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Neurological Manifestations of Non-Severe COVID-19-A Multidirectional Approach. Brain Sci 2023; 13:brainsci13020355. [PMID: 36831898 PMCID: PMC9953805 DOI: 10.3390/brainsci13020355] [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: 01/09/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
COVID-19 remains a significant clinical issue worldwide, with frequent neurological manifestations. In this study, the authors combine data obtained from the patient's medical history, physical examinations, and additional test results in the pursuit of any clinically relevant connections. Fifty-eight adult patients hospitalized in the Department of Neurology and Infectiology over a five-months period were retrospectively enrolled in this study. On admission, all patients included in this study were classified as mild or moderate COVID-19 cases, according to the World Health Organization (WHO) guidelines. Laboratory tests, Electroencephalography (EEG), and Magnetic Resonance Imaging (MRI) were performed. There was no statistically significant difference in the Neutrophil-Lymphocyte Ratio (NLR), C-reactive protein (CRP), and Interleukin 6 (IL-6) in patients who reported to the hospital within a week from the symptoms' onset and in those who reported later. In total, 49.06% of patients with eligible EEG recordings presented abnormal brain activity, while 27.59% of the study population had COVID-19-associated MRI findings. EEG and MRI abnormality occurrence did not correlate with the incidence of mild neurological symptoms (headache, olfactory, and gustatory disorders) of the SARS-CoV-2 infection. In three patients in this study population, unprovoked generalized epileptic seizures occurred for the first time in their life. Non-severe SARS-CoV-2 infection causes functional and structural abnormalities within the central nervous system. Brain microhemorrhages are frequently present in non-severe COVID-19 patients. There is no significant association between mild neurological symptoms of COVID-19 and additional test abnormalities. The time from SARS-CoV-2 infection's onset to hospital admission does not seem to influence the prognostic value of CRP, IL-6, and NLR in non-severe COVID-19. Mild-to-moderate SARS-CoV-2 infection can be a trigger factor for epilepsy and epileptic seizures.
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Broni E, Miller WA. Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes. Biomedicines 2023; 11:512. [PMID: 36831052 PMCID: PMC9953644 DOI: 10.3390/biomedicines11020512] [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: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global challenge requiring urgent and permanent therapeutic solutions. These solutions can only be engineered if the patterns and rate of mutations of the virus can be elucidated. Predicting mutations and the structure of proteins based on these mutations have become necessary for early drug and vaccine design purposes in anticipation of future viral mutations. The amino acid composition (AAC) of proteomes and individual viral proteins provide avenues for exploitation since AACs have been previously used to predict structure, shape and evolutionary rates. Herein, the frequency of amino acid residues found in 1637 complete proteomes belonging to 11 SARS-CoV-2 variants/lineages were analyzed. Leucine is the most abundant amino acid residue in the SARS-CoV-2 with an average AAC of 9.658% while tryptophan had the least abundance of 1.11%. The AAC and ranking of lysine and glycine varied in the proteome. For some variants, glycine had higher frequency and AAC than lysine and vice versa in other variants. Tryptophan was also observed to be the most intolerant to mutation in the various proteomes for the variants used. A correlogram revealed a very strong correlation of 0.999992 between B.1.525 (Eta) and B.1.526 (Iota) variants. Furthermore, isoleucine and threonine were observed to have a very strong negative correlation of -0.912, while cysteine and isoleucine had a very strong positive correlation of 0.835 at p < 0.001. Shapiro-Wilk normality test revealed that AAC values for all the amino acid residues except methionine showed no evidence of non-normality at p < 0.05. Thus, AACs of SARS-CoV-2 variants can be predicted using probability and z-scores. AACs may be beneficial in classifying viral strains, predicting viral disease types, members of protein families, protein interactions and for diagnostic purposes. They may also be used as a feature along with other crucial factors in machine-learning based algorithms to predict viral mutations. These mutation-predicting algorithms may help in developing effective therapeutics and vaccines for SARS-CoV-2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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da-Costa-Rodrigues B, Cheohen C, Sciammarella F, Pierre-Bonetti-Pozzobon A, Ribeiro L, Nepomuceno-Silva JL, Medeiros M, Mury F, Monteiro-de-Barros C, Lazoski C, Leal-da-Silva M, Tanuri A, Nunes-da-Fonseca R. SARS-CoV-2 Spatiotemporal Genomic and Molecular Analysis of the First Wave of the COVID-19 Pandemic in Macaé, the Brazilian Capital of Oil. Int J Mol Sci 2022; 23:ijms231911497. [PMID: 36232806 PMCID: PMC9569756 DOI: 10.3390/ijms231911497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/25/2022] Open
Abstract
The SARS-CoV-2 virus infection led to millions of deaths during the COVID-19 pandemic. Hundreds of workers from several other Brazilian cities, as well as from other countries, arrive daily in Macaé to work in the oil supply chain, making this city a putative hotspot for the introduction of new viral lineages. In this study, we performed a genomic survey of SARS-CoV-2 samples from Macaé during the first outbreak of COVID-19, combined with clinical data and a molecular integrative analysis. First, phylogenomic analyses showed a high occurrence of viral introduction events and the establishment of local transmissions in Macaé, including the ingression and spread of the B.1.1.28 lineage in the municipality from June to August 2020. Second, SARS-CoV-2 mutations were identified in patients with distinct levels of COVID-19 severity. Third, molecular interactions of the mutated spike protein from three B.1.1.33 local samples and human ACE2 showed higher interactions than that of the wild-type spike protein from the ancestral virus. Altogether, these results elucidate the SARS-CoV-2 genomic profile in a strategic Brazilian city and further explore the functional aspects of SARS-CoV-2 with a characterization of emerging viral mutations associated with clinical data and the potential targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Bruno da-Costa-Rodrigues
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
- Programa de Ciências Morfológicas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-170, Brazil
- Correspondence: (B.d.-C.-R.); (R.N.-d.-F.)
| | - Caio Cheohen
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Felipe Sciammarella
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Allan Pierre-Bonetti-Pozzobon
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Lupis Ribeiro
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - José Luciano Nepomuceno-Silva
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Marcio Medeiros
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Flávia Mury
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Cintia Monteiro-de-Barros
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Cristiano Lazoski
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Manuela Leal-da-Silva
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Amilcar Tanuri
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Rodrigo Nunes-da-Fonseca
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
- Programa de Ciências Morfológicas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-170, Brazil
- Correspondence: (B.d.-C.-R.); (R.N.-d.-F.)
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Tylicki L, Biedunkiewicz B, Puchalska-Reglińska E, Gellert R, Burnier M, Wolf J, Dȩbska-Ślizień A. COVID-19 vaccination reduces mortality in patients on maintenance hemodialysis. Front Med (Lausanne) 2022; 9:937167. [PMID: 36160175 PMCID: PMC9492862 DOI: 10.3389/fmed.2022.937167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with chronic kidney disease on maintenance hemodialysis (HD) have a very high risk of death in the course of COVID-19. The aim of the study was to assess the effectiveness of COVID-19 vaccination to reduce the incidence of COVID-19 and the fatality rate in HD patients. A retrospective registry-based cohort study was performed in all HD adult patients in the Pomeranian Voivodeship. Vaccinations were carried out from January to April 2021 with mRNA vaccines, either BNT162b2 or mRNA-1273 with two-dose schedule. In the first analysis (2nd pandemic wave), 1,160 unvaccinated patients were included (59.7% males, 25.7% diabetic). In the second analysis (4th pandemic wave), 1,131 (59.4% male, 30.7% diabetic) individuals were included, 1,042 (92.13%) were fully vaccinated. Three hundred and fifteen HD patients (27.2%) were COVID-19 positive during the 2nd wave, and 6.9% (78/1,131) during the 4th wave. Within the fully vaccinated patients of the 4th wave, 60 were COVID-19 positive, 5.8 vs. 20.2% of unvaccinated COVID-19 positive patients in 2nd wave, respectively. COVID-19 incidence rate ratio (IRR) was 0.21 (4th wave-vaccinated vs. 2nd wave-unvaccinated) indicating a 79% reduction. The IRR between vaccinated and unvaccinated patients of the 4th wave was 0.28 in favor of vaccinated patients with 72% reduction. In the 2nd wave, 93 patients died as a result of COVID-19 (fatality rate: 29.5%). The fatality rate of fully vaccinated patients during the 4th wave was 6.7% (p = 0.004), while the fatality rate in the 4th wave within unvaccinated patients accounted for 11.1%. Significant clinical effectiveness of COVID-19 vaccination was demonstrated in a multicenter study in HD patients.
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Affiliation(s)
- Leszek Tylicki
- Department of Nephrology, Transplantology and Internal Medicine, Medical University of Gdansk, Gdańsk, Poland
- *Correspondence: Leszek Tylicki
| | - Bogdan Biedunkiewicz
- Department of Nephrology, Transplantology and Internal Medicine, Medical University of Gdansk, Gdańsk, Poland
| | | | - Ryszard Gellert
- Department of Nephrology and Internal Medicine, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michel Burnier
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Translational Medicine Centre, Medical University of Gdańsk, Gdańsk, Poland
| | - Jacek Wolf
- Translational Medicine Centre, Medical University of Gdańsk, Gdańsk, Poland
| | - Alicja Dȩbska-Ślizień
- Department of Nephrology, Transplantology and Internal Medicine, Medical University of Gdansk, Gdańsk, Poland
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5
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Morawiec E, Miklasińska-Majdanik M, Bratosiewicz-Wąsik J, Wojtyczka RD, Swolana D, Stolarek I, Czerwiński M, Skubis-Sikora A, Samul M, Polak A, Kruszniewska-Rajs C, Pudełko A, Figlerowicz M, Bednarska-Czerwińska A, Wąsik TJ. From Alpha to Delta-Genetic Epidemiology of SARS-CoV-2 (hCoV-19) in Southern Poland. Pathogens 2022; 11:pathogens11070780. [PMID: 35890025 PMCID: PMC9316897 DOI: 10.3390/pathogens11070780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
In Poland, the first case of SARS-CoV-2 infection was confirmed in March 2020. Since then, many circulating virus lineages fueled rapid pandemic waves which inflicted a severe burden on the Polish healthcare system. Some of these lineages were associated with increased transmissibility and immune escape. Mutations in the viral spike protein, which is responsible for host cell recognition and serves as the primary target for neutralizing antibodies, are of particular importance. We investigated the molecular epidemiology of the SARS-CoV-2 clades circulating in Southern Poland from February 2021 to August 2021. The 921 whole-genome sequences were used for variant identification, spike mutation, and phylogenetic analyses. The Pango B.1.1.7 was the dominant variant (n = 730, 89.68%) from March 2021 to July 2021. In July 2021, the B.1.1.7 was displaced by the B.1.617.2 lineage with 66.66% in July 2021 and 92.3% in August 2021 frequencies, respectively. Moreover, our results were compared with the sequencing available on the GISAID platform for other regions of Poland, the Czech Republic, and Slovakia. The analysis showed that the dominant variant in the analyzed period was B.1.1.7 in all countries and Southern Poland (Silesia). Interestingly, B.1.1.7 was replaced by B.1.617.2 earlier in Southern Poland than in the rest of the country. Moreover, in the Czech Republic and Slovakia, AY lineages were predominant at that time, contrary to the Silesia region.
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Affiliation(s)
- Emilia Morawiec
- Department of Microbiology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800 Zabrze, Poland;
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800 Zabrze, Poland
| | - Maria Miklasińska-Majdanik
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
| | - Jolanta Bratosiewicz-Wąsik
- Department of Biopharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland;
| | - Robert D. Wojtyczka
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
| | - Denis Swolana
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
| | - Ireneusz Stolarek
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznań, Poland; (I.S.); (M.F.)
| | - Michał Czerwiński
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- American Medical Clinic, 40-851 Katowice, Poland
| | - Aleksandra Skubis-Sikora
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Cytophysiology, Chair of Histology and Embryology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, 40-055 Katowice, Poland
| | - Magdalena Samul
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
| | - Agnieszka Polak
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
| | - Celina Kruszniewska-Rajs
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Adam Pudełko
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- Department of Clinical Chemistry and Laboratory Diagnostics, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznań, Poland; (I.S.); (M.F.)
| | - Anna Bednarska-Czerwińska
- Gyncentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland; (M.C.); (A.S.-S.); (M.S.); (A.P.); (C.K.-R.); (A.P.); (A.B.-C.)
- American Medical Clinic, 40-851 Katowice, Poland
- Department of Gynecology and Obstetrics, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, 41-800 Zabrze, Poland
| | - Tomasz J. Wąsik
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (M.M.-M.); (R.D.W.); (D.S.)
- Correspondence: ; Tel.: +48-32-364-1621
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Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B, Pandey R. Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome. Microbiol Spectr 2022; 10:e0231121. [PMID: 35579429 PMCID: PMC9241827 DOI: 10.1128/spectrum.02311-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/17/2022] [Indexed: 12/13/2022] Open
Abstract
The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.
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Affiliation(s)
- Priti Devi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aanchal Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kriti Khare
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Shweta Sahni
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sujeet Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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7
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SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains. Viruses 2022; 14:v14061230. [PMID: 35746701 PMCID: PMC9227152 DOI: 10.3390/v14061230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/14/2022] [Accepted: 06/04/2022] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.
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Phylodynamic Dispersal of SARS-CoV-2 Lineages Circulating across Polish-German Border Provinces. Viruses 2022; 14:v14050884. [PMID: 35632625 PMCID: PMC9143188 DOI: 10.3390/v14050884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction: The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evolved into a worldwide outbreak, with significant molecular evolution over time. Large-scale phylodynamic studies allow to map the virus spread and inform preventive strategies. Aim: This study investigates the extent of binational dispersal and dynamics of SARS-CoV-2 lineages between seven border provinces of the adjacent countries of Poland and Germany to reconstruct SARS-CoV-2 transmission networks. Methods: Following three pandemic waves from March 2020 to the end of May 2021, we analysed a dataset of 19,994 sequences divided into B.1.1.7|Alpha and non-Alpha lineage groups. We performed phylogeographic analyses using the discrete diffusion models to identify the pathways of virus spread. Results: Based on population dynamics inferences, in total, 673 lineage introductions (95% HPD interval 641−712) for non-Alpha and 618 (95% HPD interval 599−639) for B.1.1.7|Alpha were identified in the area. For non-Alpha lineages, 5.05% binational, 86.63% exclusively German, and 8.32% Polish clusters were found, with a higher frequency of international clustering observed for B.1.1.7|Alpha (13.11% for binational, 68.44% German and 18.45% Polish, p < 0.001). We identified key transmission hubs for the analysed lineages, namely Saxony, West Pomerania and Lower Silesia. Conclusions: Clustering patterns between Poland and Germany reflect the viral variant transmission dynamics at the international level in the borderline area. Tracing the spread of the virus between two adjacent large European countries may provide a basis for future intervention policies in cross-border cooperation efforts against the spread of the pandemics.
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Klempt P, Brzoň O, Kašný M, Kvapilová K, Hubáček P, Briksi A, Bezdíček M, Koudeláková V, Lengerová M, Hajdúch M, Dřevínek P, Pospíšilová Š, Kriegová E, Macek M, Kvapil P. Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic. Microorganisms 2021; 9:microorganisms9081671. [PMID: 34442750 PMCID: PMC8397935 DOI: 10.3390/microorganisms9081671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/03/2023] Open
Abstract
In the Czech Republic, the current pandemic led to over 1.67 million SARS-CoV-2- positive cases since the recording of the first case on 1 March 2020. SARS-CoV-2 genome analysis is an important tool for effective real-time quantitative PCR (RT-qPCR) diagnostics, epidemiology monitoring, as well as vaccination strategy. To date, there is no comprehensive report on the distribution of SARS-CoV-2 genome variants in either the Czech Republic, including Central and Eastern Europe in general, during the first year of pandemic. In this study, we have analysed a representative cohort of SARS-CoV-2 genomes from 229 nasopharyngeal swabs of COVID-19 positive patients collected between March 2020 and February 2021 using validated reference-based sequencing workflow. We document the changing frequency of dominant variants of SARS-CoV-2 (from B.1 -> B.1.1.266 -> B.1.258 -> B.1.1.7) throughout the first year of the pandemic and list specific variants that could impact the diagnostic efficiency RT-qPCR assays. Moreover, our reference-based workflow provided evidence of superinfection in several samples, which may have contributed to one of the highest per capita numbers of COVID-19 cases and deaths during the first year of the pandemic in the Czech Republic.
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Affiliation(s)
- Petr Klempt
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
- Correspondence: ; Tel.: +420-739-394-373
| | - Ondřej Brzoň
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Kašný
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
| | - Kateřina Kvapilová
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Petr Hubáček
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Úvalu 84, 150 06 Prague, Czech Republic; (P.H.); (A.B.); (P.D.)
| | - Aleš Briksi
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Úvalu 84, 150 06 Prague, Czech Republic; (P.H.); (A.B.); (P.D.)
| | - Matěj Bezdíček
- Center of Molecular Biology and Genetics, Department of Internal Medicine-Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00 Brno, Czech Republic; (M.B.); (M.L.); (Š.P.)
| | - Vladimira Koudeláková
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 5, 77 515 Olomouc, Czech Republic; (V.K.); (M.H.)
| | - Martina Lengerová
- Center of Molecular Biology and Genetics, Department of Internal Medicine-Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00 Brno, Czech Republic; (M.B.); (M.L.); (Š.P.)
| | - Marian Hajdúch
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 5, 77 515 Olomouc, Czech Republic; (V.K.); (M.H.)
| | - Pavel Dřevínek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Úvalu 84, 150 06 Prague, Czech Republic; (P.H.); (A.B.); (P.D.)
| | - Šárka Pospíšilová
- Center of Molecular Biology and Genetics, Department of Internal Medicine-Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00 Brno, Czech Republic; (M.B.); (M.L.); (Š.P.)
| | - Eva Kriegová
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University Olomouc and University Hospital, Hněvotínská 3, 775 15 Olomouc, Czech Republic;
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine-Charles University and Motol University Hospital, V Úvalu 84, 150 05 Prague, Czech Republic;
| | - Petr Kvapil
- Institute of Applied Biotechnologies, Služeb 3056/4, 108 00 Prague, Czech Republic; (O.B.); (M.K.); (K.K.); (P.K.)
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