Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality
Abstract Background The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissi...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Infectious Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12879-023-08527-y |
| _version_ | 1797577915654733824 |
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| author | Amr Kandeel Yassmin Moatasim Manal Fahim Hala Bahaaeldin Rabeh El-Shesheny Wael H. Roshdy Mina N. Kamel Shaymaa Shawky Mokhtar Gomaa Amel Naguib Nancy El Guindy Ola Deghedy Reham Kamel Mohamed Khalifa Ramy Galal Mohamed Hassany Galal Mahmoud Ahmed Kandeil Salma Afifi Amira Mohsen Mohammad Abdel Fattah Ghazi Kayali Mohamed A. Ali Khaled Abdelghaffar |
| author_facet | Amr Kandeel Yassmin Moatasim Manal Fahim Hala Bahaaeldin Rabeh El-Shesheny Wael H. Roshdy Mina N. Kamel Shaymaa Shawky Mokhtar Gomaa Amel Naguib Nancy El Guindy Ola Deghedy Reham Kamel Mohamed Khalifa Ramy Galal Mohamed Hassany Galal Mahmoud Ahmed Kandeil Salma Afifi Amira Mohsen Mohammad Abdel Fattah Ghazi Kayali Mohamed A. Ali Khaled Abdelghaffar |
| author_sort | Amr Kandeel |
| collection | DOAJ |
| description | Abstract Background The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissibility and lower vaccine efficacy against omicron. There is an urgent need to better describe how omicron will impact clinical presentation and vaccine efficacy. This study aims at comparing the epidemiologic, clinical, and genomic characteristics of the omicron variant prevalent during the fifth wave with those of other VOCs between May 2020 and April 2022. Methods Epidemiological data were obtained from the National Electronic Diseases Surveillance System. Secondary data analysis was performed on all confirmed COVID-19 patients. Descriptive data analysis was performed for demographics and patient outcome and the incidence of COVID-19 was calculated as the proportion of SARS-CoV-2 confirmed patients out of the total population of Egypt. Incidence and characteristics of the omicron cohort from January- April 2022, were compared to those confirmed from May 2020-December 2021. We performed the whole-genome sequencing of SARS-CoV-2 on 1590 specimens using Illumina sequencing to describe the circulation of the virus lineages in Egypt. Results A total of 502,629 patients enrolled, including 60,665 (12.1%) reported in the fifth wave. The incidence rate of omicron was significantly lower than the mean of incidences in the previous subperiod (60.1 vs. 86.3/100,000 population, p < 0.001). Symptoms were reported less often in the omicron cohort than in patients with other variants, with omicron having a lower hospitalization rate and overall case fatality rate as well. The omicron cohort tended to stay fewer days at the hospital than did those with other variants. We analyzed sequences of 2433 (1590 in this study and 843 were obtained from GISAID platform) Egyptian SARS-CoV-2 full genomes. The first wave that occurred before the emergence of global variants of concern belonged to the B.1 clade. The second and third waves were associated with C.36. Waves 4 and 5 included B.1.617.2 and BA.1 clades, respectively. Conclusions The study indicated that Omicron-infected patients had milder symptoms and were less likely to be hospitalized; however, patients hospitalized with omicron had a more severe course and higher fatality rates than those hospitalized with other variants. Our findings demonstrate the importance of combining epidemiological data and genomic analysis to generate actionable information for public health decision-making. |
| first_indexed | 2024-03-10T22:14:45Z |
| format | Article |
| id | doaj.art-de66e86522c5413fb014319526de82ac |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-03-10T22:14:45Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-de66e86522c5413fb014319526de82ac2023-11-19T12:30:09ZengBMCBMC Infectious Diseases1471-23342023-08-0123111210.1186/s12879-023-08527-yComparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortalityAmr Kandeel0Yassmin Moatasim1Manal Fahim2Hala Bahaaeldin3Rabeh El-Shesheny4Wael H. Roshdy5Mina N. Kamel6Shaymaa Shawky7Mokhtar Gomaa8Amel Naguib9Nancy El Guindy10Ola Deghedy11Reham Kamel12Mohamed Khalifa13Ramy Galal14Mohamed Hassany15Galal Mahmoud16Ahmed Kandeil17Salma Afifi18Amira Mohsen19Mohammad Abdel Fattah20Ghazi Kayali21Mohamed A. Ali22Khaled Abdelghaffar23Preventive Sector, Ministry of Health and PopulationCentre of Scientific Excellence for Influenza Viruses, National Research CentreDepartment of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and PopulationDepartment of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and PopulationCentre of Scientific Excellence for Influenza Viruses, National Research CentreCentral Public Health Laboratory, Ministry of Health and PopulationCentre of Scientific Excellence for Influenza Viruses, National Research CentreCentral Public Health Laboratory, Ministry of Health and PopulationCentre of Scientific Excellence for Influenza Viruses, National Research CentreCentral Public Health Laboratory, Ministry of Health and PopulationCentral Public Health Laboratory, Ministry of Health and PopulationDepartment of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and PopulationDepartment of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and PopulationCentral Public Health Laboratory, Ministry of Health and PopulationPublic Health InitiativesNational Hepatology and Tropical Medicine Research Institute, Ministry of Health and PopulationCentral Public Health Laboratory, Ministry of Health and PopulationCentre of Scientific Excellence for Influenza Viruses, National Research CentreMinistry of Health and Population ConsultantCommunity Medicine Department, National Research CentrePreventive Sector, Central Administration for Preventive Affairs, Ministry of Health and PopulationHuman LinkCentre of Scientific Excellence for Influenza Viruses, National Research CentreMinister of Health and PopulationAbstract Background The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissibility and lower vaccine efficacy against omicron. There is an urgent need to better describe how omicron will impact clinical presentation and vaccine efficacy. This study aims at comparing the epidemiologic, clinical, and genomic characteristics of the omicron variant prevalent during the fifth wave with those of other VOCs between May 2020 and April 2022. Methods Epidemiological data were obtained from the National Electronic Diseases Surveillance System. Secondary data analysis was performed on all confirmed COVID-19 patients. Descriptive data analysis was performed for demographics and patient outcome and the incidence of COVID-19 was calculated as the proportion of SARS-CoV-2 confirmed patients out of the total population of Egypt. Incidence and characteristics of the omicron cohort from January- April 2022, were compared to those confirmed from May 2020-December 2021. We performed the whole-genome sequencing of SARS-CoV-2 on 1590 specimens using Illumina sequencing to describe the circulation of the virus lineages in Egypt. Results A total of 502,629 patients enrolled, including 60,665 (12.1%) reported in the fifth wave. The incidence rate of omicron was significantly lower than the mean of incidences in the previous subperiod (60.1 vs. 86.3/100,000 population, p < 0.001). Symptoms were reported less often in the omicron cohort than in patients with other variants, with omicron having a lower hospitalization rate and overall case fatality rate as well. The omicron cohort tended to stay fewer days at the hospital than did those with other variants. We analyzed sequences of 2433 (1590 in this study and 843 were obtained from GISAID platform) Egyptian SARS-CoV-2 full genomes. The first wave that occurred before the emergence of global variants of concern belonged to the B.1 clade. The second and third waves were associated with C.36. Waves 4 and 5 included B.1.617.2 and BA.1 clades, respectively. Conclusions The study indicated that Omicron-infected patients had milder symptoms and were less likely to be hospitalized; however, patients hospitalized with omicron had a more severe course and higher fatality rates than those hospitalized with other variants. Our findings demonstrate the importance of combining epidemiological data and genomic analysis to generate actionable information for public health decision-making.https://doi.org/10.1186/s12879-023-08527-ySARS-CoV-2 variantsSequencingWhole genomeEpidemiology |
| spellingShingle | Amr Kandeel Yassmin Moatasim Manal Fahim Hala Bahaaeldin Rabeh El-Shesheny Wael H. Roshdy Mina N. Kamel Shaymaa Shawky Mokhtar Gomaa Amel Naguib Nancy El Guindy Ola Deghedy Reham Kamel Mohamed Khalifa Ramy Galal Mohamed Hassany Galal Mahmoud Ahmed Kandeil Salma Afifi Amira Mohsen Mohammad Abdel Fattah Ghazi Kayali Mohamed A. Ali Khaled Abdelghaffar Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality BMC Infectious Diseases SARS-CoV-2 variants Sequencing Whole genome Epidemiology |
| title | Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality |
| title_full | Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality |
| title_fullStr | Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality |
| title_full_unstemmed | Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality |
| title_short | Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality |
| title_sort | comparison of sars cov 2 omicron variant with the previously identified sars cov 2 variants in egypt 2020 2022 insight into sars cov 2 genome evolution and its impact on epidemiology clinical picture disease severity and mortality |
| topic | SARS-CoV-2 variants Sequencing Whole genome Epidemiology |
| url | https://doi.org/10.1186/s12879-023-08527-y |
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