Home Medicine It did not stop there: rapid substitution of circulating SARS-CoV-2 variant of concern B.1.1.7 (Alpha) by variant of concern B.1.617.2 (Delta) and further evolution of different Delta sublineages in Southern Saxony-Anhalt in late summer 2021
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It did not stop there: rapid substitution of circulating SARS-CoV-2 variant of concern B.1.1.7 (Alpha) by variant of concern B.1.617.2 (Delta) and further evolution of different Delta sublineages in Southern Saxony-Anhalt in late summer 2021

  • Markus Glaß , Laura Michaela Schian , Danny Misiak , Claudia Misiak , Simon Müller , Alexander Rausch , Katharina Angermann , Mariann Hoyer , Ramona Zabel , Ramyatha Battula , Astrid Kehlen , Beate Möbius , Jessica Weickert , Stefan Hüttelmaier and Matthias Karrasch EMAIL logo
Published/Copyright: December 14, 2021
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Journal of Laboratory Medicine
From the journal Journal of Laboratory Medicine Volume 46 Issue 1

Keywords: SARS-CoV-2; surveillance; whole genome sequencing (WGS)

To the Editor,

In a recently published manuscript in the Journal of Laboratory Medicine [1], we reported about the establishment of a regional SARS-CoV-2 surveillance program using whole genome sequencing (WGS) of SARS-CoV-2 isolates. Specimens were collected over a period of 5 months (January to May 2021) from patients suffering from COVID-19 and from outpatients without any clinical signs or symptoms. Sequence libraries were constructed from total RNA extracts using the Illumina COVIDSeq Test kit (Illumina, San Diego, US). During this time frame, the majority of the obtained sequences (252/364=69%) were assigned to the SARS-CoV-2 variant of concern (VOC) Alpha (B.1.1.7), and only very few other VOCs were found in our cohort [Beta (B.1.351, n=2); Delta (B.1.617.2, n=1)]. This situation rapidly changed throughout the sommer months of June to September 2021, in which VOC Delta (B.1.617.2 and sublineages AY.xx) rapidly became the dominant SARS-CoV-2 lineage in our study population within only one month (see Figure 1). In the months August and September 2021, a multitude of further Delta sublineages emerged (Figure 1). This spread of VOC Delta could also be observed when comparing SARS-CoV-2 genome sequences from the entire country of Germany collected in the same time period, and submitted to GISAID (gisaid.org) [2]. A similar development was reported from other European countries [3, 4]. We have created interactive websites providing up-to-date SARS-CoV-2 lineage distribution from our local area. All unfolding data determined by our surveillance program are accessible via the URL https://ngs-info.medizin.uni-halle.de/shiny/SARS_CoV2/SARS_CoV2.html. As already mentioned in our previously published manuscript [1], this fast changing situation further fosters the need for an established SARS-CoV-2 testing by WGS as an important surveillance tool for early detection of upcoming new lineages of concern [4, 5].

Figure 1: SARS-CoV-2 lineage distribution from June to September 2021.
Figure 1:

SARS-CoV-2 lineage distribution from June to September 2021.

While in June all sequenced SARS-CoV-2 genomes from the study population were classified as B.1.1.7 (VoC Alpha), from July on only B.1.617.2 and its sublineages AY.xx (VoC Delta) were found.

Corresponding author: Matthias Karrasch, MD, Department of Laboratory Medicine, Unit III, Halle University Hospital, Halle (Saale), Germany, E-mail:
Stefan Hüttelmaier and Matthias Karrasch contributed equally to this work.

Acknowledgments

The authors would like to thank Anke Cachay, Monique Dreher, Anastassia Teuber, Gabriele Unger and Nancy Wurg (Department of Laboratory Medicine, Unit III, Molecular Diagnostic Section, Halle University Hospital) for specimen handling, SARS-CoV-2 RNA isolation/inactivation and SNP-PCR, as well as Michael Böttcher and Ghanem El Kassem (Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany) for cooperation with the Illumina MiniSeq. We further acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s hCov19 Database.

  1. Research funding: None declared.

  2. Author contributions: All authors have accepted responsibility for the entire content of this manuscript and approved its submission.

  3. Competing interests: Authors state no conflict of interest.

  4. Informed consent: Informed consent was obtained from all individuals included in this study.

  5. Ethical approval: The local Institutional Review Board deemed the study exempt from review.

References

1. Glaß, M, Misiak, D, Misiak, C, Müller, S, Rausch, A, Angermann, K, et al.. Fast forward evolution in real time: the Rapid spread of SARS-CoV-2 variant of concern lineage B.1.1.7. In Saxony-Anhalt over a period of 5 months. J Lab Med 2022;46:71–5. https://doi.org/10.1515./labmed-2021-0092.10.1515/labmed-2021-0092Search in Google Scholar

2. Calvignac-Spencer, S, Budt, M, Huska, M, Richard, H, Leipold, L, Grabenhenrich, L, et al.. Rise and fall of SARS-CoV-2 lineage A.27 in Germany. Viruses 2021;13:1491.10.3390/v13081491Search in Google Scholar PubMed PubMed Central

3. Mishra, S, Mindermann, S, Sharma, M, Whittaker, C, Mellan, TA, Wilton, T, et al.. Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England. EClinicalMedicine 2021;39:101064.10.1016/j.eclinm.2021.101064Search in Google Scholar PubMed PubMed Central

4. Molenkamp, R, Fanoy, E, Derickx, L, de Groot, T, Jonges, M, Leenstra, T, et al.. Supplementing SARS-CoV-2 genomic surveillance with PCR-based variant detection for real-time actionable information, The Netherlands, June to July 2021. Euro Surveill 2021;26:2100921.10.2807/1560-7917.ES.2021.26.40.2100921Search in Google Scholar PubMed PubMed Central

5. Gravagnuolo, AM, Faqih, L, Cronshaw, C, Wynn, J, Klapper, P, Wigglesworth, M. High throughput diagnostics and dynamic risk assessment of SARS-CoV-2 variants of concern. EBioMedicine 2021;70:103540.10.1016/j.ebiom.2021.103540Search in Google Scholar PubMed PubMed Central

Received: 2021-11-10
Accepted: 2021-11-26
Published Online: 2021-12-14
Published in Print: 2022-02-23

© 2021 Markus Glaß et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  1. Frontmatter
  2. Obituary
  3. In Memoriam of Beniam Ghebremedhin
  4. Review
  5. New and emerging technologies for the diagnosis of urinary tract infections
  6. Original Articles
  7. Blood indices and circulating tumor cells for predicting metastasis of hepatocellular carcinoma after liver transplantation
  8. Comparison of APACHE II scores and mortality with CRP/albumin, neutrophil/lymphocyte and thrombocyte/lymphocyte ratios in patients admitted to internal medicine and anesthesia reanimation intensive care unit
  9. The correlation between the prevalence of gestational diabetes mellitus and maternal age in Southern China
  10. The investigation of serum protein profiles in anal fistula for potential biomarkers
  11. Evaluation of antioxidant and antiinflammatory activity of ethanolic extracts of Polygonum senticosum in lipopolysaccharide-induced RAW 264.7 macrophages
  12. Prevalence of SARS-CoV-2 antibodies in hospital employees, Central Germany
  13. Fast forward evolution in real time: the rapid spread of SARS-CoV-2 variant of concern lineage B.1.1.7 in Saxony-Anhalt over a period of 5 months
  14. Letters to the Editor
  15. It did not stop there: rapid substitution of circulating SARS-CoV-2 variant of concern B.1.1.7 (Alpha) by variant of concern B.1.617.2 (Delta) and further evolution of different Delta sublineages in Southern Saxony-Anhalt in late summer 2021
  16. In reply to a review article “Review of potentials and limitations of indirect approaches for estimating reference limits/intervals of quantitative procedures in laboratory medicine”
  17. Reply to the letter of Katayev and Fleming
https://doi.org/10.1515/labmed-2021-0168
Keywords for this article
SARS-CoV-2; surveillance; whole genome sequencing (WGS)
Creative Commons
BY 4.0

Articles in the same Issue

  1. Frontmatter
  2. Obituary
  3. In Memoriam of Beniam Ghebremedhin
  4. Review
  5. New and emerging technologies for the diagnosis of urinary tract infections
  6. Original Articles
  7. Blood indices and circulating tumor cells for predicting metastasis of hepatocellular carcinoma after liver transplantation
  8. Comparison of APACHE II scores and mortality with CRP/albumin, neutrophil/lymphocyte and thrombocyte/lymphocyte ratios in patients admitted to internal medicine and anesthesia reanimation intensive care unit
  9. The correlation between the prevalence of gestational diabetes mellitus and maternal age in Southern China
  10. The investigation of serum protein profiles in anal fistula for potential biomarkers
  11. Evaluation of antioxidant and antiinflammatory activity of ethanolic extracts of Polygonum senticosum in lipopolysaccharide-induced RAW 264.7 macrophages
  12. Prevalence of SARS-CoV-2 antibodies in hospital employees, Central Germany
  13. Fast forward evolution in real time: the rapid spread of SARS-CoV-2 variant of concern lineage B.1.1.7 in Saxony-Anhalt over a period of 5 months
  14. Letters to the Editor
  15. It did not stop there: rapid substitution of circulating SARS-CoV-2 variant of concern B.1.1.7 (Alpha) by variant of concern B.1.617.2 (Delta) and further evolution of different Delta sublineages in Southern Saxony-Anhalt in late summer 2021
  16. In reply to a review article “Review of potentials and limitations of indirect approaches for estimating reference limits/intervals of quantitative procedures in laboratory medicine”
  17. Reply to the letter of Katayev and Fleming
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