Öz
Abstract
Objective: Our study focused on retrospectively assessing variant of concern, specified by the World Health Organization (WHO), with one-step reverse transcription and real-time polymerase chain reaction (RT-PCR) test in SARS-CoV-2 positive patients after three doses of attenuated COVID-19 vaccine.
Methods: 8.520 samples transported with viral nucleic acid buffer (vNAT) tubes between June 2021 and January 31, 2022, were tested and included in the study. All the patients whose samples were included in our research had 3 doses of CoronaVac (Sinovac Life Science Co, Ltd, Beijing, China). Gender distribution was 4686 (55%) female and 3834 ( 45%) males. Variant specific genome regions only found in B.1.351, P.1 and B.1.1.7 as well as ORF1ab and N gene regions are investigated by the Bio-Speedy® Emerging Plus kit (Bioeksen AR-GE Technologies, Turkey) used to identify the variants in the study.
Results: All 8.520 samples were SARS-CoV-2 RT-PCR positive. Our study detected alpha and delta variants in 1460 (17.14%) and 3570 (41.9%) patients respectively. 2570 (30.16%) patients did not have any variants according to test results. It was observed that the spread of beta, gamma and other suspicious variants remained at relatively low rates.
Conclusion: The delta variant became dominant from July until to the end of the year. Declining delta variant rates and increasing cases of suspected variants towards the beginning of December 2021 suggest the omicron variant. Therefore, molecular surveillance studies that are planned to take epidemiological data into consideration and to examine the prevalence and gene-based analysis of local and worldwide variants are required.
Anahtar Kelimeler
sars-cov-2 variants of concern variant B.1.1.7 variant B.1.351 variant P.1 variant B.1.617.2
Kaynakça
- 1.World Health Organization Coronavirus (COVID-19) Situation Report-114. 13 May 2020. [cited 25.05.2023]. Available from: https://apps.who.int/iris/handle/10665/332089,
- 2. WHO Coronavirus (COVID-19) Dashboard. [cited 25.05.2023]. Available from: https://covid19.who.int,
- 3. Carabelli AM, Peacock TP, Thorne LG , Harvey WT, Hughes J, et al.SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol. 2023;21(3):162-177. doi: 10.1038/s41579-022-00841-7.
- 4. Vitiello, A., Ferrara, F., Auti, A. M., Di Domenico, M., & Boccellino, M. Advances in the Omicron variant development. J Intern Med 2022;292(1):81-90.doi: 10.1111/joim.13478. Epub 2022 Mar 22.
- 5. Chenchula, S., & Karunakaran, P. Current Evidence on Efficacy of COVID‐19 Booster Dose Vaccination Against the Omicron Variant. A Systematic Review. J Med Virol 2022;94(7):2969-2976. doi: 10.1002/jmv.27697. Epub 2022 Mar 14.
- 6. McEwen AE, Cohen S, Bryson-Cahn C, Liu C, Pergam SA, Lynch J, et al. Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State. Clin Infect Dis 2022;74(6):1089-1092. doi: 10.1093/cid/ciab581.
- 7. Chavda, V. P., & Apostolopoulos, V. Is Booster Dose Strategy Sufficient for Omicron Variant of SARS-CoV-2?. Vaccines. 2022;10 (3):367. doi: 10.3390/vaccines10030367.
- 8. McLaughlin, J., & Castrodale, L. Effectiveness of COVID-19 Vaccine Booster Dose Against COVID-19 During the SARS CoV-2 B. 1.1. 529 (Omicron) Wave - Alaska, December 2021–January 2022. State of Alaska Epidemiology Bulletin 2022;2
- 9.Centers for Disease Control and Prevention (CDC). [cited 25.05.2023]. Available from: https://www.cdc.gov/vaccines/hcp/conversations/understanding-vacc-work.html.
- 10. REUTERS. Chilean Sinovac trial leaders recommend third dose of COVID-19 vaccine. [cited 25.05.2023]. Available from: https://www.reuters.com/world/americas/chilean-sinovac-trial-leaders-recommend-third-dose-covid-19-vaccine-2021-07-15/
- 11. The Wall Street Journal. China to Keep Covid-19 Border Restrictions for Another Year [cited 25.05.2023]. Available from: https:// www.wsj.com/articles/china-to-keep-covid-19-border-restrictions-for-another-year-11624361777.
- 12. Erensoy MS, Midilli K, Gökahmetoğlu S, et al. SARS-CoV-2 variants affect the course of pandemic why and how should effective and comprehensive genomic surveillance be done? STED. 2021:30:37-40. Turkish
- 13. Garcia-Beltran WF, Lam EC, Denis KS, Nitido AD, Garcia ZH, Hauser BM, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 2021;184:2523.
- 14. Nemet, I., Kliker, L., Lustig, Y., Zuckerman, N., Erster, O., Cohen, C. et al. Third BNT162b2 vaccination neutralization of SARS-CoV-2 Omicron infection. N Engl J Med, 2022;386:492-94
- 15.Baric RS. Emergence of a highly fit SARS-CoV-2 variant. N Engl J Med. 2020;383(27):2684-6.
- 16. Tekin S, Demirtürk N. COVID-19: Risk factors increasing disease and scoring. Klimik Derg. 2021;34(3):155-5. Turkish.
- 17. Vasireddy D, Vanaparthy R, Mohan G, Malayala SV, Atluri P. Review of COVID-19 variants and COVID-19 vaccine efficacy: what the clinician should know? J Clin Med Res. 2021;13(6):317-25. Erratum in: J Clin Med Res. 2021;13(7):412.
- 18. Abdool Karim SS, de Oliveira T. New SARS-CoV-2 variants - clinical, public health, and vaccine implications. N Engl J Med. 2021;384(19):1866-8.
Öz
ÖZ
Amaç: Çalışmamızda, üç doz atenüe COVID-19 aşısı sonrası SARS-CoV-2 polimeraz zincir reaksiyonu (PCR) testi pozitif saptanan hastalarda Dünya Sağlık Örgütü (DSÖ) tarafından endişe verici varyantların (“variants of concern – VOCs”) dağılımının geriye dönük olarak değerlendirilmesi amaçlandı.
Gereç ve Yöntemler: Haziran 2021-31 Ocak 2022 tarihleri arasında laboratuvara rutin çalışma kapsamında viral nükleik asit tamponu (vNAT) tüpü ile gelen ve SARS-CoV-2 RT-PCR testi istenen 8520 örnek çalışmaya dahil edildi. Örneklerin hepsi, 3 doz CoronaVac (Sinovac Life Science Co, Ltd, Beijing, China) aşı geçmişine sahip ve son doz aşıdan en az 28 gün geçtikten sonra alınmış, cinsiyet dağılımı 4686 (%55)’sı kadın 3834 (%45)’ü erkektir. SARS-CoV-2 varyantları; ORF1ab ve N gen bölgelerinin yanı sıra yalnızca B.1.1.7, B.1.351 ve P.1’de bulunan varyant spesifik genom bölgelerini de hedefleyen Bio-Speedy® SARS- CoV-2 Emerging Plus kiti (Bioeksen AR-GE Teknolojileri, Türkiye) ile saptandı.
Bulgular: 8.520 numunenin tamamı SARS-CoV-2 RT-PCR pozitifti. Çalışmamızda sırasıyla 1460 (%17,14) ve 3570 (%41,9) hastada alfa ve delta varyantları saptandı. 2570 (%30,16) hastanın test sonuçlarında göre herhangi bir varyantı yoktu. Beta, gama ve diğer şüpheli varyantların yayılımının nispeten düşük oranlarda kaldığı gözlemlendi.
Sonuç: Çalışmamızda,Temmuz ayından yıl sonuna kadar ise delta varyantının baskın hale geldiği tespit edildi. Bu bağlamda epidemiyolojik veriler ışığında planlanmış, bölgesel ve küresel çapta varyantların sıklığını ve genomik analizlerini irdeleyen moleküler sürveyans çalışmalarının yapılması gerekmektedir.
Anahtar Kelimeler
Kaynakça
- 1.World Health Organization Coronavirus (COVID-19) Situation Report-114. 13 May 2020. [cited 25.05.2023]. Available from: https://apps.who.int/iris/handle/10665/332089,
- 2. WHO Coronavirus (COVID-19) Dashboard. [cited 25.05.2023]. Available from: https://covid19.who.int,
- 3. Carabelli AM, Peacock TP, Thorne LG , Harvey WT, Hughes J, et al.SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol. 2023;21(3):162-177. doi: 10.1038/s41579-022-00841-7.
- 4. Vitiello, A., Ferrara, F., Auti, A. M., Di Domenico, M., & Boccellino, M. Advances in the Omicron variant development. J Intern Med 2022;292(1):81-90.doi: 10.1111/joim.13478. Epub 2022 Mar 22.
- 5. Chenchula, S., & Karunakaran, P. Current Evidence on Efficacy of COVID‐19 Booster Dose Vaccination Against the Omicron Variant. A Systematic Review. J Med Virol 2022;94(7):2969-2976. doi: 10.1002/jmv.27697. Epub 2022 Mar 14.
- 6. McEwen AE, Cohen S, Bryson-Cahn C, Liu C, Pergam SA, Lynch J, et al. Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State. Clin Infect Dis 2022;74(6):1089-1092. doi: 10.1093/cid/ciab581.
- 7. Chavda, V. P., & Apostolopoulos, V. Is Booster Dose Strategy Sufficient for Omicron Variant of SARS-CoV-2?. Vaccines. 2022;10 (3):367. doi: 10.3390/vaccines10030367.
- 8. McLaughlin, J., & Castrodale, L. Effectiveness of COVID-19 Vaccine Booster Dose Against COVID-19 During the SARS CoV-2 B. 1.1. 529 (Omicron) Wave - Alaska, December 2021–January 2022. State of Alaska Epidemiology Bulletin 2022;2
- 9.Centers for Disease Control and Prevention (CDC). [cited 25.05.2023]. Available from: https://www.cdc.gov/vaccines/hcp/conversations/understanding-vacc-work.html.
- 10. REUTERS. Chilean Sinovac trial leaders recommend third dose of COVID-19 vaccine. [cited 25.05.2023]. Available from: https://www.reuters.com/world/americas/chilean-sinovac-trial-leaders-recommend-third-dose-covid-19-vaccine-2021-07-15/
- 11. The Wall Street Journal. China to Keep Covid-19 Border Restrictions for Another Year [cited 25.05.2023]. Available from: https:// www.wsj.com/articles/china-to-keep-covid-19-border-restrictions-for-another-year-11624361777.
- 12. Erensoy MS, Midilli K, Gökahmetoğlu S, et al. SARS-CoV-2 variants affect the course of pandemic why and how should effective and comprehensive genomic surveillance be done? STED. 2021:30:37-40. Turkish
- 13. Garcia-Beltran WF, Lam EC, Denis KS, Nitido AD, Garcia ZH, Hauser BM, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 2021;184:2523.
- 14. Nemet, I., Kliker, L., Lustig, Y., Zuckerman, N., Erster, O., Cohen, C. et al. Third BNT162b2 vaccination neutralization of SARS-CoV-2 Omicron infection. N Engl J Med, 2022;386:492-94
- 15.Baric RS. Emergence of a highly fit SARS-CoV-2 variant. N Engl J Med. 2020;383(27):2684-6.
- 16. Tekin S, Demirtürk N. COVID-19: Risk factors increasing disease and scoring. Klimik Derg. 2021;34(3):155-5. Turkish.
- 17. Vasireddy D, Vanaparthy R, Mohan G, Malayala SV, Atluri P. Review of COVID-19 variants and COVID-19 vaccine efficacy: what the clinician should know? J Clin Med Res. 2021;13(6):317-25. Erratum in: J Clin Med Res. 2021;13(7):412.
- 18. Abdool Karim SS, de Oliveira T. New SARS-CoV-2 variants - clinical, public health, and vaccine implications. N Engl J Med. 2021;384(19):1866-8.
Ayrıntılar
| Birincil Dil | İngilizce |
|---|---|
| Konular | Bulaşıcı Hastalıklar, Klinik Mikrobiyoloji |
| Bölüm | Orjinal Araştırma |
| Yazarlar | |
| Yayımlanma Tarihi | 30 Eylül 2023 |
| Kabul Tarihi | 11 Eylül 2023 |
| Yayımlandığı Sayı | Yıl 2023 Cilt: 13 Sayı: 5 |
