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Omicron variant: Clinical severity and hospitalisation profile in South Africa

A new South African study suggests that the Omicron variant boosts immunity to Delta and might displace it, while another found that it may be less pathogenic than previous variants.

The study, published in MedRxiv, and which covered only a small group of people and has not been peer-reviewed, found that people who were infected with Omicron, especially those who were vaccinated, developed enhanced immunity to the Delta variant.

The analysis enrolled 33 vaccinated and unvaccinated people who were infected with the Omicron variant. Although the authors found that neutralisation of Omicron increased 14-fold over 14 days after the enrolment, they also found that there was a 4.4-fold increase in neutralisation of the Delta variant, reports Reuters.

“The increase in Delta variant neutralisation in individuals infected with Omicron may result in decreased ability of Delta to re-infect those people,” said the scientists who conducted the study.

The results of the study are “consistent with Omicron displacing the Delta variant, since it can elicit immunity which neutralises Delta, making re-infection with Delta less likely”, they said.

According to the team, implications of this displacement would depend on whether or not Omicron is less pathogenic compared with Delta. “If so, then the incidence of COVID-19 severe disease would be reduced and the infection may shift to become less disruptive to individuals and society.”

Alex Sigal, a professor at the Africa Health Research Institute in South Africa, said that if Omicron were less pathogenic as it looked to be from the South African experience, “this will help push out Delta”.

According to an earlier South African study, there is reduced risk of hospitalisation and severe disease in people infected with Omicron compared with the Delta variant, though the authors say some of that is possibly due to high population immunity.

Study details 1

Omicron infection enhances neutralizing immunity against the Delta variant

Khadija Khan, Farina Karim, Sandile Cele, James Emmanuel San , Gila Lustig, Houriiyah Tegally, Mallory Bernstein, Yashica Ganga, Zesuliwe Jule, Kajal Reedoy, Nokuthula Ngcobo, Matilda Mazibuko, Ntombifuthi Mthabela, Zoey Mhlane, Nikiwe Mbatha, Jennifer Giandhari, Yajna Ramphal, Taryn Naidoo, Nithendra Manickchund, Nombulelo Magula, Salim Abdool Karim, Glenda Gray, Willem Hanekom, Anne von Gottberg, Bernadett Gosnell, Richard Lessells, Penny Moore, Tulio de Oliveira, Mahomed-Yunus Moosa, Alex Sigal.

Published on MedRxiv on 27 December 2021

Omicron has been shown to be highly transmissible and have extensive evasion of neutralising antibody immunity elicited by vaccination and previous SARS-CoV-2 infection. Omicron infections are rapidly expanding worldwide, often in the face of high levels of Delta infections. We characterised developing immunity to Omicron and investigated whether neutralising immunity elicited by Omicron also enhances neutralising immunity of the Delta variant. We enrolled both previously vaccinated and unvaccinated individuals who were infected with SARS-CoV-2 in the Omicron infection wave in South Africa soon after symptom onset.

We then measured their ability to neutralise both Omicron and Delta virus at enrollment versus a median of 14 days after enrollment. Neutralisation of Omicron increased 14-fold over this time, showing a developing antibody response to the variant. Importantly, there was an enhancement of Delta virus neutralisation, which increased 4.4-fold. The increase in Delta variant neutralisation in individuals infected with Omicron may result in decreased ability of Delta to re-infect those individuals.

Along with emerging data indicating that Omicron, at this time in the pandemic, is less pathogenic than Delta, such an outcome may have positive implications in terms of decreasing the COVID-19 burden of severe disease.

Study details 2

Characteristics and Outcomes of Hospitalized Patients in South Africa During the COVID-19 Omicron Wave Compared With Previous Waves

Caroline Maslo, Richard Friedland, Mande Toubkin, Anchen Laubscher, Teshlin Akaloo, Boniswa Kama.

Published in JAMA Network on 31 December 2021

On 24 November 2021, a SARS-CoV-2 variant of concern, Omicron (B.1.1.529), was identified in South Africa as responsible for a fourth wave of COVID-19. The high number of spike mutations has raised concerns about its ability to evade vaccine and spread. We assessed hospitalised patients with a positive SARS-CoV-2 test result during the fourth wave compared with previous waves.

Netcare is a private health care group consisting of 49 acute care hospitals (>10 000 beds) across South Africa. South Africa has experienced 3 COVID-19 waves: (1) June to August 2020 (ancestral variant), (2) November 2020 to January 2021 (Beta), and (3) May to September 2021 (Delta). Cases again started to increase beginning 15 November 2021, coinciding with the identification of Omicron; as of 7 December, 26% community positivity rates were reached. We identified the period when 26% positivity rates were reached in the previous waves (wave 1: 14 June to 6 July 2020; wave 2: 1-23 December 2020; wave 3: 1-23 June  2021) and compared them with the fourth wave (15 November to 7 December 2021). For triage purposes, Netcare’s policy is to test all admitted patients for COVID-19 with reverse transcriptase–polymerase chain reaction or, from wave 2 onward, a rapid antigen test obtained from a nasopharyngeal swab. All patients hospitalised with a positive COVID-19 result were included. Patient characteristics, need for oxygen supply and mechanical ventilation, admission to intensive care, length of stay (LOS), and mortality rates were extracted from the electronic administration system. Follow-up was until 20 December 2021.

The number of patients treated in the hospitals during the same early period of each wave differed (2351 in wave 4 vs maximum 6342 in wave 3); however, 68% to 69% of patients presenting to the emergency department with a positive COVID-19 result were admitted to the hospital in the first 3 waves vs 41.3% in wave 4. Patients hospitalised during wave 4 were younger (median age, 36 years vs maximum 59 years in wave 3; P < .001) with a higher proportion of females. Significantly fewer patients with comorbidities were admitted in wave 4, and the proportion presenting with an acute respiratory condition was lower (31.6% in wave 4 vs maximum 91.2% in wave 3, P < .001). Of 971 patients admitted in wave 4, 24.2% were vaccinated, 66.4% were unvaccinated, and vaccination status was unknown for 9.4%. The proportion of patients requiring oxygen therapy significantly decreased (17.6% in wave 4 vs 74% in wave 3, P < .001) as did the percentage receiving mechanical ventilation. Admission to intensive care was 18.5% in wave 4 vs 29.9% in wave 3 (P < .001). The median LOS (between 7 and 8 days in previous waves) decreased to 3 days in wave 4. The death rate was between 19.7% in wave 1 and 29.1% in wave 3 and decreased to 2.7% in wave 4.

A different pattern of characteristics and outcomes in patients hospitalised with COVID-19 was observed in the early phase of the fourth wave compared with earlier waves in South Africa, with younger patients having fewer comorbidities, fewer hospitalisations and respiratory diagnoses, and a decrease in severity and mortality.
The study has several limitations. First, patients’ virus genotyping was not available. The Omicron variant was estimated to be 81% of the variants isolated by November and 95% isolated by December 2021. Second, 7% of the patients were still hospitalised as of 20 December  Third, patients’ behaviour and the profile of admissions could have differed between waves as different national restrictions and lockdowns were implemented. These factors should not have affected urgent admissions. Fourth, patients admitted for COVID-19 could not be differentiated from asymptomatic patients admitted for other diagnoses with an incidental positive test result, and this likely differed between waves, suggested by the lower proportion admitted with respiratory diagnoses in wave 4.

Further research is needed to determine if the differences between waves are affected by preexisting acquired or natural immunity (44.3% of the adult South African population was vaccinated as of December 2021 and >50% of the population has had previous exposure to SARS-CoV-2) or if Omicron may be less pathogenic than previous variants.


Reuters article – South Africa study suggests Omicron could displace Delta (Open access)


MedRxiv article – Omicron infection enhances neutralizing immunity against the Delta variant (Open access)


JAMA Network article – Characteristics and Outcomes of Hospitalized Patients in South Africa During the COVID-19 Omicron Wave Compared With Previous Waves (Open access)


See more from MedicalBrief archives:


Increased risk of SARS-CoV-2 reinfection associated with Omicron — South African study


Previous infection + vaccines deliver ’stronger than basic' Omicron defence — China in-vitro study


So far, milder disease seen with Omicron, with shorter hospital stays — SA hospitals analysis


Discovery Health’s large real-world analysis of Omicron


Two-dose vaccines induce lower antibodies against Omicron — Oxford study



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