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Smith L, Morris CP, Jibowu MH, Fallon S, Ray SC, Cosgrove SE, Curless MS, Fabre V, Karaba SM, Maragakis LL, Milstone AM, Sick-Samuels AC, Trexler P, Mostafa HH, Rock C. Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) exposure investigations using genomic sequencing among healthcare workers and patients in a large academic center. Infect Control Hosp Epidemiol 2023; 44:798-801. [PMID: 35232508 PMCID: PMC8943229 DOI: 10.1017/ice.2022.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/04/2023]
Abstract
Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) transmissions among healthcare workers and hospitalized patients are challenging to confirm. Investigation of infected persons often reveals multiple potential risk factors for viral acquisition. We combined exposure investigation with genomic analysis confirming 2 hospital-based clusters. Prolonged close contact with unmasked, unrecognized infectious, individuals was a common risk.
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Affiliation(s)
- Leigh Smith
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - C. Paul Morris
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Morgan H. Jibowu
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - Susan Fallon
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - Stuart C. Ray
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sara E. Cosgrove
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - Melanie S. Curless
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - Valeria Fabre
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - Sara M. Karaba
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lisa L Maragakis
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - Aaron M Milstone
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anna C. Sick-Samuels
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Polly Trexler
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
| | - Heba H. Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland
| | - Clare Rock
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, Maryland
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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.
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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
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Vukovikj M, Boshevska G, Janchevska E, Buzharova T, Preshova A, Simova M, Peshnacka A, Kocinski D, Kuzmanovska G, Memeti S, Gjorgoski I. In-depth genetic characterization of the SARS-CoV-2 pandemic in a two-year frame in North Macedonia using second and third generation sequencing technologies. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2022.1064882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a persistent negative impact on both the public health and the global economy. To comprehend the origin, transmission routes and discover the mutations that alter the virus’s transmissibility and pathogenicity, full-length SARS-CoV-2 genomes have to be molecularly characterized. Focusing on a two-year time frame (2020-2021), we provide an in-depth virologic and epidemiological overview of the SARS-CoV-2 pandemic in the Republic of North Macedonia by assessing the frequency and distribution of the circulating SARS-CoV-2 variants. Using genetic characterization and phylogenetic analysis we shed light on the molecular evolution of the virus as well as test for a possible connection between specific SARS-CoV-2 haplotypes and the severity of the clinical symptoms. Our results show that one fifth (21.51%) of the tested respiratory samples for SARS-CoV-2 were positive. A noticeable trend in the incidence and severity of the COVID-19 infections was observed in the 60+ age group between males and females. Of the total number of positive cases, the highest incidence of SARS-CoV-2 was noticed in 60+ males (4,170.4/100,000), with a statistically significant (0,0001) difference between the two sexes. Additionally, a 1.8x increase in male mortality and consequentially significantly higher number of death cases was observed compared to females of the same age group (0.001). A total of 327 samples were sequenced in the period March 2020 - August 2021, showing the temporal distribution of SARS-CoV-2 variants circulating in North Macedonia. The phylogenetic analysis showed that most of the viral genomes were closely related and clustered in four distinctive lineages, B.1, B.1.1.7, B.1.351 and B.1.617.2. A statistically significant difference was observed in the 2C_1 haplotype (p=0.0013), where 10.5% of the patients were hospitalized due to severe clinical condition. By employing genetic sequencing, coupled with epidemiological investigations, we investigated viral distribution patterns, identified emerging variants and detected vaccine breakthrough infections. The present work is the first molecular study giving a comprehensive overview of the genetic landscape of circulating SARS-CoV-2 viruses in North Macedonia in a period of two years.
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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.
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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
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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.
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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
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Kim Y, Bae JY, Kwon K, Chang HH, Lee WK, Park H, Kim J, Choi I, Park MS, Kim SW. Kinetics of neutralizing antibodies against SARS-CoV-2 infection according to sex, age, and disease severity. Sci Rep 2022; 12:13491. [PMID: 35931794 PMCID: PMC9356129 DOI: 10.1038/s41598-022-17605-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Knowledge of the factors affecting the difference in kinetics and longevity of the neutralizing antibody (nAb) response to SARS-CoV-2 is necessary to properly prioritize vaccination. In the present study, from March to December 2020, of the 143 patients who recovered from COVID-19, 87 underwent study visits scheduled every 3 months. Patient demographics and blood samples were collected followed by a plaque reduction neutralization test to analyze nAb titers. A linear mixed model was used to compare the effects of sex, age, and disease severity over time. Results demonstrated a gradual reduction in nAb titers over time with a significant decrease from 6 to 9 months post-COVID-19 infection (p < 0.001). In time-to-sex, age, and disease severity comparisons, reduction in nAb titers over time was unaffected by sex (p = 0.167), age (p = 0.188), or disease severity (p = 0.081). Additionally, the nAb titer was 1.46 times significantly higher in those aged ≥ 50 years than in those aged < 50 years (p = 0.036) irrespective of time Moreover, the nAb titer was 2.41 times higher in the moderate or above than that in the below moderate disease severity group (p < 0.001). However, no significant differences were observed in terms of sex (p = 0.300). Given the reduction in nAbs over time, maintaining protective neutralizing antibodies regardless of sex, age, or disease severity is needed.
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Affiliation(s)
- Yoonjung Kim
- Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, 130, Dongdeok-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Biosafety center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kitae Kwon
- Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, 130, Dongdeok-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Hyun-Ha Chang
- Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, 130, Dongdeok-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Won Kee Lee
- Department of Medical Informatics, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Biosafety center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jeonghun Kim
- Department of Microbiology, Institute for Viral Diseases, Biosafety center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Isaac Choi
- Department of Microbiology, Institute for Viral Diseases, Biosafety center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Biosafety center, College of Medicine, Korea University, Seoul, Republic of Korea.
| | - Shin-Woo Kim
- Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, 130, Dongdeok-ro, Jung-gu, Daegu, 41944, Republic of Korea.
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Talap J, Shen M, Yu L, Zeng S, Cai S. RT-LAMP assay combining multi-fluorescent probes for SARS-CoV-2 RNA detection and variant differentiation. Talanta 2022; 248:123644. [PMID: 35660994 PMCID: PMC9158328 DOI: 10.1016/j.talanta.2022.123644] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/15/2022]
Abstract
Simple and accurate testing tools for SARS-CoV-2 viral RNA detection are essential for the prevention of the spread of the virus and timely governmental actions. Herein, we present a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the simultaneous detection of ORF1ab and N gene fragments of SARS-CoV-2 in one pot. Using two primer sets and two molecular beacon (MB) probes respectively labelled with different fluorophore, positive results were obtained with a limit of detection of 20 and 2 copies/μL for ORF1ab and N gene fragments, respectively. Moreover, the RT-LAMP based assay was applied to detect single-site differences in S genes using two one-step displacement (OSD) probes targeting wild-type and mutant (P681R mutation was chosen as model) genes. Through that, the wild type strain and P681R mutant variant were well distinguished from each other, and a preliminary observation was also made on other mutations at this site such as P681H. The proposed method has high sensitivity for quantification and high specificity for mutation differentiation. In addition, it does not require accurate sophisticated thermal cycler instrumentation and can be used in clinical settings in resource-limited regions.
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Affiliation(s)
- Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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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.
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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.
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9
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Ciubotariu II, Dorman J, Perry NM, Gorenstein L, Kattoor JJ, Fola AA, Zine A, Hendrix GK, Wilkes RP, Kitchen A, Carpi G. Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant. Open Forum Infect Dis 2022; 9:ofac268. [PMID: 35818365 PMCID: PMC9213861 DOI: 10.1093/ofid/ofac268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Using a combination of data from routine surveillance, genomic sequencing, and phylogeographic analysis we tracked the spread and introduction events of SARS-CoV-2 variants focusing on a large university community.
Methods
Here, we sequenced and analyzed 677 high-quality SARS-CoV-2 genomes from positive RNA samples collected from Purdue University students, faculty, and staff who tested positive for the virus between January 2021 and May 2021, comprising an average of 32% of weekly cases across the time frame.
Results
Our analysis of circulating SARS-CoV-2 variants over time revealed periods when Variant of Concern (VOC) Alpha (B.1.1.7) and Iota (B.1.526) reached rapid dominance and documented that VOC Gamma (P.1) was increasing in frequency as campus surveillance was ending. Phylodynamic analysis of Gamma genomes from campus alongside a subsampling of >20,000 previously published P.1 genomes revealed ten independent introductions of this variant into the Purdue community, predominantly from elsewhere in the United States, with introductions from within the state of Indiana and from Illinois, and possibly Washington and New York, suggesting a degree of domestic spread.
Conclusions
We conclude that a robust and sustained active and passive surveillance program coupled with genomic sequencing during a pandemic offers important insights into the dynamics of pathogen arrival and spread in a campus community and can help guide mitigation measures.
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Affiliation(s)
- Ilinca I. Ciubotariu
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Jack Dorman
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Nicole M. Perry
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Lev Gorenstein
- Purdue University Information Technology Research Computing, , West Lafayette, Indiana 47907, USA
| | - Jobin J. Kattoor
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Abebe A. Fola
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Amy Zine
- University of Iowa Department of Anthropology, , Iowa City, Iowa, USA
| | - G. Kenitra Hendrix
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Rebecca P. Wilkes
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Andrew Kitchen
- University of Iowa Department of Anthropology, , Iowa City, Iowa, USA
| | - Giovanna Carpi
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation , Immunology and Infectious Disease, West Lafayette, Indiana 47907, USA
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10
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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.
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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
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11
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Almutairi MS, Assiri AM, Almohammed OA. Predictors of Poor Outcome among Critically Ill COVID-19 Patients: A Nationally Representative Sample of the Saudi Arabian Population. J Clin Med 2022; 11:jcm11102818. [PMID: 35628942 PMCID: PMC9147701 DOI: 10.3390/jcm11102818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 01/08/2023] Open
Abstract
The outbreak and continuing impact of COVID-19 have significantly increased the rates of hospitalization and admissions to intensive care units (ICU). This study evaluates clinical outcomes in critically ill patients and investigates variables tied to poor prognosis. A secondary database analysis was conducted to investigate the predictors of poor outcome among critically ill COVID-19 patients in Saudi Arabia. Multivariable logistic regression analysis was used to assess the association between various demographic characteristics, comorbidities, and COVID-19 symptoms and patients’ poor prognosis, as a composite outcome. A total of 2257 critically ill patients were identified (male (71.8%), and elderly (37.3%)). The mortality rate was 50.0%, and the composite poor outcome was 68.4%. The predictors of poor outcome were being elderly (OR = 4.79, 95%CI 3.19−7.18), obesity (OR = 1.43, 95%CI 1.1−1.87), having a severe or critical case at admission (OR = 6.46, 95%CI 2.34−17.8; OR = 22.3, 95%CI 11.0−45, respectively), and some signs and symptoms of COVID-19 such as shortness of breath, feeling fatigued or headache, respiratory rate ≥ 30/min, PaO2/FiO2 ratio < 300, and altered consciousness. In conclusion, identifying high-risk populations that are expected to have a poor prognosis based on their criteria upon admission helps policymakers and practitioners better triage patients when faced with limited healthcare resources.
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Affiliation(s)
- Masaad Saeed Almutairi
- Department of Pharmacy Practice, College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia;
| | - Ahmed M. Assiri
- Health Volunteering Center, Ministry of Health, Riyadh 11176, Saudi Arabia;
| | - Omar A. Almohammed
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Pharmacoeconomics Research Unit, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: ; Tel.: +966-555-10-4065
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12
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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: 6] [Impact Index Per Article: 3.0] [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.
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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
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13
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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: 23] [Impact Index Per Article: 11.5] [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.
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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
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14
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Fall A, Eldesouki RE, Sachithanandham J, Paul Morris C, 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. [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] [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.
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15
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Mendiola-Pastrana IR, López-Ortiz E, Río de la Loza-Zamora JG, González J, Gómez-García A, López-Ortiz G. SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review. Life (Basel) 2022; 12:life12020170. [PMID: 35207458 PMCID: PMC8879159 DOI: 10.3390/life12020170] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/19/2022] Open
Abstract
Background: From the start of the COVID-19 pandemic, new SARS-CoV-2 variants have emerged that potentially affect transmissibility, severity, and immune evasion in infected individuals. In the present systematic review, the impact of different SARS-CoV-2 variants on clinical outcomes is analyzed. Methods: A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020. Two databases (PubMed and ScienceDirect) were searched for original articles published from 1 January 2020 to 23 November 2021. The articles that met the selection criteria were appraised according to the Newcastle–Ottawa Quality Assessment Scale. Results: Thirty-three articles were included, involving a total of 253,209 patients and 188,944 partial or complete SARS-CoV-2 sequences. The most reported SARS-CoV-2 variants showed changes in the spike protein, N protein, RdRp and NSP3. In 28 scenarios, SARS-CoV-2 variants were found to be associated with a mild to severe or even fatal clinical outcome, 15 articles reported such association to be statistically significant. Adjustments in eight of them were made for age, sex and other covariates. Conclusions: SARS-CoV-2 variants can potentially have an impact on clinical outcomes; future studies focused on this topic should consider several covariates that influence the clinical course of the disease.
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Affiliation(s)
- Indira R. Mendiola-Pastrana
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - Eduardo López-Ortiz
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - José G. Río de la Loza-Zamora
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
| | - James González
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico;
| | - Anel Gómez-García
- Centro de Investigación Biomédica de Michoacán, Instituto Mexicano del Seguro Social, Morelia 58351, Mexico;
| | - Geovani López-Ortiz
- Subdivisión de Medicina Familiar, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico; (I.R.M.-P.); (E.L.-O.); (J.G.R.d.l.L.-Z.)
- Correspondence:
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16
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Schmidt M, Arshad M, Bernhart SH, Hakobyan S, Arakelyan A, Loeffler-Wirth H, Binder H. The Evolving Faces of the SARS-CoV-2 Genome. Viruses 2021; 13:1764. [PMID: 34578345 PMCID: PMC8472651 DOI: 10.3390/v13091764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023] Open
Abstract
Surveillance of the evolving SARS-CoV-2 genome combined with epidemiological monitoring and emerging vaccination became paramount tasks to control the pandemic which is rapidly changing in time and space. Genomic surveillance must combine generation and sharing sequence data with appropriate bioinformatics monitoring and analysis methods. We applied molecular portrayal using self-organizing maps machine learning (SOM portrayal) to characterize the diversity of the virus genomes, their mutual relatedness and development since the beginning of the pandemic. The genetic landscape obtained visualizes the relevant mutations in a lineage-specific fashion and provides developmental paths in genetic state space from early lineages towards the variants of concern alpha, beta, gamma and delta. The different genes of the virus have specific footprints in the landscape reflecting their biological impact. SOM portrayal provides a novel option for 'bioinformatics surveillance' of the pandemic, with strong odds regarding visualization, intuitive perception and 'personalization' of the mutational patterns of the virus genomes.
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Affiliation(s)
- Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Mamoona Arshad
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Stephan H. Bernhart
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Siras Hakobyan
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia
| | - Arsen Arakelyan
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
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17
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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: 80] [Impact Index Per Article: 26.7] [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.
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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
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