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Swami A, Mohanty A, Jamwal A, Turbadkar D, Baveja S, Shastri J, Chitalia V. A comparative analysis of the second and third wave of the Covid-19 pandemic: an experience from a tertiary care hospital in Western India. J Med Microbiol 2023; 72. [PMID: 37171852 DOI: 10.1099/jmm.0.001685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Introduction. As the world was still recovering from the 2020 pandemic, the devastating impact of Covid-19 driven by the Delta variant shook the world in 2021. As the second wave was declining, there was an unusual surge in Covid-19 positive cases by the end of 2021 which led to global concern about the change in virus characteristics.Hypothesis/gap statement. Whole genome sequencing is critical for understanding a rapidly progressing pandemic.Aim. To provide an insight into the major differences encountered in the changing characteristics between the second and third waves of the pandemic at a tertiary care hospital in India.Methods. A retrospective observational cohort analysis was conducted on Covid-positive patients during the second wave of the Covid-19 pandemic (from March 2021 to April 2021) and the third wave of the Covid-19 pandemic (from December 2021 to January 2022).Results. Out of 303 Covid-19 positive cases, 52 samples were tested by whole genome sequencing during the second wave and 108 during the third wave. A decline of 18.5 % was observed in the case fatality rate from the second wave to the third wave. There was a 5 % decline in the number of patients admitted with ARDS and a 16.3 % decline in the number of patients with co-morbidities.In total, 51.9 percent of cases were due to the Delta variant during the second wave and 95 percent due to the Omicron variant during the third wave. We found that 36.5 % of Covid-positive patients during the second wave had been vaccinated compared to 40 % in the third wave.Conclusion. Whole genome sequencing of clinical samples from a wide range of individuals during a viral epidemic will enable us to develop a more rapid public health response to new variants and identify the required vaccine modifications more quickly.
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Affiliation(s)
- Anjali Swami
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ankita Mohanty
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Ashima Jamwal
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Dilip Turbadkar
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Sujata Baveja
- Department of Microbiology, Lokmanya Tilak Municipal Medical College and General Hospital, Sion, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Department of Microbiology, T.N.Medical college and B.Y.L Nair Charitable Hospital and Lab Director, Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Vidushi Chitalia
- Molecular Lab, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
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Paulino-Ramírez R, López P, Mueses S, Cuevas P, Jabier M, Rivera-Amill V. Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085503. [PMID: 37107785 PMCID: PMC10138544 DOI: 10.3390/ijerph20085503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10-3 (95% HPD: 1.2358 × 10-3, 1.8635 × 10-3) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.
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Affiliation(s)
- Robert Paulino-Ramírez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Correspondence:
| | - Pablo López
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
| | - Sayira Mueses
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Paula Cuevas
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Maridania Jabier
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic
| | - Vanessa Rivera-Amill
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
- Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA
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Lawrence Panchali MJ, Kim CM, Lee YM, Seo JW, Kim DY, Yun NR, Kim DM. Diagnostic Sensitivity of Saliva and Other Respiratory Tract Samples of SARS-CoV-2 Variants in Patients with COVID-19. Microbiol Spectr 2023; 11:e0307622. [PMID: 36976007 PMCID: PMC10100734 DOI: 10.1128/spectrum.03076-22] [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] [Received: 08/08/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge during the ongoing coronavirus disease 2019 (COVID-19) pandemic. Contrasting studies on the omicron variant have demonstrated higher viral loads in different clinical specimens, which is consistent with its high transmissibility. We investigated the viral load in clinical specimens that were infected with the SARS-CoV-2 wild-type, delta, and omicron variants, and we analyzed the diagnostic accuracy of upper and lower respiratory specimens for these variants. We performed nested reverse transcription (RT)-polymerase chain reaction (PCR), targeting the spike gene and sequencing for variant classification. RT-PCR was performed using upper and lower respiratory specimens, including saliva from 78 COVID-19 patients (wild-type, delta, and omicron variants). A comparison of the sensitivity and specificity, using the area under the receiver operating characteristic curve (AUC) values from the N gene, showed that the omicron variant saliva samples had a higher sensitivity (AUC = 1.000) than did the delta (AUC = 0.875) and the wild-type (AUC = 0.878) variant samples. The sensitivity of the omicron saliva samples was greater than that of the wild-type nasopharynx and sputum samples (P < 0.001). The viral loads of the saliva samples containing the wild-type, delta, and omicron variants were 8.18 × 105, 2.77 × 106, and 5.69 × 105, respectively, which did not differ significantly (P = 0.610). Statistically significant differences were not observed in the saliva viral loads between vaccinated and nonvaccinated patients who were infected with the omicron variant (P = 0.120). In conclusion, omicron saliva samples had higher sensitivity than did wild-type and delta samples, and the viral load did not significantly differ between vaccinated and nonvaccinated patients. Further research is necessary to elucidate the mechanisms underlying the sensitivity differences. IMPORTANCE Owing to the vast heterogeneity of the studies focused on the correlation between the SARS-CoV-2 omicron variant and COVID-19, accurate comparisons of the specificity and sensitivity of samples and associated outcomes are still inconclusive. Moreover, limited information is available on the leading causes of infection and the factors that are associated with the conditions that underlie the spread of infection. Although several studies have contributed important knowledge regarding infectious specimens, the impact of saliva samples remains unknown. This study showed that the sensitivity of the omicron variant saliva samples was higher than that of the wild-type nasopharyngeal and sputum samples. Moreover, neither vaccinated nor nonvaccinated patients who were infected with the omicron variant showed any significant differences in SARS-CoV-2 viral loads. Hence, this study is an important step toward understanding how saliva sample results are correlated with other specimen results, regardless of the vaccination status of patients who are infected with the SARS-CoV-2 omicron variant.
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Affiliation(s)
| | - Choon-Mee Kim
- Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Yu-Mi Lee
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Jun-Won Seo
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Da Young Kim
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Na Ra Yun
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Dong-Min Kim
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
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Yin Y, Zeng T, Lai M, Luan Z, Wang K, Ma Y, Hu Z, Wang K, Peng Z. Impact of antibody-level on viral shedding in B.1.617.2 (Delta) variant-infected patients analyzed using a joint model of longitudinal and time-to-event data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:8875-8891. [PMID: 37161226 DOI: 10.3934/mbe.2023390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Knowledge of viral shedding remains limited. Repeated measurement data have been rarely used to explore the influencing factors. In this study, a joint model was developed to explore and validate the factors influencing the duration of viral shedding based on longitudinal data and survival data. We divided 361 patients infected with Delta variant hospitalized in Nanjing Second Hospital into two groups (≤ 21 days group and > 21 days group) according to the duration of viral shedding, and compared their baseline characteristics. Correlation analysis was performed to identify the factors influencing the duration of viral shedding. Further, a joint model was established based on longitudinal data and survival data, and the Markov chain Monte Carlo algorithm was used to explain the influencing factors. In correlation analysis, patients having received vaccination had a higher antibody level at admission than unvaccinated patients, and with the increase of antibody level, the duration of viral shedding shortened. The linear mixed-effects model showed the longitudinal variation of logSARS-COV-2 IgM sample/cutoff (S/CO) values, with a parameter estimate of 0.193 and a standard error of 0.017. Considering gender as an influencing factor, the parameter estimate of the Cox model and their standard error were 0.205 and 0.1093 (P = 0.608), the corresponding OR value was 1.228. The joint model output showed that SARS-COV-2 IgM (S/CO) level was strongly associated with the risk of a composite event at the 95% confidence level, and a doubling of SARS-COV-2 IgM (S/CO) level was associated with a 1.38-fold (95% CI: [1.16, 1.72]) increase in the risk of viral non-shedding. A higher antibody level in vaccinated patients, as well as the presence of IgM antibodies in serum, can accelerate shedding of the mutant virus. This study provides some evidence support for vaccine prevention and control of COVID-19 variants.
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Affiliation(s)
- Yi Yin
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ting Zeng
- College of Public Health, Xinjiang Medical University, Urumqi 830017, China
| | - Miao Lai
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zemin Luan
- College of Public Health, Xinjiang Medical University, Urumqi 830017, China
| | - Kai Wang
- Jiangsu Provincial Key Laboratory of Geriatrics, Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing 211166, China
| | - Yuhang Ma
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiliang Hu
- Department of Infectious Disease, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Kai Wang
- Department of Medical Engineering and Technology, Xinjiang Medical University, Urumqi 830017, China
| | - Zhihang Peng
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Baker FL, Zúñiga TM, Smith KA, Batatinha H, Kulangara TS, Seckeler MD, Burgess SC, Katsanis E, Simpson RJ. Exercise mobilizes diverse antigen specific T-cells and elevates neutralizing antibodies in humans with natural immunity to SARS CoV-2. Brain Behav Immun Health 2023; 28:100600. [PMID: 36743994 PMCID: PMC9886396 DOI: 10.1016/j.bbih.2023.100600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/03/2023] Open
Abstract
Epidemiological data suggest that physical activity protects against severe COVID-19 and improves clinical outcomes, but how exercise augments the SARS-CoV-2 viral immune response has yet to be elucidated. Here we determine the antigen-specific CD4 and CD8 T-cell and humoral immunity to exercise in non-vaccinated individuals with natural immunity to SARS CoV-2, using whole-blood SARS-CoV-2 peptide stimulation assays, IFN-γ ELISPOT assays, 8-color flow cytometry, deep T-cell receptor (TCR) β sequencing, and anti-RBD-1 neutralizing antibody serology. We found that acute exercise reliably mobilized (∼2.5-fold increase) highly functional SARS-CoV-2-specific T-cells to the blood compartment in those with natural immunity to the virus. The mobilized cells reacted with spike protein (including alpha (α) and delta (δ)-variants), membrane, and nucleocapsid peptides in those previously infected but not in controls. Both groups reliably mobilized T-cells reacting with Epstein-Barr viral peptides. Exercise mobilized SARS-CoV-2 specific T-cells maintained broad TCR-β diversity with no impact on CDR3 length or V and J family gene usage. Exercise predominantly mobilized MHC I restricted (i.e. CD8+) SARS-CoV-2 specific T-cells that recognized ORF1ab, surface, ORF7b, nucleocapsid, and membrane proteins. SARS-CoV-2 neutralizing antibodies were transiently elevated ∼1.5-fold during exercise after infection. In conclusion, we provide novel data on a potential mechanism by which exercise could increase SARS-CoV-2 immunosurveillance via the mobilization and redistribution of antigen-specific CD8 T-cells and neutralizing antibodies. Further research is needed to define the tissue specific disease protective effects of exercise as SARS-CoV-2 continues to evolve, as well as the impact of COVID-19 vaccination on this response.
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Affiliation(s)
- Forrest L. Baker
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States,Department of Pediatrics, The University of Arizona, Tucson, AZ, United States,Corresponding author. School of Nutritional Sciences and Wellness, The University of Arizona, 1177 E. Fourth Street Shantz Building Room 308, Tucson, AZ, 85721, United States
| | - Tiffany M. Zúñiga
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Kyle A. Smith
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Helena Batatinha
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Terese S. Kulangara
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States
| | - Michael D. Seckeler
- Department of Pediatrics (Cardiology), The University of Arizona, Tucson, AZ, United States
| | - Shane C. Burgess
- Department of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, United States,Department of Immunobiology, The University of Arizona, Tucson, AZ, United States
| | - Emmanuel Katsanis
- Department of Pediatrics, The University of Arizona, Tucson, AZ, United States,Department of Immunobiology, The University of Arizona, Tucson, AZ, United States,The University of Arizona Cancer Center, Tucson, AZ, United States,Department of Medicine, The University of Arizona, Tucson, AZ, United States,Department of Pathology, The University of Arizona, Tucson, AZ, United States
| | - Richard J. Simpson
- School of Nutritional Sciences and Wellness, The University of Arizona, Tucson, AZ, United States,Department of Pediatrics, The University of Arizona, Tucson, AZ, United States,Department of Immunobiology, The University of Arizona, Tucson, AZ, United States,The University of Arizona Cancer Center, Tucson, AZ, United States
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He J, Wei Z, Leng T, Bao J, Gao X, Chen F. Vaccination options for pregnant women during the Omicron period. J Reprod Immunol 2023; 156:103798. [PMID: 36640675 PMCID: PMC9817340 DOI: 10.1016/j.jri.2023.103798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/02/2022] [Accepted: 01/05/2023] [Indexed: 01/08/2023]
Abstract
Omicron exhibits reduced pathogenicity in general population than the previous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. However, the severity of disease and pregnancy outcomes of Omicron infection among pregnant women have not yet been definitively established. Meanwhile, substantial proportions of this population have doubts about the necessity of vaccination given the reports of declining efficacy of coronavirus disease 2019 (COVID-19) vaccines. Herein, we comprehensively discuss the clinical outcomes of infected pregnant women during the Omicron period and summarize the available data on the safety and efficacy profile of COVID-19 vaccination. The results found that the incidence of moderate and severe disease, maternal mortality, pregnancy loss, preterm delivery, stillbirth, preeclampsia/eclampsia, and gestational hypertension during the Omicron period are similar to those during the Pre-Delta period. In view of the effects of mass vaccination and previous natural infection on disease severity, the virulence of Omicron in pregnant women may be comparable to or even higher than that of the Pre-Delta variant. Moreover, the currently approved COVID-19 vaccines are safe and effective for pregnant women. Particularly, those who received a second or third dose had significantly less severe disease with little progression to critical illness or death compared with those who were unvaccinated or received only one dose. Therefore, in the case of the rapid spread of Omicron, pregnant women should still strictly follow preventive measures to avoid infection and receive the COVID-19 vaccine in a timely manner.
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Affiliation(s)
- Jiarui He
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Zichun Wei
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Taiyang Leng
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Jiaqi Bao
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Xinyao Gao
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Fei Chen
- Jining Medical University, 133 Hehua Rd, Jining 272067, China.
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Wang H, Lan Y. The global dynamic transmissibility of COVID-19 and its influencing factors: an analysis of control measures from 176 countries. BMC Public Health 2023; 23:404. [PMID: 36855085 PMCID: PMC9971674 DOI: 10.1186/s12889-023-15174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023] Open
Abstract
OBJECTIVE To summarise the dynamic characteristics of COVID-19 transmissibility; To analyse and quantify the effect of control measures on controlling the transmissibility of COVID-19; To predict and compare the effectiveness of different control measures. METHODS We used the basic reproduction number ([Formula: see text]) to measure the transmissibility of COVID-19, the transmissibility of COVID-19 and control measures of 176 countries and regions from January 1, 2020 to May 14, 2022 were included in the study. The dynamic characteristics of COVID-19 transmissibility were summarised through descriptive research and a Dynamic Bayesian Network (DBN) model was constructed to quantify the effect of control measures on controlling the transmissibility of COVID-19. RESULTS The results show that the spatial transmissibility of COVID-19 is high in Asia, Europe and Africa, the temporal transmissibility of COVID-19 increases with the epidemic of Beta and Omicron strains. Dynamic Bayesian Network (DBN) model shows that the transmissibility of COVID-19 is negatively correlated with control measures. Restricting population mobility has the strongest effect, nucleic acid testing (NAT) has a strong effect, and vaccination has the weakest effect. CONCLUSION Strict control measures are essential for controlling the COVID-19 outbreak; Restricting population mobility and nucleic acid testing (NAT) have significant impacts on controlling the COVID-19 transmissibility, while vaccination has no significant impact. In light of these findings, future control measures may include the widespread use of new NAT technology and the promotion of booster immunization.
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Affiliation(s)
- Hongjian Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yajia Lan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
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Piranej S, Zhang L, Bazrafshan A, Marin M, Melikyan GB, Salaita K. Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530294. [PMID: 36909543 PMCID: PMC10002644 DOI: 10.1101/2023.02.27.530294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Assays detecting viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here we present Rolosense, a virus sensing platform that transduces the motion of synthetic DNA-based motors transporting 5-micron particles on RNA fuel chips. Motors and chips are modified with virus-binding aptamers that lead to stalling of motion. Therefore, motors perform a "mechanical test" of viral target and stall in the presence of whole virions which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as we demonstrated one-pot detection of influenza A and SARS-CoV-2. As a proof-of-concept, we show readout can be achieved using a smartphone camera in as little as 15 mins without any sample preparation steps. Taken together, mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost, point-of-care screening of circulating viruses.
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Affiliation(s)
- Selma Piranej
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
| | - Luona Zhang
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
| | | | - Mariana Marin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322 (USA)
- Children’s Healthcare of Atlanta, Atlanta, Georgia 30322 (USA)
| | - Gregory B. Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322 (USA)
- Children’s Healthcare of Atlanta, Atlanta, Georgia 30322 (USA)
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322 (USA)
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Karimizadeh Z, Dowran R, Mokhtari-azad T, Shafiei-Jandaghi NZ. The reproduction rate of severe acute respiratory syndrome coronavirus 2 different variants recently circulated in human: a narrative review. Eur J Med Res 2023; 28:94. [PMID: 36823532 PMCID: PMC9950018 DOI: 10.1186/s40001-023-01047-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
SARS-COV-2 is responsible for the current worldwide pandemic, which started on December 2019 in Wuhan, China. On March 2020 World Health Organization announced COVID-19 as the new pandemic. Some SARS-COV-2 variants have increased transmissibility, cause more severe disease (e.g., increased hospitalizations or deaths), are resistant to antibodies produced by the previous infection or vaccination, and there is more difficulty in treatment and diagnosis of them. World Health Organization considered them as SARS-CoV-2 variants of concern. The introductory reproduction rate (R0) is an epidemiologic index of the transmissibility of the virus, defined as the average number of persons infected by the virus after known contact with an infectious person in a susceptible population. An R0 > 1 means that the virus is spreading exponentially, and R0 < 1, means that the outbreak is subsiding. In various studies, the estimated R and VOC growth rates were reported to be greater than the ancestral strains. However, it was also a low level of concordance between the estimated Rt of the same variant in different studies. It is because the R of a variant not only dependent on the biological and intrinsic factors of the virus but also several parameters can affect the R0, including the duration of contagiousness and the likelihood of infection per contact. Evaluation of changes in SARS-CoV-2 has shown that the rate of human-to-human transmission of this virus has increased. Like other viruses with non-human sources which succeeded in surviving in the human population, SARS-CoV-2 has gradually adapted to the human population, and its ability to transmit from human to human has increased. Of course, due to the continuous changes in this virus, it is crucial to survey the rate of transmission of the virus over time.
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Affiliation(s)
- Zahra Karimizadeh
- grid.411705.60000 0001 0166 0922Students’ Scientific Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Razieh Dowran
- grid.411705.60000 0001 0166 0922Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-azad
- grid.411705.60000 0001 0166 0922Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Development of Next Generation Vaccines against SARS-CoV-2 and Variants of Concern. Viruses 2023; 15:v15030624. [PMID: 36992333 PMCID: PMC10057551 DOI: 10.3390/v15030624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
SARS-CoV-2 has caused the COVID-19 pandemic, with over 673 million infections and 6.85 million deaths globally. Novel mRNA and viral-vectored vaccines were developed and licensed for global immunizations under emergency approval. They have demonstrated good safety and high protective efficacy against the SARS-CoV-2 Wuhan strain. However, the emergence of highly infectious and transmissible variants of concern (VOCs) such as Omicron was associated with considerable reductions in the protective efficacy of the current vaccines. The development of next-generation vaccines that could confer broad protection against both the SARS-CoV-2 Wuhan strain and VOCs is urgently needed. A bivalent mRNA vaccine encoding the Spike proteins of both the SARS-CoV-2 Wuhan strain and the Omicron variant has been constructed and approved by the US FDA. However, mRNA vaccines are associated with instability and require an extremely low temperature (−80 °C) for storage and transportation. They also require complex synthesis and multiple chromatographic purifications. Peptide-based next-generation vaccines could be developed by relying on in silico predictions to identify peptides specifying highly conserved B, CD4+ and CD8+ T cell epitopes to elicit broad and long-lasting immune protection. These epitopes were validated in animal models and in early phase clinical trials to demonstrate immunogenicity and safety. Next-generation peptide vaccine formulations could be developed to incorporate only naked peptides, but they are costly to synthesize and production would generate extensive chemical waste. Continual production of recombinant peptides specifying immunogenic B and T cell epitopes could be achieved in hosts such as E. coli or yeast. However, recombinant protein/peptide vaccines require purification before administration. The DNA vaccine might serve as the most effective next-generation vaccine for low-income countries, since it does not require an extremely low temperature for storage or need extensive chromatographic purification. The construction of recombinant plasmids carrying genes specifying highly conserved B and T cell epitopes meant that vaccine candidates representing highly conserved antigenic regions could be rapidly developed. Poor immunogenicity of DNA vaccines could be overcome by the incorporation of chemical or molecular adjuvants and the development of nanoparticles for effective delivery.
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Albreiki M, Mousa M, Azman SK, Vurivi H, Alhalwachi Z, Alshehhi F, AlShamsi S, Marzouqi NA, Alawadi T, Alrand H, Oulhaj A, Fikri A, Alsafar H. Risk of hospitalization and vaccine effectiveness among COVID-19 patients in the UAE during the Delta and Omicron outbreaks. Front Immunol 2023; 14:1049393. [PMID: 36860855 PMCID: PMC9969353 DOI: 10.3389/fimmu.2023.1049393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/20/2023] [Indexed: 02/17/2023] Open
Abstract
Introduction A rapid increase in COVID-19 cases due to the spread of the Delta and Omicron variants in vaccinated populations has raised concerns about the hospitalization risk associated with, and the effectiveness of, COVID-19 vaccines. Method This case-control study aims to determine the hospitalization risk associated with the inactivated BBIBP-CorV (Sinopharm) and mRNA BNT162b2 (Pfizer-BionTech) vaccines, and their effectiveness reducing the rate of hospital admission between 28 May 2021 and 13 January 2022, during the Delta and Omicron outbreaks. The estimation of vaccine effectiveness of 4,618 samples was based on the number of patients hospitalized at different vaccination statuses, adjusted for confounding variables. Results Hospitalization risk increases in patients affected with the Omicron variant if patients are aged ≤ 18 years (OR 6.41, 95% CI 2.90 to 14.17; p < 0.001), and in patients affected with the Delta variant if they are aged > 45 years (OR 3.41, 95% CI 2.21 to 5.50; p < 0.001). Vaccine effectiveness reducing the rate of hospital admission for fully vaccinated participants infected with the Delta and Omicron variants was similar for both the BBIBP-CorV (94%, 95% CI 90% to 97%; 90%, 95% CI 74% to 96%) and BNT162b2 vaccines (95%, 95% CI 61% to 99.3%; 94%, 95% CI 53% to 99%), respectively. Discussion The BBIBP-CorV and BNT162b2 vaccines utilized in the UAE vaccination program were highly effective in reducing the rate of COVID-19-related hospitalization during the Delta and Omicron outbreaks, and further effort must be taken to achieve high vaccine coverage rates in children and adolescents in the global context to reduce the hospitalization risk associated with COVID-19 on an international scale.
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Affiliation(s)
- Mohammed Albreiki
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Nuffield Department of Women’s and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Syafiq Kamarul Azman
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hema Vurivi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Zainab Alhalwachi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Fatima Alshehhi
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Safiya AlShamsi
- National Center for Health Research, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Nada Al Marzouqi
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Tayba Alawadi
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Hussain Alrand
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Abderrahim Oulhaj
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
- Research and Data Intelligence Support Center, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Asma Fikri
- National Center for Health Research, Ministry of Health and Prevention, Dubai, United Arab Emirates
- Faculty of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Emirates Health Services Establishment, Dubai, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
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Cunningham CL, Frye CJ, Makowski JA, Kensinger AH, Shine M, Milback EJ, Lackey PE, Evanseck JD, Mihailescu MR. Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.528014. [PMID: 36798421 PMCID: PMC9934655 DOI: 10.1101/2023.02.10.528014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The stem loop 2 motif (s2m), a highly conserved 41-nucleotide hairpin structure in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a greater than 99% correlation of a single nucleotide mutation at the 15 th position (G15U) in Delta SARS-CoV-2. Based on 1 H NMR assignments comparing the imino proton resonance region of s2m and the G15U at 19°C, we find that the U15-A29 base pair closes resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we find that the s2m G15U mutation drastically reduces the binding affinity of the host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on the immune response.
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Characterization of a Vesicular Stomatitis Virus-Vectored Recombinant Virus Bearing Spike Protein of SARS-CoV-2 Delta Variant. Microorganisms 2023; 11:microorganisms11020431. [PMID: 36838396 PMCID: PMC9960918 DOI: 10.3390/microorganisms11020431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
The frequent emergence of SARS-CoV-2 variants thwarts the prophylactic and therapeutic countermeasures confronting COVID-19. Among them, the Delta variant attracts widespread attention due to its high pathogenicity and fatality rate compared with other variants. However, with the emergence of new variants, studies on Delta variants have been gradually weakened and ignored. In this study, a replication-competent recombinant virus carrying the S protein of the SARS-CoV-2 Delta variant was established based on the vesicular stomatitis virus (VSV), which presented a safe alternative model for studying the Delta variant. The recombinant virus showed a replication advantage in Vero E6 cells, and the viral titers reach 107.3 TCID50/mL at 36 h post-inoculation. In the VSV-vectored recombinant platform, the spike proteins of the Delta variant mediated higher fusion activity and syncytium formation than the wild-type strain. Notably, the recombinant virus was avirulent in BALB/c mice, Syrian hamsters, 3-day ICR suckling mice, and IFNAR/GR-/- mice. It induced protective neutralizing antibodies in rodents, and protected the Syrian hamsters against the SARS-CoV-2 Delta variant infection. Meanwhile, the eGFP reporter of recombinant virus enabled the visual assay of neutralizing antibodies. Therefore, the recombinant virus could be a safe and convenient surrogate tool for authentic SARS-CoV-2. This efficient and reliable model has significant potential for research on viral-host interactions, epidemiological investigation of serum-neutralizing antibodies, and vaccine development.
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Khatri R, Siddqui G, Sadhu S, Maithil V, Vishwakarma P, Lohiya B, Goswami A, Ahmed S, Awasthi A, Samal S. Intrinsic D614G and P681R/H mutations in SARS-CoV-2 VoCs Alpha, Delta, Omicron and viruses with D614G plus key signature mutations in spike protein alters fusogenicity and infectivity. Med Microbiol Immunol 2023; 212:103-122. [PMID: 36583790 PMCID: PMC9801140 DOI: 10.1007/s00430-022-00760-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022]
Abstract
The SARS-CoV-2 virus has been rapidly evolving over the time and the genetic variation has led to the generation of Variants of Concerns (VoC), which have shown increased fitness. These VoC viruses contain the key mutations in the spike protein which have allowed better survival and evasion of host defense mechanisms. The D614G mutation in the spike domain is found in the majority of VoC; additionally, the P681R/H mutation at the S1/S2 furin cleavage site junction is also found to be highly conserved in major VoCs; Alpha, Delta, Omicron, and its' current variants. The impact of these genetic alterations of the SARS-CoV-2 VoCs on the host cell entry, transmissibility, and infectivity has not been clearly identified. In our study, Delta and D614G + P681R synthetic double mutant pseudoviruses showed a significant increase in the cell entry, cell-to-cell fusion and infectivity. In contrast, the Omicron and P681H synthetic single mutant pseudoviruses showed TMPRSS2 independent cell entry, less fusion and infectivity as compared to Delta and D614G + P681R double mutants. Addition of exogenous trypsin further enhanced fusion in Delta viruses as compared to Omicron. Furthermore, Delta viruses showed susceptibility to both E64d and Camostat mesylate inhibitors suggesting, that the Delta virus could exploit both endosomal and TMPRSS2 dependent entry pathways as compared to the Omicron virus. Taken together, these results indicate that the D614G and P681R/H mutations in the spike protein are pivotal which might be favoring the VoC replication in different host compartments, and thus allowing a balance of mutation vs selection for better long-term adaptation.
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Affiliation(s)
- Ritika Khatri
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Gazala Siddqui
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Srikanth Sadhu
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
- Immunobiology and Immunology Core Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Vikas Maithil
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Preeti Vishwakarma
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Bharat Lohiya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Abhishek Goswami
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Shubbir Ahmed
- Centralized Core Research Facility (CCRF), All India Institute of Medical Science (AIIMS), Delhi, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
- Immunobiology and Immunology Core Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Sweety Samal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India.
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Cox M, Peacock TP, Harvey WT, Hughes J, Wright DW, Willett BJ, Thomson E, Gupta RK, Peacock SJ, Robertson DL, Carabelli AM. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nat Rev Microbiol 2023; 21:112-124. [PMID: 36307535 PMCID: PMC9616429 DOI: 10.1038/s41579-022-00809-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 01/20/2023]
Abstract
Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.
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Affiliation(s)
- MacGregor Cox
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Derek W Wright
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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Gomes da Silva P, Gonçalves J, Torres Franco A, Rodriguez E, Diaz I, Orduña Domingo A, Garcinuño Pérez S, March Roselló GA, Dueñas Gutiérrez CJ, São José Nascimento M, Sousa SI, Garcia Encina P, Mesquita JR. Environmental Dissemination of SARS-CoV-2 in a University Hospital during the COVID-19 5th Wave Delta Variant Peak in Castile-León, Spain. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1574. [PMID: 36674328 PMCID: PMC9866319 DOI: 10.3390/ijerph20021574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
The dominant SARS-CoV-2 Delta variant (B.1.617.2) became the main circulating variant among countries by mid 2021. Attention was raised to the increased risk of airborne transmission, leading to nosocomial outbreaks even among vaccinated individuals. Considering the increased number of COVID-19 hospital admissions fueled by the spread of the variant, with Spain showing the highest COVID-19 rates in mainland Europe by July 2021, the aim of this study was to assess SARS-CoV-2 environmental contamination in different areas of a University Hospital in the region of Castile-León, Spain, during the peak of the 5th wave of COVID-19 in the country (July 2021). Air samples were collected from sixteen different areas of the Hospital using a Coriolis® μ air sampler. Surface samples were collected in these same areas using sterile flocked plastic swabs. RNA extraction followed by a one-step RT-qPCR were performed for detection of SARS-CoV-2 RNA. Of the 21 air samples, only one was positive for SARS-CoV-2 RNA, from the emergency waiting room. Of the 40 surface samples, 2 were positive for SARS-CoV-2 RNA, both from the microbiology laboratory. These results may be relevant for risk assessment of nosocomial infection within healthcare facilities, thus helping prevent and minimize healthcare staff's exposure to SARS-CoV-2, reinforcing the importance of always wearing appropriate and well-fit masks at all times and proper PPE when in contact with infected patients.
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Affiliation(s)
- Priscilla Gomes da Silva
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 1800-412 Porto, Portugal
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 1800-412 Porto, Portugal
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 1800-412 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 1800-412 Porto, Portugal
| | - José Gonçalves
- Institute of Sustainable Processes, Valladolid University, Dr. Mergelina S/N., 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., 47011 Valladolid, Spain
| | - Andrés Torres Franco
- Institute of Sustainable Processes, Valladolid University, Dr. Mergelina S/N., 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., 47011 Valladolid, Spain
| | - Elisa Rodriguez
- Institute of Sustainable Processes, Valladolid University, Dr. Mergelina S/N., 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., 47011 Valladolid, Spain
| | - Israel Diaz
- Institute of Sustainable Processes, Valladolid University, Dr. Mergelina S/N., 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., 47011 Valladolid, Spain
| | - Antonio Orduña Domingo
- Microbiology Service, Valladolid University Clinical Hospital (HCUV), Faculty of Medicine, University of Valladolid, 47011 Valladolid, Spain
| | | | | | - Carlos Jesús Dueñas Gutiérrez
- Internal Medicine, Infectious Diseases Section, Valladolid University Clinical Hospital (HCUV), 47011 Valladolid, Spain
| | | | - Sofia I.V. Sousa
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 1800-412 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 1800-412 Porto, Portugal
| | - Pedro Garcia Encina
- Institute of Sustainable Processes, Valladolid University, Dr. Mergelina S/N., 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., 47011 Valladolid, Spain
| | - João R. Mesquita
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 1800-412 Porto, Portugal
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 1800-412 Porto, Portugal
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Dwivedi R, Sharma P, Eilts F, Zhang F, Linhardt RJ, Tandon R, Pomin VH. Anti-SARS-CoV-2 and anticoagulant properties of Pentacta pygmaea fucosylated chondroitin sulfate depend on high molecular weight structures. Glycobiology 2023; 33:75-85. [PMID: 36136750 PMCID: PMC9829039 DOI: 10.1093/glycob/cwac063] [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: 07/14/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 01/28/2023] Open
Abstract
Fucosylated chondroitin sulfate (FucCS) is a unique marine glycosaminoglycan that exhibits diverse biological functions, including antiviral and anticoagulant activity. In previous work, the FucCS derived from Pentacta pygmaea (PpFucCS) showed moderate anticoagulant effect but high inhibitory activity against the Wuhan strain of severe acute respiratory syndrome coronavirus (SARS-CoV-2). In this study, we perform free-radical depolymerization of PpFucCS by the copper-based Fenton method to generate low molecular weight (MW) oligosaccharides. PpFucCS oligosaccharides were structurally analyzed by 1H nuclear magnetic resonance spectroscopy and were used to conduct structure-activity relationship studies regarding their effects against SARS-CoV-2 and clotting. Anticoagulant properties were measured by activated partial thromboplastin time, protease (factors Xa and IIa) inhibition by serine protease inhibitors (antithrombin [AT] and heparin cofactor II [HCII]), and competitive surface plasmon resonance (SPR) assay using AT, HCII, and IIa. Anti-SARS-CoV-2 properties were measured by the concentration-response inhibitory curves of HEK-293T-human angiotensin-converting enzyme-2 cells infected with a baculovirus pseudotyped SARS-CoV-2 Delta variant spike (S)-protein and competitive SPR assays using multiple S-proteins (Wuhan, N501Y [Alpha], K417T/E484K/N501Y [Gamma], L542R [Delta], and Omicron [BA.2 subvariant]). Cytotoxicity of native PpFucCS and oligosaccharides was also assessed. The PpFucCS-derived oligosaccharide fraction of the highest MW showed great anti-SARS-CoV-2 Delta activity and reduced anticoagulant properties. Results have indicated no cytotoxicity and MW dependency on both anti-SARS-CoV-2 and anticoagulant effects of PpFucCS, as both actions were reduced accordingly to the MW decrease of PpFucCS. Our results demonstrate that the high-MW structures of PpFucCS is a key structural element to achieve the maximal anti-SARS-CoV-2 and anticoagulant effects.
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Affiliation(s)
- Rohini Dwivedi
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Poonam Sharma
- Center for Immunology and Microbial Research, Department of Cell Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Friederike Eilts
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Giessen 35390, Germany
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Ritesh Tandon
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Center for Immunology and Microbial Research, Department of Cell Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- School of Pharmacy, Research Institute of Pharmaceutical Sciences, University of Mississippi, Oxford, MS 38677, United States
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Stein SJ, Ravnholdt AR, Herrera VL, Rivera DN, Williams PT, Santarpia JL. SARS-CoV-2 Aerosol and Surface Detections in COVID-19 Testing Centers and Implications for Transmission Risk in Public Facing Workers. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:976. [PMID: 36673732 PMCID: PMC9859205 DOI: 10.3390/ijerph20020976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and resulting COVID-19 (coronavirus disease 2019) pandemic have required mass diagnostic testing, often taking place in testing sites within hospitals, clinics, or at satellite locations. To establish the potential of SARS-CoV-2 aerosol transmission and to identify junctures during testing that result in increased viral exposure, aerosol and surface samples were examined for the presence of SARS-CoV-2 RNA from locations within Nebraska Medicine COVID-19 testing and vaccine clinics. Aerosols containing SARS-CoV-2 RNA detected within clinics suggest viral shedding from infected individuals. SARS-CoV-2 RNA detection in aerosol samples was shown to correlate with clinic operation and patient infection, as well as with community infection findings. Additionally, SARS-CoV-2 RNA was detected in surface samples collected from clinics. The presence of SARS-CoV-2 RNA in aerosols in these clinics supports the continued use of respiratory protection and sanitization practices for healthcare workers, and other workers with public facing occupations.
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Affiliation(s)
- Sarah J. Stein
- Department of Pathology and Microiology, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | - Ashley R. Ravnholdt
- Department of Pathology and Microiology, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | - Vicki L. Herrera
- Department of Pathology and Microiology, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | - Danielle N. Rivera
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE 68106, USA
- National Strategic Research Institute, Omaha, NE 68106, USA
| | - Paul T. Williams
- Department of Pathology and Microiology, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | - Joshua L. Santarpia
- Department of Pathology and Microiology, University of Nebraska Medical Center, Omaha, NE 68106, USA
- Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE 68106, USA
- National Strategic Research Institute, Omaha, NE 68106, USA
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Ye Q, Liu H, Mao J, Shu Q. Nonpharmaceutical interventions for COVID-19 disrupt the dynamic balance between influenza A virus and human immunity. J Med Virol 2023; 95:e28292. [PMID: 36367115 PMCID: PMC9877879 DOI: 10.1002/jmv.28292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
During the COVID-19 epidemic, nonpharmaceutical interventions (NPIs) blocked the transmission route of respiratory diseases. This study aimed to investigate the impact of NPIs on the influenza A virus (IAV) outbreak. The present study enrolled all children with respiratory tract infections who came to the Children's Hospital of Zhejiang University between January 2019 and July 2022. A direct immunofluorescence assay kit detected IAV. Virus isolation and Sanger sequencing were performed. From June to July 2022, in Hangzhou, China, the positive rate of IAV infection in children has increased rapidly, reaching 30.41%, and children over 3 years old are the main infected population, accounting for 75% of the total number of infected children. Influenza A (H3N2) viruses are representative strains during this period. In this outbreak, H3N2 was isolated from a cluster of its own and is highly homologous with A/South_Dakota/22/2022 (2021-2022 Northern Hemisphere). Between isolated influenza A (H3N2) viruses and A/South_Dakota/22/2022, the nucleotide homology of the HA gene ranged from 97.3% to 97.5%; the amino acid homology was 97%-97.2%, and the genetic distance of nucleotides ranged from 0.05 to 0.052. Compared with A/South_Dakota/22/2022, the isolated H3N2 showed S156H, N159Y, I160T, D186S, S198P, I48T, S53D, and K171N mutations. There was no variation in 13 key amino acid sites associated with neuraminidase inhibitor resistance in NA protein. Long-term NPIs have significantly affected the evolution and transmission of the influenza virus and human immunity, breaking the dynamic balance between the IAV and human immunity.
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Affiliation(s)
- Qing Ye
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Huihui Liu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Qiang Shu
- Department of Thoracic & Cardiovascular Surgery, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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70
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Wang M, Yan H, Chen L, Wang Y, Li L, Zhang H, Miao L. Oxalic acid blocked the binding of spike protein from SARS-CoV-2 Delta (B.1.617.2) and Omicron (B.1.1.529) variants to human angiotensin-converting enzymes 2. PLoS One 2023; 18:e0285722. [PMID: 37200310 DOI: 10.1371/journal.pone.0285722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023] Open
Abstract
An epidemic of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading worldwide. Moreover, the emergence of SARS-CoV-2 variants of concern, such as Delta and Omicron, has seriously challenged the application of current therapeutics including vaccination and drugs. Relying on interaction of spike protein with receptor angiotensin-converting enzymes 2 (ACE2), SARS-CoV-2 successfully invades to the host cells, which indicates a strategy that identification of small-molecular compounds to block the entry is of great significance for COVID-19 prevention. Our study evaluated the potential efficacy of natural compound oxalic acid (OA) as an inhibitory agent against SARS-CoV-2 invasion, particular on the interaction of the receptor binding domain (RBD) of Delta and Omicron variants to ACE2. By employing a competitive binding assay in vitro, OA significantly blocked the binding of RBDs from Delta B.1.617.2 and Omicron B.1.1.529 to ACE2, but has no effect on the wide-type SARS-CoV-2 strain. Furthermore, OA inhibited the entries of Delta and Omicron pseudovirus into ACE2 high expressing-HEK293T cells. By surface plasmon resonance (SPR) assay, the direct bindings of OA to RBD and ACE2 were analyzed and OA had both affinities with RBDs of B.1.617.2 and B.1.1.529 and with ACE2. Molecular docking predicted the binding sites on the RBD-ACE2 complex and it showed similar binding abilities to both complex of variant Delta or Omicron RBD and ACE2. In conclusion, we provided a promising novel small-molecule compound OA as an antiviral candidate by blocking the cellular entries of SARS-CoV-2 variants.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Huimin Yan
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lu Chen
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yu Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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71
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O'Grady HM, Harrison R, Snedeker K, Trufen L, Yue P, Ward L, Fifen A, Jamieson P, Weiss A, Coulthard J, Lynch T, Croxen MA, Li V, Pabbaraju K, Wong A, Zhou HY, Dingle TC, Hellmer K, Berenger BM, Fonseca K, Lin YC, Evans D, Conly JM. A two-ward acute care hospital outbreak of SARS-CoV-2 delta variant including a point-source outbreak associated with the use of a mobile vital signs cart and sub-optimal doffing of personal protective equipment. J Hosp Infect 2023; 131:1-11. [PMID: 36195200 PMCID: PMC9527227 DOI: 10.1016/j.jhin.2022.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND The arrival of the Delta variant of SARS-CoV-2 was associated with increased transmissibility and illness of greater severity. Reports of nosocomial outbreaks of Delta variant COVID-19 in acute care hospitals have been described but control measures varied widely. AIM Epidemiological investigation of a linked two-ward COVID-19 Delta variant outbreak was conducted to elucidate its source, risk factors, and control measures. METHODS Investigations included epidemiologic analysis, detailed case review serial SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) testing of patients and healthcare workers (HCWs), viral culture, environmental swabbing, HCW-unaware personal protective equipment (PPE) audits, ventilation assessments, and the use of whole genome sequencing (WGS). FINDINGS This linked two-ward outbreak resulted in 17 patient and 12 HCW cases, despite an 83% vaccination rate. In this setting, suboptimal adherence and compliance to PPE protocols, suboptimal hand hygiene, multi-bedded rooms, and a contaminated vital signs cart with potential fomite or spread via the hands of HCWs were identified as significant risk factors for nosocomial COVID-19 infection. Sudden onset of symptoms, within 72 h, was observed in 79% of all Ward 2 patients, and 93% of all cases (patients and HCWs) on Ward 2 occurred within one incubation period, consistent with a point-source outbreak. RT-PCR assays showed low cycle threshold (CT) values, indicating high viral load from environmental swabs including the vital signs cart. WGS results with ≤3 SNP differences between specimens were observed. CONCLUSION Outbreaks on both wards settled rapidly, within 3 weeks, using a `back-to-basics' approach without extraordinary measures or changes to standard PPE requirements. Strict adherence to recommended PPE, hand hygiene, education, co-operation from HCWs, including testing and interviews, and additional measures such as limiting movement of patients and staff temporarily were all deemed to have contributed to prompt resolution of the outbreak.
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Affiliation(s)
- H M O'Grady
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - R Harrison
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada; Workplace Health and Safety, Alberta Health Services, Edmonton, Alberta, Canada
| | - K Snedeker
- Provincial Population and Public Health, Alberta Health Services, Calgary, Alberta, Canada
| | - L Trufen
- Workplace Health and Safety, Alberta Health Services, Edmonton, Alberta, Canada
| | - P Yue
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - L Ward
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - A Fifen
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - P Jamieson
- Department of Family Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - A Weiss
- Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - J Coulthard
- Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - T Lynch
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Genomics and Bioinformatics, Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada; Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - M A Croxen
- Alberta Public Heath Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada; Department of Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - V Li
- Alberta Public Heath Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - K Pabbaraju
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - A Wong
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - H Y Zhou
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - T C Dingle
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - K Hellmer
- Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - B M Berenger
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - K Fonseca
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Y-C Lin
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada; Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - D Evans
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada; Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - J M Conly
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada; Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; W21C Research and Innovation Centre, O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada; Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada.
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72
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Mousavi SF, Ebrahimi M, Moghaddam SAA, Moafi N, Jafari M, Tavakolian A, Heidary M. Evaluating the characteristics of patients with SARS-CoV-2 infection admitted during COVID-19 peaks: A single-center study. VACUNAS 2023; 24:27-36. [PMID: 36062028 PMCID: PMC9424515 DOI: 10.1016/j.vacun.2022.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/13/2022] [Indexed: 02/08/2023]
Abstract
Background Nowadays, the world is facing a coronavirus disease (COVID-19) pandemic, elicited by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the time of studying, five COVID-19 waves occurred in Iran. We aimed to evaluate the characteristics of patients with SARS-CoV-2 infection admitted to Vasei Hospital of Sabzevar, Iran during COVID-19 peaks. Methods Clinical manifestations, laboratory findings, radiological findings, and underlying diseases of patients with COVID-19 were obtained from electronic medical records. Then, this information was compared in patients with SARS-CoV-2 infection to the peaks of COVID-19. Results The highest and lowest respiratory involvements were observed in the third (74.6%) and fourth (38.8%) peaks, respectively. The most common radiological finding in all peaks was ground-glass opacity (28.98%), followed by consolidation, which was the highest (14.6%) in peak three. The lymphocyte count decreased in all peaks. Its highest reduction (16.12) occurred in the third peak. The SpO2 was lower than normal range in all peaks, except for the second (90.77%) and fifth (91.06%) peaks. Dyspnea (52.36%) was the most and dizziness (1.26%) and sore throat (0.6%) were the least frequent symptoms. The mortality rates were 14. 4%, 18.2%, 23%, 9.02%, and 9.4% in the first to fifth peaks, respectively. Conclusion As different variants of the SARS-CoV-2 virus were predominant in each wave, COVID-19 patients had different features in various peaks. The fifth wave of COVID-19 had the highest number of hospitalized patients, while the first peak had the lowest number. Perhaps, the significant increase in testing capacity in the fifth wave and its long time period are the reasons for this growth. Most of the clinical symptoms were similar in all peaks, but the incidence was different. As patients hospitalized in the third peak had the highest rate of underlying disease, it can be a reason for the increase in the death rate of patients. We did not observe any significant differences in laboratory tests among the patients during different peaks. Thus, we should be vigilant in continuously studying the characteristics of the disease, and be able to modify treatments rapidly if necessary.
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Affiliation(s)
| | | | | | - Narges Moafi
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahbobe Jafari
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Ayoub Tavakolian
- Emergency Medicine Department, Faculty of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mohsen Heidary
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran,Corresponding authors
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73
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Mousavi SF, Ebrahimi M, Moghaddam SAA, Moafi N, Jafari M, Tavakolian A, Heidary M. Evaluating the characteristics of patients with SARS-CoV-2 infection admitted during COVID-19 peaks: A single-center study. VACUNAS (ENGLISH EDITION) 2023; 24. [PMCID: PMC9969536 DOI: 10.1016/j.vacune.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Background Nowadays, the world is facing a coronavirus disease (COVID-19) pandemic, elicited by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the time of studying, five COVID-19 waves occurred in Iran. We aimed to evaluate the characteristics of patients with SARS-CoV-2 infection admitted to Vasei Hospital of Sabzevar, Iran during COVID-19 peaks. Methods Clinical manifestations, laboratory findings, radiological findings, and underlying diseases of patients with COVID-19 were obtained from electronic medical records. Then, this information was compared in patients with SARS-CoV-2 infection to the peaks of COVID-19. Results The highest and lowest respiratory involvements were observed in the third (74.6%) and fourth (38.8%) peaks, respectively. The most common radiological finding in all peaks was ground-glass opacity (28.98%), followed by consolidation, which was the highest (14.6%) in peak three. The lymphocyte count decreased in all peaks. Its highest reduction (16.12) occurred in the third peak. The SpO2 was lower than normal range in all peaks, except for the second (90.77%) and fifth (91.06%) peaks. Dyspnea (52.36%) was the most and dizziness (1.26%) and sore throat (0.6%) were the least frequent symptoms. The mortality rates were 14. 4%, 18.2%, 23%, 9.02%, and 9.4% in the first to fifth peaks, respectively. Conclusion As different variants of the SARS-CoV-2 virus were predominant in each wave, COVID-19 patients had different features in various peaks. The fifth wave of COVID-19 had the highest number of hospitalized patients, while the first peak had the lowest number. Perhaps, the significant increase in testing capacity in the fifth wave and its long time period are the reasons for this growth. Most of the clinical symptoms were similar in all peaks, but the incidence was different. As patients hospitalized in the third peak had the highest rate of underlying disease, it can be a reason for the increase in the death rate of patients. We did not observe any significant differences in laboratory tests among the patients during different peaks. Thus, we should be vigilant in continuously studying the characteristics of the disease, and be able to modify treatments rapidly if necessary.
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Affiliation(s)
| | | | | | - Narges Moafi
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahbobe Jafari
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Ayoub Tavakolian
- Emergency Medicine Department, Faculty of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mohsen Heidary
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran,Corresponding authors
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74
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Talasaz AH, Sadeghipour P, Mehdizadeh K, Khoshnam Rad N, Bikdeli B, Lip GYH, Harenberg J. Knowledge Gaps for Prophylactic Use of Antithrombotic Agents in Patients with COVID-19: Insights into New SARS-CoV-2 Variants, Vaccination Status, and Emerging Oral Antivirals. Thromb Haemost 2022; 123:186-191. [PMID: 36206775 PMCID: PMC9904967 DOI: 10.1055/a-1956-9641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Data suggest that coronavirus disease 2019 (COVID-19) results in a prothrombotic state leading to arterial and venous thromboses. Vaccination, novel antiviral drugs, and emerging variants have changed the course of the disease in many ways; however, their effects on the incidence of thrombotic events and the efficacy of preventative antithrombotic agents have not been yet evaluated. A systematic search was conducted to identify studies reported on the incidence of thrombotic events based on vaccination status, use of novel antiviral drugs, and emerging viral variants. Similarly, we screened the ongoing/published randomized trials of preventative antithrombotic therapy in any COVID-19 population to assess whether subgroup-specific results were reported based on any of these variants. Upon searching a total of 3,451 records, only one entry fulfilled the inclusion criteria of our systematic review, which was a self-controlled case series on 29,121,633 vaccinated individuals, the incidence rate ratio of thrombotic complication after breakthrough infection was 13.86 (95% confidence interval [CI]: 12.76-15.05) compared with 1.10 (95% CI: 1.02-1.18) during the 28-day postvaccination. In conclusion, although the mortality benefit of mass vaccination and the early promising results of the new antiviral therapies are well known, we were unable to find clinical evidence on whether vaccination, the use of novel antiviral agents, and emerging viral variants have affected the incidence rate of thrombotic events or impacted the efficacy of prophylactic antithrombotic therapy in patients with COVID-19. Analyses from existing trials and large-scale registries can provide interim knowledge and any findings of relevance should be incorporated in the design of future trials.
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Affiliation(s)
- Azita H. Talasaz
- Department of Clinical Pharmacy, Tehran University of Medical Sciences, Tehran, Iran,Department of Pharmacotherapy and Outcome Sciences, Virginia Commonwealth University, Richmond, Virginia, United States,Address for correspondence Azita H. Talasaz, PharmD, BCPS, BCCP Department of Clinical Pharmacy, Tehran University of Medical Sciences16 Azar St., TehranIran
| | - Parham Sadeghipour
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular, Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran,Clinical Trial Center, Rajaie Cardiovascular, Medical, and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Kasra Mehdizadeh
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular, Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Niloofar Khoshnam Rad
- Department of Clinical Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Behnood Bikdeli
- Cardiovascular Medicine Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States,Thrombosis Research Group, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States,Yale/YNHH Center for Outcomes Research and Evaluation (CORE), New Haven, Connecticut, United States,Cardiovascular Research Foundation (CRF), New York, New York, United States
| | - Gregory Y. H. Lip
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart and Chest Hospital, Liverpool, United Kingdom,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Job Harenberg
- Ruprecht Karls University, Heidelberg, Germany,Ruperto Carola University of Heidelberg, Heidelberg, Germany,Job Harenberg, MD Department of MedicineDOASENSE GmbH, Waldhofer Strasse 102, 69123 HeidelbergGermany
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75
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Robalo Q, De Mot L, Vandromme M, Van Goethem N, Gabrio A, Chung PYJ, Meurisse M, Catteau L, Thijs C, Blot K. Association between COVID-19 Primary Vaccination and Severe Disease Caused by SARS-CoV-2 Delta Variant among Hospitalized Patients: A Belgian Retrospective Cohort Study. Vaccines (Basel) 2022; 11:vaccines11010014. [PMID: 36679859 PMCID: PMC9866568 DOI: 10.3390/vaccines11010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
We aimed to investigate vaccine effectiveness against progression to severe COVID-19 (acute respiratory distress syndrome (ARDS), intensive care unit (ICU) admission and/or death) and in-hospital death in a cohort of hospitalized COVID-19 patients. Mixed effects logistic regression analyses were performed to estimate the association between receiving a primary COVID-19 vaccination schedule and severe outcomes after adjusting for patient, hospital, and vaccination characteristics. Additionally, the effects of the vaccine brands including mRNA vaccines mRNA-1273 and BNT162b2, and adenovirus-vector vaccines ChAdOx1 (AZ) and Ad26.COV2.S (J&J) were compared to each other. This retrospective, multicenter cohort study included 2493 COVID-19 patients hospitalized across 73 acute care hospitals in Belgium during the time period 15 August 2021-14 November 2021 when the Delta variant (B1.617.2) was predominant. Hospitalized COVID-19 patients that received a primary vaccination schedule had lower odds of progressing to severe disease (OR (95% CI); 0.48 (0.38; 0.60)) and in-hospital death (OR (95% CI); 0.49 (0.36; 0.65)) than unvaccinated patients. Among the vaccinated patients older than 75 years, mRNA vaccines and AZ seemed to confer similar protection, while one dose of J&J showed lower protection in this age category. In conclusion, a primary vaccination schedule protects against worsening of COVID-19 to severe outcomes among hospitalized patients.
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Affiliation(s)
- Queeny Robalo
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
- Correspondence:
| | - Laurane De Mot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | - Mathil Vandromme
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
- Natuurpunt Studie vzw, 2800 Mechelen, Belgium
| | - Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | - Andrea Gabrio
- Department of Methodology and Statistics, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Pui Yan Jenny Chung
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | - Marjan Meurisse
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | | | - Lucy Catteau
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
| | - Carel Thijs
- Maastricht University Medical Centre+, Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Koen Blot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium
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Šimičić P, Židovec-Lepej S. A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2. Viruses 2022; 15:1. [PMID: 36680042 PMCID: PMC9866536 DOI: 10.3390/v15010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
RNA viruses are characterised by extremely high genetic variability due to fast replication, large population size, low fidelity, and (usually) a lack of proofreading mechanisms of RNA polymerases leading to high mutation rates. Furthermore, viral recombination and reassortment may act as a significant evolutionary force among viruses contributing to greater genetic diversity than obtainable by mutation alone. The above-mentioned properties allow for the rapid evolution of RNA viruses, which may result in difficulties in viral eradication, changes in virulence and pathogenicity, and lead to events such as cross-species transmissions, which are matters of great interest in the light of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemics. In this review, we aim to explore the molecular mechanisms of the variability of viral RNA genomes, emphasising the evolutionary trajectory of SARS-CoV-2 and its variants. Furthermore, the causes and consequences of coronavirus variation are explored, along with theories on the origin of human coronaviruses and features of emergent RNA viruses in general. Finally, we summarise the current knowledge on the circulating variants of concern and highlight the many unknowns regarding SARS-CoV-2 pathogenesis.
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Affiliation(s)
| | - Snježana Židovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
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Infectious diseases genomic surveillance capacity in the Caribbean: A retrospective analysis of SARS-CoV-2. LANCET REGIONAL HEALTH. AMERICAS 2022; 18:100411. [PMID: 36567881 PMCID: PMC9761298 DOI: 10.1016/j.lana.2022.100411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/02/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
Background The ongoing coronavirus diseases 2019 (COVID-19) pandemic with its numerous variants of concern has shown the need to have a robust and complete global infectious diseases genomic surveillance network worldwide. Various clinical and research institutions have stepped up to perform SARS-CoV-2 sequencing thus enhancing the understanding of this virus' global evolution. However, given that genomic sequencing capacities and capabilities are not available in every region or country, significant gaps exist, which lead to geographic blind spots. One such region is the Caribbean. This paper measures the Caribbean region's SARS-CoV-2 genomic sequencing capacity and highlights the need to improve further regional genomics surveillance capacities and capabilities, which are essential for efficient health interventions for infectious diseases. Methods A map showing SARS-CoV-2 sequences available for each Caribbean Island was constructed using SARS-CoV-2 genomic, epidemiological and populational data obtained from GISAID, the World Health Organization, the United Nations, and the World Bank. The number of reported SARS-CoV-2 cases and the proportion of cases sequenced in each Caribbean Island was then analysed by the Gross Domestic Product per capita and political status. Findings As of August 6, 2022, the number of SARS-CoV-2 sequences from the Caribbean are underrepresented with only 40,190 (1.07%) of the over 3.76 million documented cases sequenced, which is further exacerbated by a disparity based not only on the country's income but also on its political status (sovereign country versus dependent or integrated) and accessibility to sequencing technologies. There are a limited number of sequencing centres based in the Caribbean islands with the majority located on the American and European continents. Using mobile sequencing technologies while concomitantly investing in data analysis training could lead to greater and more sustainable coverage. Interpretation Considering the Caribbean region's dispersed heterogeneous populations, varying political regimes, and resource-constrained healthcare systems, further development of local next-generation sequencing capacity and capabilities in the Caribbean region is needed to achieve global public health goals. Funding No funding source was required for this study.
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Abavisani M, Rahimian K, Mahdavi B, Tokhanbigli S, Mollapour Siasakht M, Farhadi A, Kodori M, Mahmanzar M, Meshkat Z. Mutations in SARS-CoV-2 structural proteins: a global analysis. Virol J 2022; 19:220. [PMID: 36528612 PMCID: PMC9759450 DOI: 10.1186/s12985-022-01951-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally. METHODS We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022. The presence and location of mutations were then investigated by aligning the sequences to the reference sequence and categorizing them based on frequency and continent. Finally, the related human genes with the viral structural genes were discovered, and their interactions were reported. RESULTS The results indicated that the most relative mutations among the E, M, N, and S AASs occurred in the regions of 7 to 14, 66 to 88, 164 to 205, and 508 to 635 AAs, respectively. The most frequent mutations in E, M, N, and S proteins were T9I, I82T, R203M/R203K, and D614G. D614G was the most frequent mutation in all six geographical areas. Following D614G, L18F, A222V, E484K, and N501Y, respectively, were ranked as the most frequent mutations in S protein globally. Besides, A-kinase Anchoring Protein 8 Like (AKAP8L) was shown as the linkage unit between M, E, and E cluster genes. CONCLUSION Screening the structural protein mutations can help scientists introduce better drug and vaccine development strategies.
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Affiliation(s)
- Mohammad Abavisani
- grid.411583.a0000 0001 2198 6209Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Karim Rahimian
- grid.46072.370000 0004 0612 7950Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- grid.417689.5Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- grid.411463.50000 0001 0706 2472Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Mahsa Mollapour Siasakht
- grid.5645.2000000040459992XDepartment of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- grid.412462.70000 0000 8810 3346Department of Biology, Payame Noor University, Tehran, Iran
| | - Mansoor Kodori
- grid.510756.00000 0004 4649 5379Non Communicable Diseases Research Center, Bam University of Medical Sciences, Bam, Iran
| | - Mohammadamin Mahmanzar
- grid.46072.370000 0004 0612 7950Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran
| | - Zahra Meshkat
- grid.411583.a0000 0001 2198 6209Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Jain N, Hamilton D, Mital S, Ilias A, Brinkmann M, McPhedran K. Long-term passive wastewater surveillance of SARS-CoV-2 for seven university dormitories in comparison to municipal surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158421. [PMID: 36058330 PMCID: PMC9433341 DOI: 10.1016/j.scitotenv.2022.158421] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 05/28/2023]
Abstract
Wastewater-based surveillance (WBS) has been an effective tool for monitoring and understanding potential SARS-CoV-2 transmission across small and large-scale communities. In this study at the University of Saskatchewan, the assessment of SARS-CoV-2 was done over eight months during the 2021-2022 academic year. Wastewater samples were collected using passive samplers that were deployed in domestic sewer lines near adjacent campus residences and extracted for viral RNA, followed by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR). The results showed similar trends for SARS-CoV-2 detection frequencies and viral loads across university residences, the whole campus, and from related WBS at Saskatoon Wastewater Treatment Plant. The maximum daily detection frequency for seven dormitories considered was about 75 %, while maximum daily case numbers for the residences and campus-wide were about 11 and 75 people, respectively. In addition, self-reported rates of infection on campus peaked during similar time frames as increases in viral load were detected at the Saskatoon wastewater treatment plant. These similarities indicate the usefulness and cost-effectiveness of monitoring the spread of COVID-19 in small-scale communities using WBS.
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Affiliation(s)
- N Jain
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - D Hamilton
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - S Mital
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - A Ilias
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - M Brinkmann
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Centre for Hydrology, University of Saskatchewan, Saskatoon, SK, Canada.
| | - K McPhedran
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
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Arslan A, Sahbudak Bal Z, Yildirim Arslan S, Bilen NM, Guner Ozenen G, Yazıcı Özkaya P, Yurtseven A, Çiçek C, Durusoy İR, Ozkinay F, Kurugol Z. The longitudinal evaluation of COVID-19 in pediatric patients and the impact of delta variant. J Trop Pediatr 2022; 69:6972188. [PMID: 36611014 DOI: 10.1093/tropej/fmac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Pediatric patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) displayed milder symptoms than adults. However, they play an important role in case numbers and virus transmission. Therefore, we aimed to determine the epidemiological features of all pediatric patients infected with SARS-CoV-2 and put forth case numbers longitudinally throughout the delta variant dominant period. METHODS A retrospective study was conducted at a university hospital and included patients between 0 and18 years old with a SARS-CoV-2 polymerase chain reaction (PCR) positive result, including inpatients and outpatients. Epidemiological and clinical features were recorded from electronic files, and telephone visits were performed between March 2020 and December 2021. RESULTS During the study period, 3175 coronavirus disease 2019 (COVID-19) pediatric patients were admitted to our hospital with a mean age of 10.61 ± 4.6 years. Of the 1815 patients who could be interviewed, 85.7% reported at least one symptom. Before the delta variant period, 0-4 years aged children were more commonly infected, while school-aged children and adolescents were more common, and the rate of pediatric cases to all COVID-19 cases increased to 35.8% after the delta variant became dominant. Symptomatic cases were significantly higher before the delta variant (87.8% vs. 84.06%, p = 0.016). The hospitalization rate was higher before the delta variant (p < 0.001), whereas PICU admission showed no statistical difference. CONCLUSIONS The frequency of school-aged children and adolescents raised with the impact of both school openings and the delta variant, and the rate of pediatric cases increased in total COVID-19 patient numbers.
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Affiliation(s)
- Asli Arslan
- Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Zumrut Sahbudak Bal
- Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Sema Yildirim Arslan
- Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Nimet Melis Bilen
- Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Gizem Guner Ozenen
- Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Pınar Yazıcı Özkaya
- Division of Pediatric İntensive Care Unit, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Ali Yurtseven
- Division of Emergency Medicine, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Candan Çiçek
- Department of Microbiology, Medical School of Ege University, Izmir 35100, Turkey
| | - İsabel Raika Durusoy
- Department of Public Health, Medical School of Ege University, Izmir 35100, Turkey
| | - Ferda Ozkinay
- Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
| | - Zafer Kurugol
- Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir 35100, Turkey
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81
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Zhou YQ, Wang K, Wang XY, Cui HY, Zhao Y, Zhu P, Chen ZN. SARS-CoV-2 pseudovirus enters the host cells through spike protein-CD147 in an Arf6-dependent manner. Emerg Microbes Infect 2022; 11:1135-1144. [PMID: 35343395 PMCID: PMC9037224 DOI: 10.1080/22221751.2022.2059403] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants is threatening public health around the world. Endocytosis functions as an important way for viral infection, and SARS-CoV-2 bears no exception. However, the specific endocytic mechanism of SARS-CoV-2 remains unknown. In this study, we used endocytic inhibitors to evaluate the role of different endocytic routes in SARS-CoV-2 pseudovirus infection and found that the viral infection was associated with caveolar/lipid raft- and cytoskeleton-mediated endocytosis, but independent of the clathrin-mediated endocytosis and macropinocytosis. Meanwhile, the knockdown of CD147 and Rab5a in Vero E6 and Huh-7 cells inhibited SARS-CoV-2 pseudovirus infection, and the co-localization of spike protein, CD147, and Rab5a was observed in pseudovirus-infected Vero E6 cells, which was weakened by CD147 silencing, illustrating that SARS-CoV-2 pseudovirus entered the host cells via CD147-mediated endocytosis. Additionally, Arf6 silencing markedly inhibited pseudovirus infection in Vero E6 and Huh-7 cells, while little change was observed in CD147 knockout-Vero E6 cells. This finding indicated Arf6-mediated CD147 trafficking plays a vital role in SARS-CoV-2 entry. Taken together, our findings provide new insights into the CD147-Arf6 axis in mediating SARS-CoV-2 pseudovirus entry into the host cells, and further suggest that blockade of this pathway seems to be a feasible approach to prevent the SARS-CoV-2 infection clinically.
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Affiliation(s)
- Yun-Qi Zhou
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People's Republic of China.,National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Ke Wang
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Xue-Yan Wang
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People's Republic of China.,National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Hong-Yong Cui
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Yongxiang Zhao
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People's Republic of China
| | - Ping Zhu
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Zhi-Nan Chen
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People's Republic of China.,National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, People's Republic of China
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82
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Wu K, Wang D, Wang J, Zhou Y. Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs. Virol Sin 2022; 37:813-822. [PMID: 36075564 PMCID: PMC9444306 DOI: 10.1016/j.virs.2022.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/01/2022] [Indexed: 12/27/2022] Open
Abstract
The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA (gRNA) or canonical subgenomic RNAs (sgRNAs). Here, we systematically investigated the translation landscape of SARS-CoV-2, especially its noncanonical sgRNAs. We first constructed a strict pipeline, named vipep, for identifying reliable peptides derived from RNA viruses using RNA-seq and mass spectrometry data. We applied vipep to analyze 24 sets of mass spectrometry data related to SARS-CoV-2 infection. In addition to known canonical proteins, we identified many noncanonical sgRNA-derived peptides, which stably increase after viral infection. Furthermore, we explored the potential functions of those proteins encoded by noncanonical sgRNAs and found that they can bind to viral RNAs and may have immunogenic activity. The generalized vipep pipeline is applicable to any RNA viruses and these results have expanded the SARS-CoV-2 translation map, providing new insights for understanding the functions of SARS-CoV-2 sgRNAs.
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Affiliation(s)
- Kai Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Dehe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junhao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China,TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, 430072, China,Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China,Corresponding author
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83
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Kim J, Jeong J, Lee CM, Lee DW, Kang CK, Choe PG, Kim NJ, Oh MD, Lee CH, Park WB, Lee KH, Im SA. Prospective longitudinal analysis of antibody response after standard and booster doses of SARS-COV2 vaccination in patients with early breast cancer. Front Immunol 2022; 13:1028102. [DOI: 10.3389/fimmu.2022.1028102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants brought waves of pandemics with breakthrough infections in vaccinated individuals. We analyzed the antibody responses after primary and booster vaccination in healthy controls (HC) and patients with early breast cancer (BC).MethodsIn this prospective longitudinal cohort study, the binding activity of serum antibody level against spike proteins and antigens of SARS-CoV-2 variants was measured within 21 days after each vaccination in the BC group and HC group.ResultsAll participants, 40 in the BC and 20 in the HC group, had increased antibody response after vaccination. BC group, however, had weaker humoral responses than the HC group (IgG: 1.5, 2.3, 2.5-folds in BC vs. 1.9, 3.6, 4.0-folds in HC after each dose; IgA: 2.1, 3.0, 3.6-folds in BC vs. 4.2, 10.4, 5.2-folds in HC after each dose, respectively). Those under concurrent cytotoxic chemotherapy had weaker antibody response than the non-cytotoxic treatment group and HC. Adjunct use of steroids and age were not significant risk factors. The levels of binding antibody against the Delta and the Omicron (BA1) variants were lower than the wild-type, especially in BC.ConclusionIn the waves of new sub-variants, our study suggests that an additional dose of vaccinations should be recommended according to the anti-cancer treatment modality in patients with BC who had received booster vaccination.
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84
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Chavda VP, Bezbaruah R, Deka K, Nongrang L, Kalita T. The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far. Vaccines (Basel) 2022; 10:1926. [PMID: 36423021 PMCID: PMC9698608 DOI: 10.3390/vaccines10111926] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 07/30/2023] Open
Abstract
The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus's capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40-60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the "Delta plus" variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380008, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Kangkan Deka
- NETES Institute of Pharmaceutical Science, Mirza, Guwahati 781125, Assam, India
| | - Lawandashisha Nongrang
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Tutumoni Kalita
- Girijananda Chowdhury Institute of Pharmaceutical Science, Azara, Guwahati 781017, Assam, India
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Langan LM, O’Brien M, Lovin LM, Scarlett KR, Davis H, Henke AN, Seidel SE, Archer N, Lawrence E, Norman RS, Bojes HK, Brooks BW. Quantitative Reverse Transcription PCR Surveillance of SARS-CoV-2 Variants of Concern in Wastewater of Two Counties in Texas, United States. ACS ES&T WATER 2022; 2:2211-2224. [PMID: 37552718 PMCID: PMC9291321 DOI: 10.1021/acsestwater.2c00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 06/02/2023]
Abstract
After its emergence in late November/December 2019, the severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) rapidly spread globally. Recognizing that this virus is shed in feces of individuals and that viral RNA is detectable in wastewater, testing for SARS-CoV-2 in sewage collections systems has allowed for the monitoring of a community's viral burden. Over a 9 month period, the influents of two regional wastewater treatment facilities were concurrently examined for wild-type SARS-CoV-2 along with variants B.1.1.7 and B.1.617.2 incorporated as they emerged. Epidemiological data including new confirmed COVID-19 cases and associated hospitalizations and fatalities were tabulated within each location. RNA from SARS-CoV-2 was detectable in 100% of the wastewater samples, while variant detection was more variable. Quantitative reverse transcription PCR (RT-qPCR) results align with clinical trends for COVID-19 cases, and increases in COVID-19 cases were positively related with increases in SARS-CoV-2 RNA load in wastewater, although the strength of this relationship was location specific. Our observations demonstrate that clinical and wastewater surveillance of SARS-CoV-2 wild type and constantly emerging variants of concern can be combined using RT-qPCR to characterize population infection dynamics. This may provide an early warning for at-risk communities and increases in COVID-19 related hospitalizations.
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Affiliation(s)
- Laura M. Langan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Megan O’Brien
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
| | - Lea M. Lovin
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Kendall R. Scarlett
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Haley Davis
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Abigail N. Henke
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Biology, Baylor
University, One Bear Place #97388, Waco, Texas 76798, United
States
| | - Sarah E. Seidel
- Center for Health
Statistics, Texas Department of State Health Services, Austin, Texas
78756, United States
| | - Natalie Archer
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Eric Lawrence
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - R. Sean Norman
- Department of Environmental Health Sciences, Arnold School of
Public Health, University of South Carolina, 921 Assembly
Street Columbia, South Carolina 29208, United States
| | - Heidi K. Bojes
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Bryan W. Brooks
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
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Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters. Nat Commun 2022; 13:6644. [PMID: 36333374 PMCID: PMC9636174 DOI: 10.1038/s41467-022-34439-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Current COVID-19 vaccines are based on prototypic spike sequences from ancestral 2019 SARS-CoV-2 strains. However, the ongoing pandemic is fueled by variants of concern (VOC) escaping vaccine-mediated protection. Here we demonstrate how immunization in hamsters using prototypic spike expressed from yellow fever 17D (YF17D) as vector blocks ancestral virus (B lineage) and VOC Alpha (B.1.1.7) yet fails to fully protect from Beta (B.1.351). However, the same YF17D vectored vaccine candidate with an evolved antigen induced considerably improved neutralizing antibody responses against VOCs Beta, Gamma (P.1) and the recently predominant Omicron (B.1.1.529), while maintaining immunogenicity against ancestral virus and VOC Delta (B.1.617.2). Thus vaccinated animals resisted challenge by all VOCs, including vigorous high titre exposure to the most difficult to cover Beta, Delta and Omicron variants, eliminating detectable virus and markedly improving lung pathology. Finally, vaccinated hamsters did not transmit Delta variant to non-vaccinated cage mates. Overall, our data illustrate how current first-generation COVID-19 vaccines may need to be updated to maintain efficacy against emerging VOCs and their spread at community level.
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87
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Bauer G, Struck F, Staschik E, Maile J, Wochinz‐Richter K, Motz M, Soutschek E. Differential avidity determination of IgG directed towards the receptor-binding domain (RBD) of SARS-CoV-2 wild-type and its variants in one assay: Rational tool for the assessment of protective immunity. J Med Virol 2022; 94:5294-5303. [PMID: 35851961 PMCID: PMC9349558 DOI: 10.1002/jmv.28006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/02/2022] [Accepted: 07/14/2022] [Indexed: 12/15/2022]
Abstract
The avidity (binding strength) of IgG directed towards the receptor-binding domain (RBD) of spike protein has been recognized as a central marker in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology. It seems to be linked to increased infection-neutralization potential and therefore might indicate protective immunity. Using a prototype line assay based on the established recomLine SARS-CoV-2 assay, supplemented with RBD of the delta and the omicron variant, differential avidity determination of IgG directed towards RBD of wild-type (WT) SARS-CoV-2 and distinct variants was possible within one assay. Our data confirm that natural SARS-CoV-2 infection or one vaccination step lead to low avidity IgG, whereas further vaccination steps gradually increase avidity to high values. High avidity is not reached by infection alone. After infection with WT SARS-CoV-2 or vaccination based on mRNA WT, the avidity of cross-reacting IgG directed towards RBD of the delta variant only showed marginal differences compared to IgG directed towards RBD WT. In contrast, the avidity of IgG cross-reacting with RBD of the omicron variant was always much lower than for IgG RBD WT, except after the third vaccination step. Therefore, parallel avidity testing of RBD WT and omicron seems to be mandatory for a significant assessment of protective immunity towards SARS-CoV-2.
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Affiliation(s)
- Georg Bauer
- Institute of Virology, Medical CenterUniversity of FreiburgFreiburgGermany,Faculty of MedicineUniversity of FreiburgFreiburgGermany
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88
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Ho HPT, Vo DNK, Lin TY, Hung JN, Chiu YH, Tsai MH. Ganoderma microsporum immunomodulatory protein acts as a multifunctional broad-spectrum antiviral against SARS-CoV-2 by interfering virus binding to the host cells and spike-mediated cell fusion. Biomed Pharmacother 2022; 155:113766. [PMID: 36271550 PMCID: PMC9515347 DOI: 10.1016/j.biopha.2022.113766] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus that has caused over 6 million fatalities. SARS-CoV-2 variants with spike mutations are frequently endowed with a strong capability to escape vaccine-elicited protection. Due to this characteristic, a broad-spectrum inhibitor against SARS-CoV-2 infection is urgently demanded. Ganoderma microsporum immunomodulatory protein (GMI) was previously reported to alleviate infection of SARS-CoV-2 through ACE2 downregulation whereas the impact of GMI on virus itself was less understood. Our study aims to determine the effects of GMI on SARS-CoV-2 pseudovirus and the more detailed mechanisms of GMI inhibition against SARS-CoV-2 pseudovirus infection. METHODS ACE2-overexpressing HEK293T cells (HEK293T/ACE2) and SARS-CoV-2 pseudoviruses carrying spike variants were used to study the effects of GMI in vitro. Infectivity was evaluated by fluorescence microscopy and flow cytometry. Fusion rate mediated by SARS-CoV-2 spike protein was examined with split fluorescent protein /luciferase systems. The interactions of GMI with SARS-CoV-2 pseudovirus and ACE2 were investigated by immunoprecipitation and immunoblotting. RESULTS GMI broadly blocked SARS-CoV-2 infection in various cell lines. GMI effectively inhibited the infection of pseudotyped viruses carrying different emerged spike variants, including Delta and Omicron strains, on HEK293T/hACE2 cells. In cell-free virus infection, GMI dominantly impeded the binding of spike-bearing pseudotyped viruses to ACE2-expressing cells. In cell-to-cell fusion model, GMI could efficiently inhibit spike-mediated syncytium without the requirement of ACE2 downregulation. CONCLUSIONS GMI, an FDA-approved dietary ingredient, acts as a multifunctional broad-spectrum antiviral against SARS-CoV-2 and could become a promising candidate for preventing or treating SARS-CoV-2 associated diseases.
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Affiliation(s)
- Ha Phan Thanh Ho
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Di Ngoc Kha Vo
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tung-Yi Lin
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jo-Ning Hung
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ya-Hui Chiu
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ming-Han Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan; Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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89
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Deminco F, Vaz SN, Santana DS, Pedroso C, Tadeu J, Stoecker A, Vieira SM, Netto E, Brites C. A Simplified Sanger Sequencing Method for Detection of Relevant SARS-CoV-2 Variants. Diagnostics (Basel) 2022; 12:2609. [PMID: 36359452 PMCID: PMC9689870 DOI: 10.3390/diagnostics12112609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 08/26/2023] Open
Abstract
Molecular surveillance of the new coronavirus through new genomic sequencing technologies revealed the circulation of important variants of SARS-CoV-2. Sanger sequencing has been useful in identifying important variants of SARS-CoV-2 without the need for whole-genome sequencing. A sequencing protocol was constructed to cover a region of 1000 base pairs, from a 1120 bp product generated after a two-step RT-PCR assay in samples positive for SARS-CoV-2. Consensus sequence construction and mutation identification were performed. Of all 103 samples sequenced, 69 contained relevant variants represented by 20 BA.1, 13 delta, 22 gamma, and 14 zeta, identified between June 2020 and February 2022. All sequences found were aligned with representative sequences of the variants. Using the Sanger sequencing methodology, we were able to develop a more accessible protocol to assist viral surveillance with a more accessible platform.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Carlos Brites
- Laboratório de Pesquisa em Infectologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA)/EBSERH, Salvador 40170-110, Bahia, Brazil
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90
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Siewiński M, Bażanów B, Orzechowska B, Gołąb K, Gburek J, Matkowski A, Rapak A, Janocha A, Krata L, Dobrzyński M, Kilar E. Use of natural cysteine protease inhibitors in limiting SARS-Co-2 fusion into human respiratory cells. Med Hypotheses 2022; 168:110965. [PMID: 36313266 PMCID: PMC9598048 DOI: 10.1016/j.mehy.2022.110965] [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: 07/07/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022]
Abstract
Specific antibodies that humans acquire as a result of disease or after vaccination are needed to effectively suppress infection with a specific variant of SARS CoV-2 virus. The S protein of the D614G variant of coronavirus is used as an antigen in known vaccines to date. It is known that COVID-19 disease resulting from infection with this coronavirus can often be very dangerous to the health and lives of patients. In contrast, vaccines produce antibodies against an older version of the protein S-D614G (January 2020) and therefore have difficulty recognizing new variants of the virus. In our project we propose to obtain specific and precise antibodies by means of so-called controlled infection against specific infectious variants of the SARS-CoV-2 virus “here and now”. Currently, several variants of this pathogen have already emerged that threaten the health and lives of patients. We propose to reduce this threat by partially, but not completely, blocking the fusion mechanism of the SARS-CoV-2 virus into human respiratory cells. According to our plan, this can be achieved by inhibiting cathepsin L activity in respiratory cells, after introducing natural and non-toxic cysteine protease inhibitors into this area. We obtain these inhibitors by our own method from natural, “human body friendly” natural resources. We hypothesize that blocking cathepsin L will reduce the number of infecting viruses in cells to such an extent that COVID-19 developing in infected individuals will not threaten their health and life. At the same time, the number of viruses will be sufficient for the body's own immune system to produce precise antibodies against a specific version of this pathogen.
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Affiliation(s)
- Maciej Siewiński
- Wroclaw Medical University, Wroclaw, Poland; TherapyRaft comp. Wroclaw, Poland
| | - Barbara Bażanów
- Wrocław University of Environmental and Life Sciences, Faculty of Veterinary Medicine, Department of Pathology, C.K.Norwida 31, 50-375 Wrocław, Poland,Corresponding author
| | - Beata Orzechowska
- Laboratory of Virology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Krzysztof Gołąb
- Department of Pharmaceutical Biochemistry, Wroclaw Medical University, Borowska 211A, Wrocław, Poland
| | - Jakub Gburek
- Department of Pharmaceutical Biochemistry, Wroclaw Medical University, Borowska 211A, Wrocław, Poland
| | - Adam Matkowski
- Wroclaw Medical University, Dept. Pharmaceutical Biology and Biotechnology
| | - Andrzej Rapak
- Department of Experimental Oncology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Wroclaw, Poland
| | - Anna Janocha
- Wroclaw Medical University, Dept. Physiology, Wrocław, Poland Chałubińskiego 10
| | | | - Maciej Dobrzyński
- Wroclaw Medical University, Dept. of Conservative Dentistry and Pedodontics: Wroclaw, Poland
| | - Ewa Kilar
- Wroclaw Medical University, Dept. of Clinical Pharmacology Wroclaw, Poland
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91
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35753493 DOI: 10.1101/2022.01.28.21268186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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92
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156932. [PMID: 35753493 PMCID: PMC9225927 DOI: 10.1016/j.scitotenv.2022.156932] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/21/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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93
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Chi WY, Li YD, Huang HC, Chan TEH, Chow SY, Su JH, Ferrall L, Hung CF, Wu TC. COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection. J Biomed Sci 2022; 29:82. [PMID: 36243868 PMCID: PMC9569411 DOI: 10.1186/s12929-022-00853-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/01/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) has been the most severe public health challenge in this century. Two years after its emergence, the rapid development and deployment of effective COVID-19 vaccines have successfully controlled this pandemic and greatly reduced the risk of severe illness and death associated with COVID-19. However, due to its ability to rapidly evolve, the SARS-CoV-2 virus may never be eradicated, and there are many important new topics to work on if we need to live with this virus for a long time. To this end, we hope to provide essential knowledge for researchers who work on the improvement of future COVID-19 vaccines. In this review, we provided an up-to-date summary for current COVID-19 vaccines, discussed the biological basis and clinical impact of SARS-CoV-2 variants and subvariants, and analyzed the effectiveness of various vaccine booster regimens against different SARS-CoV-2 strains. Additionally, we reviewed potential mechanisms of vaccine-induced severe adverse events, summarized current studies regarding immune correlates of protection, and finally, discussed the development of next-generation vaccines.
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Affiliation(s)
- Wei-Yu Chi
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Hsin-Che Huang
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy En Haw Chan
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Urology, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sih-Yao Chow
- Downstream Process Science, EirGenix Inc., Zhubei, Hsinchu, Taiwan R.O.C
| | - Jun-Han Su
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Louise Ferrall
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
- Department of Obstetrics and Gynecology, Johns Hopkins University, Baltimore, MD, USA
| | - T-C Wu
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Obstetrics and Gynecology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA.
- The Johns Hopkins Medical Institutions, CRB II Room 309, 1550 Orleans St, MD, 21231, Baltimore, USA.
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94
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A Vaccine with Multiple Receptor-Binding Domain Subunit Mutations Induces Broad-Spectrum Immune Response against SARS-CoV-2 Variants of Concern. Vaccines (Basel) 2022; 10:vaccines10101653. [PMID: 36298518 PMCID: PMC9609383 DOI: 10.3390/vaccines10101653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
With the emergence of more variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the immune evasion of these variants from existing vaccines, the development of broad-spectrum vaccines is urgently needed. In this study, we designed a novel SARS-CoV-2 receptor-binding domain (RBD) subunit (RBD5m) by integrating five important mutations from SARS-CoV-2 variants of concern (VOCs). The neutralization activities of antibodies induced by the RBD5m candidate vaccine are more balanced and effective for neutralizing different SARS-CoV-2 VOCs in comparison with those induced by the SARS-CoV-2 prototype strain RBD. Our results suggest that the RBD5m vaccine is a good broad-spectrum vaccine candidate able to prevent disease from several different SARS-CoV-2 VOCs.
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95
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Li X, Xu Y, Li X, Liu W, Yao D, Chen W, Yu H, He L, Lu S, Jiang C, Zhu W, Meng L. Real-world effectiveness and protection of SARS-CoV-2 vaccine among patients hospitalized for COVID-19 in Xi’an, China, December 8, 2021, to January 20, 2022: A retrospective study. Front Immunol 2022; 13:978977. [PMID: 36211421 PMCID: PMC9538118 DOI: 10.3389/fimmu.2022.978977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/09/2022] [Indexed: 01/08/2023] Open
Abstract
Introduction In December 2021, a large-scale epidemic broke out in Xi’an, China, due to SARS-CoV-2 infection. This study reports the effect of vaccination on COVID-19 and evaluates the impact of different vaccine doses on routine laboratory markers. Methods The laboratory data upon admission, of 231 cases with COVID-19 hospitalized from December 8, 2021 to January 20, 2022 in Xi’an, including blood routine, lymphocyte subtypes, coagulative function tests, virus specific antibodies and blood biochemical tests were collected and analyzed. Results Of the 231 patients, 21 were not vaccinated, 158 were vaccinated with two doses and 52 with three doses. Unvaccinated patients had a higher proportion of moderate and severe symptoms than vaccinated patients, while two-dose vaccinated patients had a higher proportion than three-dose vaccinated patients. SARS-CoV-2 specific IgG levels were significantly elevated in vaccinated patients compared with unvaccinated patients. Particularly, unvaccinated patients had lower counts and percentages of lymphocytes, eosinophils and CD8+ T-lymphocytes, and elevated coagulation-related markers. In addition, vaccination had no effect on liver and kidney function. Conclusions Vaccination against SARS-CoV-2, inducing high IgG level and increased CD8+ T cells and eosinophils, and regulating coagulation function, can significantly attenuate symptoms of COVID-19, suggesting that the vaccine remains protective against SARS-CoV-2.
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Affiliation(s)
- Xiaowei Li
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University, Xi’an, China
| | - Yinjuan Xu
- Department of Biochemistry and Molecular Biology, Institute of Molecular and Translational Medicine (IMTM), Xi’an Jiaotong University Health Science Center, Xi’an, China
- Department of Laboratory Medicine, Xi’an Chest Hospital, Xi'an, China
| | - Xiaomeng Li
- Department of Biochemistry and Molecular Biology, Institute of Molecular and Translational Medicine (IMTM), Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Wenbin Liu
- Department of Biochemistry and Molecular Biology, Institute of Molecular and Translational Medicine (IMTM), Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Dan Yao
- Nursing Department, Xi’an Children’s Hospital, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Weichao Chen
- Department of Respiratory Medicine, Xi’an Children’s Hospital, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Hongchuan Yu
- Department of Respiratory Medicine, Xi’an Children’s Hospital, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Langchong He
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Shemin Lu
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University, Xi’an, China
- Department of Biochemistry and Molecular Biology, Institute of Molecular and Translational Medicine (IMTM), Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Congshan Jiang
- National Regional Children’s Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi’an Key Laboratory of Children’s Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi’an Children’s Hospital, Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wenhua Zhu
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University, Xi’an, China
- Department of Biochemistry and Molecular Biology, Institute of Molecular and Translational Medicine (IMTM), Xi’an Jiaotong University Health Science Center, Xi’an, China
- *Correspondence: Liesu Meng, ; Wenhua Zhu,
| | - Liesu Meng
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University, Xi’an, China
- Department of Biochemistry and Molecular Biology, Institute of Molecular and Translational Medicine (IMTM), Xi’an Jiaotong University Health Science Center, Xi’an, China
- *Correspondence: Liesu Meng, ; Wenhua Zhu,
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96
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Rana R, Kant R, Huirem RS, Bohra D, Ganguly NK. Omicron variant: Current insights and future directions. Microbiol Res 2022; 265:127204. [PMID: 36152612 PMCID: PMC9482093 DOI: 10.1016/j.micres.2022.127204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 01/08/2023]
Abstract
The global COVID-19 outbreak has returned with the identification of the SARS-CoV-2 Omicron variant (B.1.1.529) after appearing to be persistently spreading for the more than past two years. In comparison to prior SARS-CoV-2 variants, this new variant revealed a significant amount of mutation. This novel variety may have a greater rate of transmissibility which might impede the effectiveness of current diagnostic equipment as well as vaccination efficacy and also impede immunotherapies (Antibody / monoclonal antibody based). WHO designated B.1.1.529 as a variant of concern on November 26, 2021, identified as Omicron. The Omicron variant transmission method and severity, on the other hand, are well defined. The global spread of Omicron, which has now seized many nations, has resulted in numerous speculations regarding its origin and degree of infectivity. The following sections will go over its potential for transmission, omicron structure, and impact on COVID-19 vaccines, how it is different from delta variant and diagnostics.
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Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, Delhi, India.
| | - Ravi Kant
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
| | | | - Deepika Bohra
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
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97
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A Recombinant VSV-Based Bivalent Vaccine Effectively Protects against Both SARS-CoV-2 and Influenza A Virus Infection. J Virol 2022; 96:e0133722. [PMID: 36069551 PMCID: PMC9517730 DOI: 10.1128/jvi.01337-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
COVID-19 and influenza are both highly contagious respiratory diseases that have been serious threats to global public health. It is necessary to develop a bivalent vaccine to control these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates against both SARS-CoV-2 and influenza viruses. These rVSV-based vaccines coexpress SARS-CoV-2 Delta spike protein (SP) bearing the C-terminal 17 amino acid (aa) deletion (SPΔC) and I742A point mutation, or the SPΔC with a deletion of S2 domain, or the RBD domain, and a tandem repeat harboring four copies of the highly conserved influenza M2 ectodomain (M2e) that fused with the Ebola glycoprotein DC-targeting/activation domain. Animal immunization studies have shown that these rVSV bivalent vaccines induced efficient humoral and cellular immune responses against both SARS-CoV-2 SP and influenza M2 protein, including high levels of neutralizing antibodies against SARS-CoV-2 Delta and other variant SP-pseudovirus infections. Importantly, immunization of the rVSV bivalent vaccines effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads. Overall, this study provides convincing evidence for the high efficacy of this bivalent vaccine platform to be used and/or easily adapted to produce new vaccines against new or reemerging SARS-CoV-2 variants and influenza A virus infections. IMPORTANCE Given that both COVID-19 and influenza are preferably transmitted through respiratory droplets during the same seasons, it is highly advantageous to develop a bivalent vaccine that could simultaneously protect against both COVID-19 and influenza. In this study, we generated the attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates that target both spike protein of SARS-Cov-2 Delta variant and the conserved influenza M2 domain. Importantly, these vaccine candidates effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads.
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98
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de Souza MO, Madan B, Teng IT, Huang A, Liu L, Fahad AS, Lopez Acevedo SN, Pan X, Sastry M, Gutierrez-Gonzalez M, Yin MT, Zhou T, Ho DD, Kwong PD, DeKosky BJ. Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens. Front Immunol 2022; 13:977064. [PMID: 36119018 PMCID: PMC9478573 DOI: 10.3389/fimmu.2022.977064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged continuously, challenging the effectiveness of vaccines, diagnostics, and treatments. Moreover, the possibility of the appearance of a new betacoronavirus with high transmissibility and high fatality is reason for concern. In this study, we used a natively paired yeast display technology, combined with next-generation sequencing (NGS) and massive bioinformatic analysis to perform a comprehensive study of subdomain specificity of natural human antibodies from two convalescent donors. Using this screening technology, we mapped the cross-reactive responses of antibodies generated by the two donors against SARS-CoV-2 variants and other betacoronaviruses. We tested the neutralization potency of a set of the cross-reactive antibodies generated in this study and observed that most of the antibodies produced by these patients were non-neutralizing. We performed a comparison of the specific and non-specific antibodies by somatic hypermutation in a repertoire-scale for the two individuals and observed that the degree of somatic hypermutation was unique for each patient. The data from this study provide functional insights into cross-reactive antibodies that can assist in the development of strategies against emerging SARS-CoV-2 variants and divergent betacoronaviruses.
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Affiliation(s)
- Matheus Oliveira de Souza
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Aric Huang
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Lihong Liu
- Aaron Diamond acquired immunodeficiency syndrome (AIDS) Research Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Ahmed S. Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Sheila N. Lopez Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Xiaoli Pan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Matias Gutierrez-Gonzalez
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Michael T. Yin
- Department of Medicine , Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - David D. Ho
- Aaron Diamond acquired immunodeficiency syndrome (AIDS) Research Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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99
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Saifi S, Ravi V, Sharma S, Swaminathan A, Chauhan NS, Pandey R. SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength? Genomics 2022; 114:110466. [PMID: 36041637 PMCID: PMC9419439 DOI: 10.1016/j.ygeno.2022.110466] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/12/2022] [Accepted: 08/26/2022] [Indexed: 11/29/2022]
Abstract
The global COVID-19 pandemic continues due to emerging Severe Acute Respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC). Here, we performed comprehensive analysis of in-house sequenced SARS-CoV-2 genome mutations dynamics in the patients infected with the VOCs - Delta and Omicron, within Recovered and Mortality patients. Statistical analysis highlighted significant mutations - T4685A, N4992N, and G5063S in RdRp; T19R in NTD spike; K444N and N532H in RBD spike, associated with Delta mortality. Mutations, T19I in NTD spike, Q493R and N440K in the RBD spike were significantly associated with Omicron mortality. We performed molecular docking for possible effect of significant mutations on the binding of Remdesivir. We found that Remdesivir showed less binding efficacy with the mutant Spike protein of both Delta and Omicron mortality compared to recovered patients. This indicates that mortality associated mutations could have a modulatory effect on drug binding which could be associated with disease outcome.
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Affiliation(s)
- Sheeba Saifi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Varsha Ravi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Sparsh Sharma
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Aparna Swaminathan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | | | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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100
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Richter J, Koptides D, Tryfonos C, Alexandrou D, Christodoulou C. Introduction, Spread and Impact of the SARS-CoV-2 Omicron Variants BA.1 and BA.2 in Cyprus. Microorganisms 2022; 10:1688. [PMID: 36144290 PMCID: PMC9503937 DOI: 10.3390/microorganisms10091688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/05/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Abstract
The aim of this study was to investigate and obtain insights into the appearance, spread and impact of the Omicron variants and their sub-lineages in Cyprus by analyzing 611 high-coverage full-genome sequences for the period from November 2021 until April 2022. All viruses sequenced were identified to belong to either Delta (B.1.617.2) or Omicron (lineage BA.1 and BA.2, respectively), with a variety of different sub-lineages. A detailed analysis of the mutational profile is presented and discussed. The Omicron variant BA.1 was shortly followed by BA.2; despite emerging against a background of high vaccination (81% of adult population) and pre-existing natural immunity, they gave rise to the largest waves of infection, with daily numbers rising dramatically, highlighting their increased ability for immune evasion. Within a period of only five months, the percentage of the Cypriot population with a confirmed infection increased from ~15% of the total population to >57%. Despite unprecedented case numbers, a significant reduction in hospital burden and mortality was observed. Our findings highlight the role of the importation of new variants through travel and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.
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Affiliation(s)
- Jan Richter
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Dana Koptides
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Christina Tryfonos
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Denise Alexandrou
- Medical and Public Health Services, Ministry of Health, Nicosia 1148, Cyprus
| | - Christina Christodoulou
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
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