Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa
ABSTRACT Background The SARS-CoV-2 Omicron variant of concern (VOC) almost completely replaced other variants in South Africa during November 2021, and was associated with a rapid increase in COVID-19 cases. We aimed to assess clinical severity of individuals infected with Omicron, using S Gene Target Failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.Methods We performed data linkages for (i) SARS-CoV-2 laboratory tests, (ii) COVID-19 case data, (iii) genome data, and (iv) the DATCOV national hospital surveillance system for the whole of South Africa. For cases identified using Thermo Fisher TaqPath COVID-19 PCR, infections were designated as SGTF or non-SGTF. Disease severity was assessed using multivariable logistic regression models comparing SGTF-infected individuals diagnosed between 1 October to 30 November to (i) non-SGTF in the same period, and (ii) Delta infections diagnosed between April and November 2021.Results From 1 October through 6 December 2021, 161,328 COVID-19 cases were reported nationally; 38,282 were tested using TaqPath PCR and 29,721 SGTF infections were identified. The proportion of SGTF infections increased from 3% in early October (week 39) to 98% in early December (week 48). On multivariable analysis, after controlling for factors associated with hospitalisation, individuals with SGTF infection had lower odds of being admitted to hospital compared to non-SGTF infections (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ between SGTF-infected individuals compared to non-SGTF individuals diagnosed during the same time period (aOR 0.7, 95% CI 0.3-1.4). Compared to earlier Delta infections, after controlling for factors associated with severe disease, SGTF-infected individuals had a lower odds of severe disease (aOR 0.3, 95% CI 0.2-0.5).Conclusion Early analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period. Once hospitalised, risk of severe disease was similar for SGTF- and non-SGTF infected individuals, while SGTF-infected individuals had a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reducton is likely a result of high population immunity..
| Medienart: |
|
|---|
Preprint| Erscheinungsjahr: |
2021 |
|---|---|
| Erschienen: |
2021 |
| Enthalten in: |
bioRxiv.org - (2021) vom: 23. Dez. Zur Gesamtaufnahme - year:2021 |
|---|
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Wolter, Nicole [VerfasserIn] |
|---|
| Links: |
Volltext [kostenfrei] |
|---|
| doi: |
10.1101/2021.12.21.21268116 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
XBI033268525 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | XBI033268525 | ||
| 003 | DE-627 | ||
| 005 | 20230429090038.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 211222s2021 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1101/2021.12.21.21268116 |2 doi | |
| 035 | |a (DE-627)XBI033268525 | ||
| 035 | |a (biorXiv)10.1101/2021.12.21.21268116 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 082 | 0 | |a 570 |q DE-84 | |
| 100 | 1 | |a Wolter, Nicole |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa |
| 264 | 1 | |c 2021 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 520 | |a ABSTRACT Background The SARS-CoV-2 Omicron variant of concern (VOC) almost completely replaced other variants in South Africa during November 2021, and was associated with a rapid increase in COVID-19 cases. We aimed to assess clinical severity of individuals infected with Omicron, using S Gene Target Failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.Methods We performed data linkages for (i) SARS-CoV-2 laboratory tests, (ii) COVID-19 case data, (iii) genome data, and (iv) the DATCOV national hospital surveillance system for the whole of South Africa. For cases identified using Thermo Fisher TaqPath COVID-19 PCR, infections were designated as SGTF or non-SGTF. Disease severity was assessed using multivariable logistic regression models comparing SGTF-infected individuals diagnosed between 1 October to 30 November to (i) non-SGTF in the same period, and (ii) Delta infections diagnosed between April and November 2021.Results From 1 October through 6 December 2021, 161,328 COVID-19 cases were reported nationally; 38,282 were tested using TaqPath PCR and 29,721 SGTF infections were identified. The proportion of SGTF infections increased from 3% in early October (week 39) to 98% in early December (week 48). On multivariable analysis, after controlling for factors associated with hospitalisation, individuals with SGTF infection had lower odds of being admitted to hospital compared to non-SGTF infections (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ between SGTF-infected individuals compared to non-SGTF individuals diagnosed during the same time period (aOR 0.7, 95% CI 0.3-1.4). Compared to earlier Delta infections, after controlling for factors associated with severe disease, SGTF-infected individuals had a lower odds of severe disease (aOR 0.3, 95% CI 0.2-0.5).Conclusion Early analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period. Once hospitalised, risk of severe disease was similar for SGTF- and non-SGTF infected individuals, while SGTF-infected individuals had a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reducton is likely a result of high population immunity. | ||
| 700 | 1 | |a Jassat, Waasila |e verfasserin |4 aut | |
| 700 | 1 | |a Walaza, Sibongile |e verfasserin |4 aut | |
| 700 | 1 | |a Welch, Richard |e verfasserin |4 aut | |
| 700 | 1 | |a Moultrie, Harry |e verfasserin |4 aut | |
| 700 | 1 | |a Groome, Michelle |e verfasserin |4 aut | |
| 700 | 1 | |a Amoako, Daniel Gyamfi |e verfasserin |4 aut | |
| 700 | 1 | |a Everatt, Josie |e verfasserin |4 aut | |
| 700 | 1 | |a Bhiman, Jinal N. |e verfasserin |4 aut | |
| 700 | 1 | |a Scheepers, Cathrine |e verfasserin |4 aut | |
| 700 | 1 | |a Tebeila, Naume |e verfasserin |4 aut | |
| 700 | 1 | |a Chiwandire, Nicola |e verfasserin |4 aut | |
| 700 | 1 | |a du Plessis, Mignon |e verfasserin |4 aut | |
| 700 | 1 | |a Govender, Nevashan |e verfasserin |4 aut | |
| 700 | 1 | |a Ismail, Arshad |e verfasserin |4 aut | |
| 700 | 1 | |a Glass, Allison |e verfasserin |4 aut | |
| 700 | 1 | |a Mlisana, Koleka |e verfasserin |4 aut | |
| 700 | 1 | |a Stevens, Wendy |e verfasserin |4 aut | |
| 700 | 1 | |a Treurnicht, Florette K. |e verfasserin |4 aut | |
| 700 | 1 | |a Makatini, Zinhle |e verfasserin |4 aut | |
| 700 | 1 | |a Hsiao, Nei-yuan |e verfasserin |4 aut | |
| 700 | 1 | |a Parboosing, Raveen |e verfasserin |4 aut | |
| 700 | 1 | |a Wadula, Jeannette |e verfasserin |4 aut | |
| 700 | 1 | |a Hussey, Hannah |e verfasserin |4 aut | |
| 700 | 1 | |a Davies, Mary-Ann |e verfasserin |4 aut | |
| 700 | 1 | |a Boulle, Andrew |e verfasserin |4 aut | |
| 700 | 1 | |a von Gottberg, Anne |e verfasserin |4 aut | |
| 700 | 1 | |a Cohen, Cheryl |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t bioRxiv.org |g (2021) vom: 23. Dez. |
| 773 | 1 | 8 | |g year:2021 |g day:23 |g month:12 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1101/2021.12.21.21268116 |z kostenfrei |3 Volltext |
| 912 | |a GBV_XBI | ||
| 912 | |a SSG-OLC-PHA | ||
| 951 | |a AR | ||
| 952 | |j 2021 |b 23 |c 12 | ||
| 953 | |2 045F |a 570 | ||