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Kohler C, King J, Stacker L, Goller KV, Moritz J, Pohlmann A, Nath N, Tzvetkova A, Rieck M, Paraskevopoulou S, Beslic D, Hölzer M, Fuchs S, Ziemann J, Kaderali L, Beer M, Hübner NO, Becker K. Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020-2022. Emerg Microbes Infect 2023; 12:2245916. [PMID: 37585712 PMCID: PMC10446807 DOI: 10.1080/22221751.2023.2245916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/03/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023]
Abstract
ABSTRACTGlobal and even national genome surveillance approaches do not provide the resolution necessary for rapid and accurate direct response by local public health authorities. Hence, a regional network of microbiological laboratories in collaboration with the health departments of all districts of the German federal state of Mecklenburg-Western Pomerania (M-V) was formed to investigate the regional molecular epidemiology of circulating SARS-CoV-2 lineages between 11/2020 and 03/2022. More than 4750 samples from all M-V counties were sequenced using Illumina and Nanopore technologies. Overall, 3493 (73.5%) sequences fulfilled quality criteria for time-resolved and/or spatially-resolved maximum likelihood phylogenic analyses and k-mean/ median clustering (KMC). We identified 116 different Pangolin virus lineages that can be assigned to 16 Nextstrain clades. The ten most frequently detected virus lineages belonged to B.1.1.7, AY.122, AY.43, BA.1, B.1.617.2, BA.1.1, AY.9.2, AY.4, P.1 and AY.126. Time-resolved phylogenetic analyses showed the occurrence of virus clades as determined worldwide, but with a substantial delay of one to two months. Further spatio-temporal phylogenetic analyses revealed a regional outbreak of a Gamma variant limited to western M-V counties. Finally, KMC elucidated a successive introduction of the various virus lineages into M-V, possibly triggered by vacation periods with increased (inter-) national travel activities. The COVID-19 pandemic in M-V was shaped by a combination of several SARS-CoV-2 introductions, lockdown measures, restrictive quarantine of patients and the lineage specific replication rate. Complementing global and national surveillance, regional surveillance adds value by providing a higher level of surveillance resolution tailored to local health authorities.
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Affiliation(s)
- Christian Kohler
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Lina Stacker
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katja V. Goller
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Juliane Moritz
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Ana Tzvetkova
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Maximilian Rieck
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | | | - Denis Beslic
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Stephan Fuchs
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Janine Ziemann
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Nils-Olaf Hübner
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
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Kawashima S, Matsui Y, Adachi T, Morikawa Y, Inoue K, Takebayashi S, Nobori H, Rokushima M, Tachibana Y, Kato T. Ensitrelvir is effective against SARS-CoV-2 3CL protease mutants circulating globally. Biochem Biophys Res Commun 2023; 645:132-136. [PMID: 36689809 PMCID: PMC9839456 DOI: 10.1016/j.bbrc.2023.01.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a public health concern worldwide. Ensitrelvir (S-217622) has been evaluated as an antiviral treatment for COVID-19, targeting SARS-CoV-2 3C-like protease (3CLpro). Ensitrelvir has been reported to have comparable antiviral activity against some of the SARS-CoV-2 variants: alpha, beta, gamma, delta, and omicron (BA.1.18). In this paper, we describe that ensitrelvir is effective against newly emerging SARS-CoV-2 variants and globally prevalent 3CLpro mutations. Ensitrelvir exhibited comparable antiviral activity against SARS-CoV-2 variants, including recently emerging ones: omicron (BA1.1, BA.2, BA.2.75, BA.4, BA.5, BQ.1.1, XBB.1, and XE), mu, lambda, and theta. Genetic surveillance of SARS-CoV-2 3CLpro, the target of ensitrelvir, was conducted using a public database and identified 11 major 3CLpro mutations circulating globally (G15S, T21I, T24I, K88R, L89F, K90R, P108S, P132H, A193V, H246Y, and A255V). The 3CLpro mutation from proline to histidine at amino acid position 132 was especially identified in the omicron variant, with prevalence of 99.69%. Enzyme kinetic assay revealed that these 3CLpro mutants have enzymatic activity comparable to that of the wild type (WT). Next, we assessed the inhibitory effect of ensitrelvir against mutated 3CLpro, with it showing inhibitory effects similar to that against the WT. These in vitro data suggest that ensitrelvir will be effective against currently circulating SARS-CoV-2 variants, including omicron variants and those carrying 3CLpro mutations, which emerging novel SARS-CoV-2 variants could carry.
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Affiliation(s)
- Sho Kawashima
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Yuki Matsui
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Takumi Adachi
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Yuji Morikawa
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Kae Inoue
- Shionogi TechnoAdvance Research CO., LTD., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Shiori Takebayashi
- Shionogi TechnoAdvance Research CO., LTD., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Haruaki Nobori
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Masatomo Rokushima
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Yuki Tachibana
- Laboratory for Medicinal Chemistry Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Teruhisa Kato
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan.
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Vukovikj M, Boshevska G, Janchevska E, Buzharova T, Preshova A, Simova M, Peshnacka A, Kocinski D, Kuzmanovska G, Memeti S, Gjorgoski I. In-depth genetic characterization of the SARS-CoV-2 pandemic in a two-year frame in North Macedonia using second and third generation sequencing technologies. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2022.1064882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a persistent negative impact on both the public health and the global economy. To comprehend the origin, transmission routes and discover the mutations that alter the virus’s transmissibility and pathogenicity, full-length SARS-CoV-2 genomes have to be molecularly characterized. Focusing on a two-year time frame (2020-2021), we provide an in-depth virologic and epidemiological overview of the SARS-CoV-2 pandemic in the Republic of North Macedonia by assessing the frequency and distribution of the circulating SARS-CoV-2 variants. Using genetic characterization and phylogenetic analysis we shed light on the molecular evolution of the virus as well as test for a possible connection between specific SARS-CoV-2 haplotypes and the severity of the clinical symptoms. Our results show that one fifth (21.51%) of the tested respiratory samples for SARS-CoV-2 were positive. A noticeable trend in the incidence and severity of the COVID-19 infections was observed in the 60+ age group between males and females. Of the total number of positive cases, the highest incidence of SARS-CoV-2 was noticed in 60+ males (4,170.4/100,000), with a statistically significant (0,0001) difference between the two sexes. Additionally, a 1.8x increase in male mortality and consequentially significantly higher number of death cases was observed compared to females of the same age group (0.001). A total of 327 samples were sequenced in the period March 2020 - August 2021, showing the temporal distribution of SARS-CoV-2 variants circulating in North Macedonia. The phylogenetic analysis showed that most of the viral genomes were closely related and clustered in four distinctive lineages, B.1, B.1.1.7, B.1.351 and B.1.617.2. A statistically significant difference was observed in the 2C_1 haplotype (p=0.0013), where 10.5% of the patients were hospitalized due to severe clinical condition. By employing genetic sequencing, coupled with epidemiological investigations, we investigated viral distribution patterns, identified emerging variants and detected vaccine breakthrough infections. The present work is the first molecular study giving a comprehensive overview of the genetic landscape of circulating SARS-CoV-2 viruses in North Macedonia in a period of two years.
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Morawiec E, Bednarska-Czerwińska A, Pudełko A, Strychalska A, Broncel M, Sagan D, Madej A, Jasińska-Balwierz A, Staszkiewicz R, Sobański D, Boroń D, Pokusa F, Grabarek B. A Retrospective Population Study of 385 191 Positive Real-Time Reverse Transcription-Polymerase Chain Reaction Tests For SARS-CoV-2 from a Single Laboratory in Katowice, Poland from April 2020 to July 2022. Med Sci Monit 2023; 29:e938872. [PMID: 36636983 PMCID: PMC9817382 DOI: 10.12659/msm.938872] [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: 12/23/2022] Open
Abstract
BACKGROUND This retrospective population study identified 385 191 positive real-time reverse transcription-polymerase chain reaction (RT-PCR) tests for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a single laboratory in Katowice, Poland, from April 2020 to July 2022. MATERIAL AND METHODS The material was nasopharyngeal, nasopharyngeal swab or bronchial lavage, and bronchoalveolar lavage (BAL) to confirm or exclude SARS-CoV-2 infection with the RT-PCR technique. Personal data are use according to the Provisions on the Protection of Personal Data by the Gyn-Centrum laboratory. RESULTS In 9 months of 2020, the number of SARS-CoV-2 results was 88 986; in 2021, it was 168 439, and in the first 7 months of 2022, it was 12 786. In 2020, the highest number of positive results was recorded in the third quarter (83 094 cases); 2021, in the 1st, 2nd, and 4th quarters (58 712; 37 720; and 71 753 cases, respectively), and in 2022, in the 1st quarter (127 613 cases) of the year. A positive result was observed more often in women and people aged 30-39, followed by those 40-49 years. Patients aged 10-19 years comprised the smallest population of SARS-CoV-2-positive cases. CONCLUSIONS In the Polish population studied, from April 2020 to July 2022, the detection rates of SARS-CoV-2 positivity were significantly higher for women than for men and in the 30-49 age group for both sexes. Also, the infection detection rate of 385 191 out of 1 332 659 patient samples, or 28.9%, supports that the Polish society adhered to public health recommendations for infection control during the COVID-19 pandemic.
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Affiliation(s)
- Emilia Morawiec
- Department of Histology, Cytophysiology and Embryology, Academy of Silesia, Katowice, Poland
| | | | - Adam Pudełko
- Department of Molecular Biology, Gyncentrum Fertility Clinic, Sosnowiec, Poland
| | - Anna Strychalska
- Department of Molecular Biology, Gyncentrum Fertility Clinic, Sosnowiec, Poland
| | - Mateusz Broncel
- Department of Molecular Biology, Gyncentrum Fertility Clinic, Sosnowiec, Poland
| | - Dorota Sagan
- Medical Center Dormed Medical SP, Busko-Zdrój, Poland
| | - Andrzej Madej
- Department of Pharmacology, Academy of Silesia, Katowice, Poland
| | | | - Rafał Staszkiewicz
- Department of Histology, Cytophysiology and Embryology, Academy of Silesia, Katowice, Poland
| | - Dawid Sobański
- Department of Histology, Cytophysiology and Embryology, Academy of Silesia, Katowice, Poland
| | - Dariusz Boroń
- Department of Histology, Cytophysiology and Embryology, Academy of Silesia, Katowice, Poland
| | - Filip Pokusa
- Faculty of Economics and Pedagogy, Higher School of Management and Administration in Opole, Opole, Poland
| | - Beniamin Grabarek
- Department of Histology, Cytophysiology and Embryology, Academy of Silesia, Katowice, Poland
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