework where knowledge-based and data-driven software solutions are integrated to streamline assay design, and increase the accuracy of target detection and quantification in the multiplex setting. We envision that concerted efforts by academic and industry scientists will help advance these technologies, to a point where they become mature and robust enough to bring about major improvements in the detection of nucleic acids across many fields.
Collapse
Affiliation(s)
- Louis Kreitmann
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
- Research & Development, BioMérieux S.A, Marcy-l’Etoile, France
| | - Luca Miglietta
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London, UK
| | - Ke Xu
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London, UK
| | | | - Giselle D’Souza
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | | | - Laurent Drazek
- Research & Development, BioMérieux S.A, Marcy-l’Etoile, France
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | | |
Collapse
|
16
|
Kim TY, Bae GE, Kim JY, Kang M, Jang JH, Huh HJ, Chung DR, Lee NY. Evaluation of the Kaira COVID-19/Flu/RSV Detection Kit for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus: A comparative study with the PowerChek SARS-CoV-2, influenza A&B, RSV Multiplex Real-time PCR Kit. PLoS One 2022; 17:e0278530. [PMID: 36516190 PMCID: PMC9750031 DOI: 10.1371/journal.pone.0278530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Co-circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses, such as influenza and respiratory syncytial virus (RSV), can be a severe threat to public health. The accurate detection and differentiation of these viruses are essential for clinical laboratories. Herein, we comparatively evaluated the performance of the Kaira COVID-19/Flu/RSV Detection Kit (Kaira; Optolane, Seongnam, Korea) for detection of SARS-CoV-2, influenza A and B, and RSV in nasopharyngeal swab (NPS) specimens with that of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit (PowerChek; Kogene Biotech, Seoul, Korea). METHODS A total of 250 archived NPS specimens collected for routine clinical testing were tested in parallel by the Kaira and PowerChek assays. RNA standards were serially diluted and tested by the Kaira assay to calculate the limit of detection (LOD). RESULTS The positive and negative percent agreements between the Kaira and PowerChek assays were as follows: 100% (49/49) and 100% (201/201) for SARS-CoV-2; 100% (50/50) and 99.0% (198/200) for influenza A; 100% (50/50) and 100% (200/200) for influenza B; and 100% (51/51) and 100% (199/199) for RSV, respectively. The LODs of the Kaira assay for SARS-CoV-2, influenza A and B, and RSV were 106.1, 717.1, 287.3, and 442.9 copies/mL, respectively. CONCLUSIONS The Kaira assay showed comparable performance to the PowerChek assay for detection of SARS-CoV-2, influenza A and B, and RSV in NPS specimens, indicating that the Kaira assay could be a useful diagnostic tool when these viruses are co-circulating.
Collapse
Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Go Eun Bae
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- * E-mail:
| | - Doo Ryeon Chung
- Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Korea
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
17
|
Morris CP, Eldesouki RE, Fall A, Gaston DC, Norton JM, Gallagher ND, Luo CH, Abdullah O, Klein EY, Mostafa HH. SARS-CoV-2 reinfections during the Delta and Omicron waves. JCI Insight 2022; 7:e162007. [PMID: 36048527 PMCID: PMC9714778 DOI: 10.1172/jci.insight.162007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDIncreased SARS-CoV-2 reinfection rates have been reported recently, with some locations basing reinfection on a second positive PCR test at least 90 days after initial infection. In this study, we used Johns Hopkins SARS-CoV-2 genomic surveillance data to evaluate the frequency of sequencing-validated, confirmed, and inferred reinfections between March 2020 and July 2022.METHODSPatients who had 2 or more positive SARS-CoV-2 tests in our system, with samples sequenced as a part of our surveillance efforts, were identified as the cohort for our study. SARS-CoV-2 genomes of patients' initial and later samples were compared.RESULTSA total of 755 patients (920 samples) had a positive test at least 90 days after the initial test, with a median time between tests of 377 days. Sequencing was attempted on 231 samples and was successful in 127. Rates of successful sequencing spiked during the Omicron surge; there was a higher median number of days from initial infection in these cases compared with those with failed sequences. A total of 122 (98%) patients showed evidence of reinfection; 45 of these patients had sequence-validated reinfection and 77 had inferred reinfections (later sequencing showed a clade that was not circulating when the patient was initially infected). Of the 45 patients with sequence-validated reinfections, 43 (96%) had reinfections that were caused by the Omicron variant, 41 (91%) were symptomatic, 32 (71%) were vaccinated prior to the second infection, 6 (13%) were immunosuppressed, and only 2 (4%) were hospitalized.CONCLUSIONSequence-validated reinfections increased with the Omicron surge but were generally associated with mild infections.FUNDINGFunding was provided by the Johns Hopkins Center of Excellence in Influenza Research and Surveillance (HHSN272201400007C), CDC (75D30121C11061), Johns Hopkins University President's Fund Research Response, Johns Hopkins Department of Pathology, and the Maryland Department of Health.
Collapse
Affiliation(s)
- C. Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland, USA
| | - Raghda E. Eldesouki
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Genetics Unit, Histology Department, School of Medicine, Suez Canal University, Ismailia, Egypt
| | - Amary Fall
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David C. Gaston
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Julie M. Norton
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas D. Gallagher
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Omar Abdullah
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eili Y. Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| | - Heba H. Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
18
|
Morris CP, Eldesouki RE, Sachithanandham J, Fall A, Norton JM, Abdullah O, Gallagher N, Li M, Pekosz A, Klein EY, Mostafa HH. Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.09.20.22280154. [PMID: 36172137 PMCID: PMC9516865 DOI: 10.1101/2022.09.20.22280154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The variant of concern, Omicron, has become the sole circulating SARS-CoV-2 variant for the past several months. Omicron subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 evolved over the time, with BA.1 causing the largest wave of infections globally in December 2021- January 2022. In this study, we compare the clinical outcomes in patients infected with different Omicron subvariants and compare the relative viral loads, and recovery of infectious virus from upper respiratory specimens. Methods SARS-CoV-2 positive remnant clinical specimens, diagnosed at the Johns Hopkins Microbiology Laboratory between December 2021 and July 2022, were used for whole genome sequencing. The clinical outcomes of infections with Omicron subvariants were compared to infections with BA.1. Cycle threshold values (Ct) and the recovery of infectious virus on VeroTMPRSS2 cell line from clinical specimens were compared. Results The BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and COVID-19 related hospitalizations at the Johns Hopkins system. After a peak in January cases fell in the spring, but the emergence of BA.2.12.1 followed by BA.5 in May 2022 led to an increase in case positivity and admissions. BA.1 infections had a lower mean Ct when compared to other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values less than 20. Conclusions Omicron subvariants continue to associate with a relatively high positivity and admissions. The BA.5 infections are more while BA.2 infections are less likely to have infectious virus, suggesting potential differences in infectibility during the Omicron waves. Funding Centers for Disease Control and Prevention contract 75D30121C11061, NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, and The Modeling Infectious Diseases in Healthcare Network (MInD) under awards U01CK000589.
Collapse
Affiliation(s)
- C. Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
- National Institute of Allergy and Infectious Disease, National Institutes of Health
| | - Raghda E. Eldesouki
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
- Suez Canal University, School of Medicine, Department of Histology, Genetics unit, Egypt
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Julie M. Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health
- Department of Emergency Medicine, Johns Hopkins School of Medicine
| | - Eili Y. Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine
- Center for Disease Dynamics, Economics, and Policy, Washington DC
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| |
Collapse
|
19
|
Huai Luo C, Paul Morris C, Sachithanandham J, Amadi A, Gaston DC, Li M, Swanson NJ, Schwartz M, Klein EY, Pekosz A, Mostafa HH. Infection With the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Variant Is Associated With Higher Recovery of Infectious Virus Compared to the Alpha Variant in Both Unvaccinated and Vaccinated Individuals. Clin Infect Dis 2022; 75:e715-e725. [PMID: 34922338 PMCID: PMC8903351 DOI: 10.1093/cid/ciab986] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VOC) B.1.617.2 (Delta) displaced B.1.1.7 (Alpha) and is associated with increases in coronavirus disease 2019 (COVID-19) cases, greater transmissibility, and higher viral RNA loads, but data are lacking regarding the infectious virus load and antiviral antibody levels in the nasal tract. METHODS Whole genome sequencing, cycle threshold (Ct) values, infectious virus, anti-SARS-CoV-2 immunoglobulin G (IgG) levels, and clinical chart reviews were combined to characterize SARS-CoV-2 lineages circulating in the National Capital Region between January and September 2021 and differentiate infections in vaccinated and unvaccinated individuals by the Delta, Alpha, and B.1.2 (the predominant lineage prior to Alpha) variants. RESULTS The Delta variant displaced the Alpha variant to constitute 99% of the circulating lineages in the National Capital Region by August 2021. In Delta infections, 28.5% were breakthrough cases in fully vaccinated individuals compared to 4% in the Alpha infected cohort. Breakthrough infections in both cohorts were associated with comorbidities, but only Delta infections were associated with a significant increase in the median days after vaccination. More than 74% of Delta samples had infectious virus compared to <30% from the Alpha cohort. The recovery of infectious virus with both variants was associated with low levels of local SARS-CoV-2 IgG. CONCLUSIONS Infection with the Delta variant was associated with more frequent recovery of infectious virus in vaccinated and unvaccinated individuals compared to the Alpha variant but was not associated with an increase in disease severity in fully vaccinated individuals. Infectious virus was correlated with the presence of low amounts of antiviral IgG in the nasal specimens.
Collapse
Affiliation(s)
- Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - C Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Washington D.C., USA
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David C Gaston
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nicholas J Swanson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USAand
- Center for Disease Dynamics, Economics, and Policy, Washington D.C., USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USAand
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
20
|
Eldesouki RE, Uhteg K, Mostafa HH. The circulation of Non-SARS-CoV-2 respiratory viruses and coinfections with SARS-CoV-2 during the surge of the Omicron variant. J Clin Virol 2022; 153:105215. [PMID: 35717769 PMCID: PMC9174098 DOI: 10.1016/j.jcv.2022.105215] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND In December 2021, the SARS-CoV-2 Omicron variant displaced the Delta variant and caused an unprecedented spike in the numbers of COVID-19 cases. This study reports the positivity rates of circulating non-SARS-CoV-2 respiratory viruses and evaluates coinfections of these viruses with SARS-CoV-2 during the Omicron surge. METHODS Data from the multiplex respiratory panels used for diagnosis at the Johns Hopkins Microbiology Laboratory were used to assess positivity rates and respiratory virus coinfections in the time frame between November 2021 and February 2022. Clinical presentations and outcomes were assessed in the cohort of 46 patients who had SARS-CoV-2 coinfections with other respiratory viruses. RESULTS Between November 2021 and February 2022, the high positivity of SARS-CoV-2 outcompeted enterovirus/rhinovirus and other circulating respiratory viruses and was associated with a notable decrease in influenza A infections. Coinfections represented 2.3% of the samples tested by the extended multiplex respiratory panel. SARS-COV-2 coinfections represented 25% of the coinfections in this time frame and were mostly SARS-COV-2/enterovirus/rhinovirus. Of the SARS-CoV-2 coinfection cohort, 3 patients were hospitalized and were coinfected with influenza-A (2) or RSV (1). Cough and shortness of breath were the most frequent symptoms (29%) followed by fever (28%). CONCLUSIONS The SARS-CoV-2 Omicron surge was associated with a change in the circulation of other respiratory viruses. Coinfections were most prevalent with viruses that showed the highest positivity in this time frame.
Collapse
Affiliation(s)
- Raghda E Eldesouki
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, United States of America
| | - Katharine Uhteg
- Johns Hopkins Hospital Medical Microbiology Laboratory, Meyer B-130, 600 North Wolfe Street, Baltimore, MD, 21287-7093, United States of America
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, United States of America.
| |
Collapse
|
21
|
Kim TY, Kim JY, Shim HJ, Yun SA, Jang JH, Huh HJ, Kim JW, Lee NY. Performance Evaluation of the PowerChek SARS-CoV-2, Influenza A & B Multiplex Real-Time PCR Kit in Comparison with the BioFire Respiratory Panel. Ann Lab Med 2022; 42:473-477. [PMID: 35177568 PMCID: PMC8859561 DOI: 10.3343/alm.2022.42.4.473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/27/2021] [Accepted: 11/26/2021] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses may pose enormous challenges to our healthcare system. We evaluated the performance of the PowerChek SARS-CoV-2, Influenza A & B Multiplex Real-time PCR Kit (PowerChek; Kogene Biotech, Seoul, Korea) in comparison with the BioFire Respiratory Panels 2 and 2.1 (RP2 and RP2.1; bioMérieux, Marcy l’Étoile, France), using 147 nasopharyngeal swabs. The limit of detection (LOD) of the PowerChek assay was determined using SARS-CoV-2, influenza A, and B RNA standards. The LOD values of the PowerChek assay for SARS-CoV-2 and influenza A and B were 1.12, 1.24, and 0.61 copies/μL, respectively. The positive and negative percent agreements of the PowerChek assay compared with RP2 and RP2.1 were 97.5% (39/40) and 100% (107/107) for SARS-CoV-2; 100% (39/39) and 100% (108/108) for influenza A; and 100% (35/35) and 100% (112/112) for influenza B, respectively. The performance of the PowerChek assay was comparable to that of RP2 and RP2.1 for detecting SARS-CoV-2 and influenza A and B, suggesting its use in diagnosing SARS-CoV-2 and influenza infections.
Collapse
Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
22
|
Mostafa HH, Luo CH, Morris CP, Li M, Swanson NJ, Amadi A, Gallagher N, Pekosz A. SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. J Clin Virol 2022; 150-151:105151. [PMID: 35398602 PMCID: PMC8979609 DOI: 10.1016/j.jcv.2022.105151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/12/2022] [Accepted: 03/31/2022] [Indexed: 01/19/2023]
Abstract
INTRODUCTION COVID-19 large scale immunization in the US has been associated with breakthrough positive molecular testing. In this study, we investigated whether a positive test is associated with a high anti-viral IgG, specific viral variant, recovery of infectious virus, or symptomatic infection during an early phase after vaccination rollout. METHODS We identified 133 SARS-CoV-2 positive patients who had received two doses of either Pfizer-BioNTech (BNT162b2) or Moderna (mRNA-1273) vaccines, the 2nd of which was received between January and April of 2021. The positive samples were collected between January and May of 2021. Samples were sequenced to characterize the whole genome and Spike protein changes and cycle thresholds that reflect viral loads were determined using a single molecular assay. Respiratory SARS-CoV-2 IgG antibodies were examined using ELISA and specimens were grown on cell culture to assess the recovery of infectious virus as compared to a control unvaccinated cohort. RESULTS Of 133 specimens, 24 failed sequencing and yielded a negative or very low viral load on the repeat PCR. Of 109 specimens that were used for further genome analysis, 68 (62.4%) were from symptomatic infections, 11 (10.1%) were admitted for COVID-19, and 2 (1.8%) required ICU admission with no associated mortality. The predominant virus variant was the Alpha (B.1.1.7), however a significant association between lineage B.1.526 and amino acid change S: E484K with positives after vaccination was noted. A significant reduction of the recovery of infectious virus on cell culture was accompanied by an increase in localized IgG levels in respiratory samples of vaccinated individuals. CONCLUSIONS Vaccination reduces the recovery of infectious virus in breakthrough infections caused primarily by the Alpha variant accompanied by an increase in upper respiratory tract IgG levels.
Collapse
Affiliation(s)
- Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, 600 N. Wolfe St, Meyer B-121F, Baltimore, MD, 21287 USA.
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, 600 N. Wolfe St, Meyer B-121F, Baltimore, MD, 21287 USA
| | - C Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, 600 N. Wolfe St, Meyer B-121F, Baltimore, MD, 21287 USA; National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Nicholas J Swanson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, 600 N. Wolfe St, Meyer B-121F, Baltimore, MD, 21287 USA
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, 600 N. Wolfe St, Meyer B-121F, Baltimore, MD, 21287 USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Emergency Medicine, Johns Hopkins School of Medicine, 615 North Wolfe Street, rm W2116, Baltimore, MD, 21205-2103 USA.
| |
Collapse
|
23
|
Morris CP, Eldesouki RE, Fall A, Gaston DC, Norton JM, Gallagher N, Luo CH, Abdullah O, Klein EY, Mostafa HH. Sequence Proven Reinfections with SARS-CoV-2 at a Large Academic Center. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.05.17.22275210. [PMID: 35665008 PMCID: PMC9164520 DOI: 10.1101/2022.05.17.22275210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background Increased reinfection rates with SARS-CoV-2 have recently been reported, with some locations basing reinfection on a second positive PCR test at least 90 days after initial infection. Methods We identified cases where patients had two positive tests for SARS-CoV-2 and evaluated which of these had been sequenced as part of our surveillance efforts, and evaluated sequencing and clinical data. Results 750 patients (920 samples) had a positive test at least 90 days after the initial test. The median time between tests was 377 days, and 724 (79%) of the post 90-day positives were collected after the emergence of the Omicron variant in November 2021. Sequencing was attempted on 231 samples and successful in 127. Successful sequencing spiked during the Omicron surge and showed higher median days from initial infection compared to failed sequences (median 398 days compared to 276 days, p<0.0005). A total of 122 (98%) patients showed evidence of reinfection, 45 of which had sequence proven reinfection and 77 had inferred reinfections (later sequence showed a clade that was not circulating when the patient was initially infected). Children accounted for only 4% of reinfections. 43 (96%) of 45 infections with sequence proven reinfection were caused by the Omicron variant, 41 (91%) were symptomatic, 32 (71%), were vaccinated prior to the second infection, and 6 (13%) were Immunosuppressed. Only 2 (4%) were hospitalized, and both had underlying conditions. Conclusion Sequence proven reinfections increased with the Omicron variant but generally caused mild infections.
Collapse
Affiliation(s)
- C. Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Raghda E. Eldesouki
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Genetics Unit Histology Department, School of Medicine, Suez Canal University, Egypt
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - David C. Gaston
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Julie M. Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eili Y. Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Center for Disease Dynamics, Economics, and Policy, Washington DC
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| |
Collapse
|
24
|
Fall A, Eldesouki RE, Sachithanandham J, Morris CP, Norton JM, Gaston DC, Forman M, Abdullah O, Gallagher N, Li M, Swanson NJ, Pekosz A, Klein EY, Mostafa HH. The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads. EBioMedicine 2022; 79:104008. [PMID: 35460989 PMCID: PMC9020587 DOI: 10.1016/j.ebiom.2022.104008] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The increase in SARS-CoV-2 infections in December 2021 was driven primarily by the Omicron variant, which largely displaced the Delta over a three-week span. Outcomes from infection with Omicron remain uncertain. We evaluated whether clinical outcomes and viral loads differed between Delta and Omicron infections during the period when both variants were co-circulating. METHODS In this retrospective observational cohort study, remnant clinical specimens, positive for SARS-CoV-2 after standard of care testing at the Johns Hopkins Microbiology Laboratory, between the last week of November and the end of December 2021, were used for whole viral genome sequencing. Cycle threshold values (Ct) for viral RNA, the presence of infectious virus, and levels of respiratory IgG were measured, and clinical outcomes were obtained. Differences in each measure were compared between variants stratified by vaccination status. FINDINGS The Omicron variant displaced Delta during the study period and constituted 95% of the circulating lineages by the end of December 2021. Patients with Omicron infections (N = 1,119) were more likely to be vaccinated compared to patients with Delta (N = 908), but were less likely to be admitted (0.33 CI 0.21-0.52), require ICU level care (0.38 CI 0.17-0.87), or succumb to infection (0.26 CI 0.06-1.02) regardless of vaccination status. There was no statistically significant difference in Ct values based on the lineage regardless of the vaccination status. Recovery of infectious virus in cell culture was reduced in boosted patients compared to fully vaccinated without a booster and unvaccinated when infected with the Delta lineage. However, in patients with Omicron infections, recovery of infectious virus was not affected by vaccination. INTERPRETATION Compared to Delta, Omicron was more likely to cause breakthrough infections of vaccinated individuals, yet admissions were less frequent. Admitted patients might develop severe disease comparable to Delta. Efforts for reducing Omicron transmission are required as, though the admission risk might be lower, the increased numbers of infections cause large numbers of hospitalizations. FUNDING NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, Centers for Disease Control and Prevention contract 75D30121C11061, and The Modeling Infectious Diseases in Healthcare Network (MInD) under awards U01CK000589.
Collapse
Affiliation(s)
- Amary Fall
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
| | - Raghda E Eldesouki
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA
| | - C Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA; National Institute of Allergy and Infectious Disease, National Institutes of Health, 615 North Wolfe Street, rm W2116, Bethesda, MD 20892, USA
| | - Julie M Norton
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
| | - David C Gaston
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
| | - Michael Forman
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
| | - Omar Abdullah
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
| | - Nicholas Gallagher
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA
| | - Nicholas J Swanson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA; Department of Emergency Medicine, Johns Hopkins School of Medicine, 5801 Smith Ave, Davis Suite 3220, Baltimore, MD 21209, USA.
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, 5801 Smith Ave, Davis Suite 3220, Baltimore, MD 21209, USA; Center for Disease Dynamics, Economics, and Policy, Washington DC, USA.
| | - Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA.
| |
Collapse
|
25
|
Morris CP, Luo CH, Amadi A, Schwartz M, Gallagher N, Ray SC, Pekosz A, Mostafa HH. An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Clin Infect Dis 2022; 74:1419-1428. [PMID: 34272947 PMCID: PMC8406876 DOI: 10.1093/cid/ciab636] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concerning for enhanced transmission, evasion of immune responses, or associated with severe disease have motivated the global increase in genomic surveillance. In the current study, large-scale whole-genome sequencing was performed between November 2020 and the end of March 2021 to provide a phylodynamic analysis of circulating variants over time. In addition, we compared the viral genomic features of March 2020 and March 2021. METHODS A total of 1600 complete SARS-CoV-2 genomes were analyzed. Genomic analysis was associated with laboratory diagnostic volumes and positivity rates, in addition to an analysis of the association of selected variants of concern/variants of interest with disease severity and outcomes. Our real-time surveillance features a cohort of specimens from patients who tested positive for SARS-CoV-2 after completion of vaccination. RESULTS Our data showed genomic diversity over time that was not limited to the spike sequence. A significant increase in the B.1.1.7 lineage (alpha variant) in March 2021 as well as a transient circulation of regional variants that carried both the concerning S: E484K and S: P681H substitutions were noted. Lineage B.1.243 was significantly associated with intensive care unit admission and mortality. Genomes recovered from fully vaccinated individuals represented the predominant lineages circulating at specimen collection time, and people with those infections recovered with no hospitalizations. CONCLUSIONS Our results emphasize the importance of genomic surveillance coupled with laboratory, clinical, and metadata analysis for a better understanding of the dynamics of viral spread and evolution.
Collapse
Affiliation(s)
- C Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, Maryland, USA
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Stuart C Ray
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| |
Collapse
|
26
|
Morris CP, Luo CH, Sachithanandham J, Li M, Schwartz M, Gaston DC, Gniazdowski V, Giraldo-Castillo N, Amadi A, Norton JM, Wright WF, Klein EY, Pekosz A, Mostafa HH. Large Scale SARS-CoV-2 Molecular Testing and Genomic Surveillance Reveal Prolonged Infections, Protracted RNA shedding, and Viral Reinfections. Front Cell Infect Microbiol 2022; 12:809407. [PMID: 35480235 PMCID: PMC9035932 DOI: 10.3389/fcimb.2022.809407] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/15/2022] [Indexed: 12/22/2022] Open
Abstract
Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for understanding cases of reinfection versus prolonged RNA shedding and protracted infections. In this study, data from a total of 22,292 clinical specimens, positive by SARS-CoV-2 molecular diagnosis at Johns Hopkins clinical virology laboratory between March 11th 2020 to September 23rd 2021, were used to identify patients with two or more positive results. A total of 3,650 samples collected from 1,529 patients who had between 2 and 20 positive results were identified in a time frame that extended up to 403 days from the first positive. Cycle threshold values (Ct) were available for 1,622 samples, the median of which was over 30 by 11 days after the first positive. Extended recovery of infectious virus on cell culture was notable for up to 70 days after the first positive in immunocompromised patients. Whole genome sequencing data generated as a part of our SARS-CoV-2 genomic surveillance was available for 1,027 samples from patients that had multiple positive tests. Positive samples collected more than 10 days after initial positive with high quality sequences (coverage >90% and mean depth >100), were more likely to be from unvaccinated, or immunosuppressed patients. Reinfections with viral variants of concern were found in 3 patients more than 130 days from prior infections with a different viral clade. In 75 patients that had 2 or more high quality sequences, the acquisition of more substitutions or deletions was associated with lack of vaccination and longer time between the recovered viruses. Our study highlights the value of integrating genomic, laboratory, and clinical data for understanding the biology of SARS-CoV-2 as well as for setting a precedent for future epidemics and pandemics.
Collapse
Affiliation(s)
- C. Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Matthew Schwartz
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - David C. Gaston
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Victoria Gniazdowski
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Nicolas Giraldo-Castillo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Julie M. Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - William F. Wright
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Eili Y. Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, United States
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| |
Collapse
|
27
|
Uhteg K, Amadi A, Forman M, Mostafa HH. Circulation of Non-SARS-CoV-2 Respiratory Pathogens and Coinfection with SARS-CoV-2 Amid the COVID-19 Pandemic. Open Forum Infect Dis 2022; 9:ofab618. [PMID: 35211632 PMCID: PMC8863080 DOI: 10.1093/ofid/ofab618] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Our understanding of the cocirculation of infrequently targeted respiratory pathogens and their contribution to symptoms during the coronavirus disease 2019 (COVID-19) pandemic is currently limited. This research aims at (1) understanding the epidemiology of respiratory pathogens since the start of the pandemic, (2) assessing the contribution of non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/influenza/respiratory syncytial virus (RSV) respiratory pathogens to symptoms, and (3) evaluating coinfection rates in SARS-CoV-2-positive patients, both vaccinated and unvaccinated. METHODS Retrospective analysis of respiratory pathogens identified by the Johns Hopkins Diagnostic Laboratory between December 2019 and October 2021 was performed. In addition, we assessed the contribution of respiratory pathogens other than SARS-CoV-2 to symptomatic disease by retesting 2 cohorts of specimens that were (1) collected from symptomatic patients and (2) received limited respiratory pathogen testing. The first cohort was patients who tested negative by the standard-of-care SARS-CoV-2/influenza/RSV testing. The second was a cohort of SARS-CoV-2-positive, symptomatic, fully COVID-19 immunized and unimmunized patients. RESULTS Between December 2019 and October 2021, a total of 11 806, 62 829, and 579 666 specimens were tested for an extended respiratory panel, influenza/RSV with or without SARS-CoV-2 panel, or SARS-CoV-2, respectively. Positivity rates of different targets differed between different months and were impacted by the COVID-19 pandemic. The SARS-CoV-2-negative cohort had 8.5% positivity for other respiratory pathogens that included primarily enterovirus/rhinovirus (5.8%). In the SARS-CoV-2-positive cohort, no other respiratory pathogens were detected. CONCLUSIONS The COVID-19 pandemic impacted the circulation of certain respiratory pathogens. Other respiratory viral pathogens were associated with symptomatic infections; however, coinfections with SARS-CoV-2 were highly uncommon.
Collapse
Affiliation(s)
- Katharine Uhteg
- Johns Hopkins Hospital Medical Microbiology Laboratory, Baltimore, Maryland, USA
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Forman
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
28
|
Fall A, Eldesouki RE, Sachithanandham J, Morris CP, Norton JM, Gaston DC, Forman M, Abdullah O, Gallagher N, Li M, Swanson NJ, Pekosz A, Klein EY, Mostafa HH. A Quick Displacement of the SARS-CoV-2 variant Delta with Omicron: Unprecedented Spike in COVID-19 Cases Associated with Fewer Admissions and Comparable Upper Respiratory Viral Loads. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.01.26.22269927. [PMID: 35118480 PMCID: PMC8811948 DOI: 10.1101/2022.01.26.22269927] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The increase in SARS-CoV-2 infections in December 2021 in the United States was driven primarily by the Omicron variant which largely displaced the Delta over a three week span. Outcomes from infection with the Omicron remain uncertain. We evaluate whether clinical outcomes and viral loads differ between Delta and Omicron infections during the period when both variants were co-circulating. METHODS Remnant clinical specimens from patients that tested positive for SARS-CoV-2 after standard of care testing between the last week of November and the end of December 2021were used for whole viral genome sequencing. Cycle threshold values (Ct) for viral RNA, the presence of infectious virus, and levels of respiratory IgG were measured, and clinical outcomes were obtained. Differences in each measure were compared between variants stratified by vaccination status. RESULTS The Omicron variant displaced the Delta during the study period and constituted 95% of the circulating lineages by the end of December 2021. Patients with Omicron infections (N= 1121) were more likely to be vaccinated compared to patients with Delta (N = 910), but were less likely to be admitted, require ICU level care, or succumb to infection regardless of vaccination status. There was no significant difference in Ct values based on the lineage regardless of the vaccination status. Recovery of infectious virus in cell culture was reduced in boosted patients compared to fully vaccinated without a booster and unvaccinated when infected with the Delta lineage. However, in patients with Omicron infections, recovery of infectious virus was not affected by vaccination. CONCLUSIONS Omicron infections of vaccinated individuals are expected, yet admissions are less frequent. Admitted patients might develop severe disease comparable to Delta. Efforts for reducing the Omicron transmission are required as even though the admission risk is lower, the numbers of infections continue to be high. RESEARCH IN CONTEXT EVIDENCE BEFORE THIS STUDY The unprecedented increase in COVID-19 cases in the month of December 2021, associated with the displacement of the Delta variant with the Omicron, triggered a lot of concerns. An understanding of the disease severity associated with infections with Omicron is essential as well as the virological determinants that contributed to its widespread predominance. We searched PubMed for articles published up to January 23, 2022, using the search terms ("Omicron") AND ("Disease severity") as well as ("Omicron") AND ("Viral load") And/ or ("Cell culture"). Our search yielded 3 main studies that directly assessed the omicron's clinical severity in South Africa, its infectious viral load compared to Delta, and the dynamics of viral RNA shedding. In South Africa, compared to Delta, Omicron infected patients showed a significant reduction in severe disease. In this study, Omicron and non-Omicron variants were characterized based on S gene target failure using the TaqPath COVID-19 PCR (Thermo Fisher Scientific). In the study from Switzerland that assessed the infectious viral load in Omicron versus Delta, the authors analyzed only 18 Omicron samples that were all from vaccinated individuals to show that compared to Delta, Omicron had equivalent infectious viral titers. The third study that assessed the Omicron viral dynamics showed that the peak viral RNA in Omicron infections is lower than Delta. No published studies assessed the clinical discrepancies of Omicron and Delta infected patients from the US, nor comprehensively assessed, by viral load and cell culture studies, the characteristics of both variants stratified by vaccination status. ADDED VALUE OF THIS STUDY To the best of our knowledge, this is the only study to date to compare the clinical characteristics and outcomes after infection with the Omicron variant compared to Delta in the US using variants characterized by whole genome sequencing and a selective time frame when both variant co-circulated. It is also the first study to stratify the analysis based on the vaccination status and to compare fully vaccinated patients who didn't receive a booster vaccination to patients who received a booster vaccination. In addition, we provide a unique viral RNA and infectious virus load analyses to compare Delta and Omicron samples from unvaccinated, fully vaccinated, and patients with booster vaccination. IMPLICATIONS OF ALL THE AVAILABLE EVIDENCE Omicron associated with a significant increase in infections in fully and booster vaccinated individuals but with less admissions and ICU level care. Admitted patients showed similar requirements for supplemental oxygen and ICU level care when compared to Delta admitted patients. Viral loads were similar in samples from Omicron and Delta infected patients regardless of the vaccination status. The recovery of infectious virus on cell culture was reduced in samples from patients infected with Delta who received a booster dose, but this was not the case with Omicron. The recovery of infectious virus was equivalent in Omicron infected unvaccinated, fully vaccinated, and samples from patients who received booster vaccination. FUNDING NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, Centers for Disease Control and Prevention contract 75D30121C11061.
Collapse
Affiliation(s)
- Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Raghda E Eldesouki
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | | | - C Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
- National Institute of Allergy and Infectious Disease, National Institutes of Health School of Public Health, Baltimore, Maryland, USA
| | - Julie M Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - David C Gaston
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Michael Forman
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Maggie Li
- National Institute of Allergy and Infectious Disease, National Institutes of Health School of Public Health, Baltimore, Maryland, USA
| | - Nicholas J Swanson
- National Institute of Allergy and Infectious Disease, National Institutes of Health School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- National Institute of Allergy and Infectious Disease, National Institutes of Health School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins School of Medicine
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine
- Center for Disease Dynamics, Economics, and Policy, Washington DC
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| |
Collapse
|
29
|
Digital Microfluidic qPCR Cartridge for SARS-CoV-2 Detection. MICROMACHINES 2022; 13:mi13020196. [PMID: 35208320 PMCID: PMC8874717 DOI: 10.3390/mi13020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023]
Abstract
Point-of-care (POC) tests capable of individual health monitoring, transmission reduction, and contact tracing are especially important in a pandemic such as the coronavirus disease 2019 (COVID-19). We develop a disposable POC cartridge that can be mass produced to detect the SARS-CoV-2 N gene through real-time quantitative polymerase chain reaction (qPCR) based on digital microfluidics (DMF). Several critical parameters are studied and improved, including droplet volume consistency, temperature uniformity, and fluorescence intensity linearity on the designed DMF cartridge. The qPCR results showed high accuracy and efficiency for two primer-probe sets of N1 and N2 target regions of the SARS-CoV-2 N gene on the DMF cartridge. Having multiple droplet tracks for qPCR, the presented DMF cartridge can perform multiple tests and controls at once.
Collapse
|
30
|
Comparison of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit and BioFire Respiratory Panel 2.1 for simultaneous detection of SARS-CoV-2, influenza A and B, and respiratory syncytial virus. J Virol Methods 2021; 298:114304. [PMID: 34592335 PMCID: PMC8482523 DOI: 10.1016/j.jviromet.2021.114304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 11/20/2022]
Abstract
The potential co-circulation of SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) could pose an unprecedented challenge to healthcare systems worldwide. Here, we compared the performance of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit (PowerChek) for simultaneous detection of SARS-CoV-2, influenza A and B, and respiratory syncytial virus with that of BioFire Respiratory Panel 2.1 (RP2.1) using 175 nasopharyngeal swab (NPS) specimens. Positive percent agreement and negative percent agreement of the PowerChek assay compared to RP2.1 were as follows: 100 % (40/40) and 100 % (135/135) for SARS-CoV-2; 100 % (39/39) and 100 % (136/136) for influenza A; 100 % (35/35) and 100 % (140/140) for influenza B; and 93.1 % (27/29) and 100 % (146/146) for RSV, respectively. The limit of detection (LOD) was accessed using RNA standards for each virus, and the LOD values of the PowerChek assay for SARS-CoV-2, influenza A and B, and RSV were 0.36, 1.24, 0.09, and 0.63 copies/μL, respectively. Our results demonstrate that the PowerChek assay is sensitive and accurate for detection of SARS-CoV-2, influenza A and B, and RSV, suggesting that this assay can be a valuable diagnostic tool when SARS-CoV-2, influenza, and RSV are co-circulating.
Collapse
|
31
|
Luo CH, Morris CP, Sachithanandham J, Amadi A, Gaston D, Li M, Swanson NJ, Schwartz M, Klein EY, Pekosz A, Mostafa HH. Infection with the SARS-CoV-2 Delta Variant is Associated with Higher Infectious Virus Loads Compared to the Alpha Variant in both Unvaccinated and Vaccinated Individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.15.21262077. [PMID: 34462756 PMCID: PMC8404894 DOI: 10.1101/2021.08.15.21262077] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND The emerging SARS-CoV-2 variant of concern (VOC) B.1.6.17.2 (Delta) quickly displaced the B.1.1.7 (Alpha) and is associated with increases in COVID-19 cases nationally. The Delta variant has been associated with greater transmissibility and higher viral RNA loads in both unvaccinated and fully vaccinated individuals. Data is lacking regarding the infectious virus load in Delta infected individuals and how that compares to individuals infected with other SARS-CoV-2 lineages. METHODS Whole genome sequencing of 2,785 clinical isolates was used to characterize the prevalence of SARS-CoV-2 lineages circulating in the National Capital Region between January and July 2021. Clinical chart reviews were performed for the Delta, Alpha, and B.1.2 (a control predominant lineage prior to both VOCs) variants to evaluate disease severity and outcome and Cycle threshold values (Cts) were compared. The presence of infectious virus was determined using Vero-TMPRSS2 cells and anti-SARS-CoV-2 IgG levels were determined from upper respiratory specimen. An analysis of infection in unvaccinated and fully vaccinated populations was performed. RESULTS The Delta variant displaced the Alpha variant to constitute 88.2% of the circulating lineages in the National Capital Region by July, 2021. The Delta variant associated with increased breakthrough infections in fully vaccinated individuals that were mostly symptomatic when compared to the Alpha breakthrough infections, though it is important to note there was a significantly longer period of time between vaccination and infection with Delta infections. The recovery of infectious virus on cell culture was significantly higher with the Delta variant compared to Alpha in both vaccinated and unvaccinated groups. The impact of vaccination on reducing the recovery of infectious virus from clinical samples was only observed with Alpha variant infections but was strongly associated with low localized SARS-CoV-2 IgG for both variants. A comparison of Ct values showed a significant decrease in the Delta compared to Alpha with no significant differences between unvaccinated and vaccinated groups. CONCLUSIONS Our data indicate that the Delta variant is associated with increased infectious virus loads when compared to the Alpha variant and decreased upper respiratory antiviral IgG levels. Measures to reduce transmission in addition to increasing vaccinations rates have to be implemented to reduce Delta variant spread. FUNDING NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, Centers for Disease Control and Prevention contract 75D30121C11061.
Collapse
Affiliation(s)
- Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - C Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
- National Institute of Allergy and Infectious Disease, National Institutes of Health
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - David Gaston
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nicholas J Swanson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine
- Center for Disease Dynamics, Economics, and Policy, Washington DC
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins School of Medicine
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| |
Collapse
|