1,052
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020–2022

ORCID Icon, ORCID Icon, , ORCID Icon, , ORCID Icon, ORCID Icon, ORCID Icon, , ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, , ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon show all
Article: 2245916 | Received 22 Mar 2023, Accepted 03 Aug 2023, Published online: 22 Aug 2023

References

  • Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382(8):727–733. doi:10.1056/NEJMoa2001017
  • Bohmer MM, Buchholz U, Corman VM, et al. Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series. Lancet Infect Dis. 2020;20(8):920–928. doi:10.1016/S1473-3099(20)30314-5
  • Saravanan KA, Panigrahi M, Kumar H, et al. Role of genomics in combating COVID-19 pandemic. Gene. 2022;823:146387. doi:10.1016/j.gene.2022.146387
  • Hadfield J, Megill C, Bell SM, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34(23):4121–4123. doi:10.1093/bioinformatics/bty407
  • Rambaut A, Holmes EC, O'Toole A, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403–1407. doi:10.1038/s41564-020-0770-5
  • Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780. doi:10.1093/molbev/mst010
  • Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313. doi:10.1093/bioinformatics/btu033
  • Saeed AI, Sharov V, White J, et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003;34(2):374–378. doi:10.2144/03342mt01
  • Brito AF, Semenova E, Dudas G, et al. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun. 2022;13(1):7003. doi:10.1038/s41467-022-33713-y
  • Fischer C, Maponga TG, Yadouleton A, et al. Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science. 2022;378(6623):eadd8737. doi:10.1126/science.add8737
  • Khare S, Gurry C, Freitas L, et al. Gisaid's role in pandemic response. People’s Republic of China CDC Wkly. 2021;3(49):1049–1051. doi:10.46234/ccdcw2021.255
  • Yi B, Poetsch AR, Stadtmuller M, et al. Phylogenetic analysis of SARS-CoV-2 lineage development across the first and second waves in Eastern Germany in 2020: insights into the cause of the second wave. Epidemiol Infect. 2021;149:e177. doi:10.1017/S0950268821001461
  • Hodcroft EB, Zuber M, Nadeau S, et al. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature. 2021;595(7869):707–712. doi:10.1038/s41586-021-03677-y
  • Zhou B, Thao TTN, Hoffmann D, et al. SARS-CoV-2 spike D614G change enhances replication and transmission. Nature. 2021;592(7852):122–127. doi:10.1038/s41586-021-03361-1
  • Hou YJ, Chiba S, Halfmann P, et al. SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science. 2020;370(6523):1464–1468. doi:10.1126/science.abe8499
  • Ulrich L, Halwe NJ, Taddeo A, et al. Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Nature. 2022;602(7896):307–313. doi:10.1038/s41586-021-04342-0
  • Volz E, Hill V, McCrone JT, et al. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell. 2021;184(1):64–75.e11. doi:10.1016/j.cell.2020.11.020
  • Tang H, Gao L, Wu Z, et al. Characterization of SARS-CoV-2 variants N501Y.V1 and N501Y.V2 spike on viral infectivity. Front Cell Infect Microbiol. 2021;11:720357. doi:10.3389/fcimb.2021.720357
  • Faria NR, Mellan TA, Whittaker C, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021;372(6544):815–821. doi:10.1126/science.abh2644
  • Nonaka CKV, Graf T, Barcia CAL, et al. SARS-CoV-2 variant of concern P.1 (Gamma) infection in young and middle-aged patients admitted to the intensive care units of a single hospital in Salvador, Northeast Brazil, February 2021. Int J Infect Dis. 2021;111:47–54. doi:10.1016/j.ijid.2021.08.003
  • Giovanetti M, Slavov SN, Fonseca V, et al. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nat Microbiol. 2022;7(9):1490–1500. doi:10.1038/s41564-022-01191-z
  • Bulfone TC, Blat C, Chen YH, et al. Outdoor activities associated with lower odds of SARS-CoV-2 acquisition: a case-control study. Int J Environ Res Public Health. 2022;19(10). doi:10.3390/ijerph19106126
  • Cherian S, Potdar V, Jadhav S, et al. SARS-CoV-2 spike mutations, L452R, T478 K, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Microorganisms. 2021;9(7). doi:10.3390/microorganisms9071542
  • Dhawan M, Sharma A, Priyanka N, et al. Delta variant (B.1.617.2) of SARS-CoV-2: mutations, impact, challenges and possible solutions. Hum Vaccin Immunother. 2022;18(5):2068883. doi:10.1080/21645515.2022.2068883
  • Control. ECfDPa. Threat assessment brief: emergence of SARS-CoV-2 B.1.617 variants in India and situation in the EU/EEA. Available from: https://wwwecdceuropaeu/sites/default/files/documents/Emergence-of-SARS-CoV-2-B1617-variants-in-India-and-situation-in-the-EUEEA_0pdf. 2021.
  • Centre SM. Expert reaction to cases of variant B.1.617 (the ‘Indian variant’) being investigated in the UK. 2021.
  • Rusnakova D, Sedlackova T, Radvak P, et al. Systematic genomic surveillance of SARS-CoV-2 virus on illumina sequencing platforms in the Slovak republic-One year experience. Viruses. 2022;14(11). doi:10.3390/v14112432
  • Morozov A, Nirca V, Victorova A, et al. SARS-CoV-2 from COVID-19 patients in the Republic of Moldova: whole-genome sequencing results. Viruses. 2022;14(10). doi:10.3390/v14102310
  • Morawiec E, Miklasinska-Majdanik M, Bratosiewicz-Wasik J, et al. From alpha to delta-genetic epidemiology of SARS-CoV-2 (hCoV-19) in southern Poland. Pathogens. 2022 Jul 8;11(7). doi:10.3390/pathogens11070780
  • Sievers C, Zacher B, Ullrich A, et al. SARS-CoV-2 Omicron variants BA.1 and BA.2 both show similarly reduced disease severity of COVID-19 compared to Delta, Germany, 2021 to 2022. Euro Surveill. 2022;27(22):1–7. doi:10.2807/1560-7917.ES.2022.27.22.2200396
  • Viana R, Moyo S, Amoako DG, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in Southern Africa. Nature. 2022;603(7902):679–686. doi:10.1038/s41586-022-04411-y
  • Yamasoba D, Kimura I, Nasser H, et al. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell. 2022;185(12):2103–2115.e19. doi:10.1016/j.cell.2022.04.035
  • WHO. COVID-19 weekly epidemiological update, edition 99 published 6 July 2022.