update on delta and other variants in south africa

UKZN INSPIRING GREATNESS

Update on Delta and other Variants in

South Africa

Prof Tulio de Oliveira and Dr. Richard Lessells, KRISP

for the Network for Genomic Surveillance South Africa (NGS-SA)


South Africa has entered exponential growth

phase (Re >1)

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Detection of Delta in South Africa

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Date

Pro

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f G

en

om

es

Variants

Other lineages

20H (Beta, V2)

20I (Alpha, V1)

21A (Delta)

21B (Kappa)

21D (Eta)

B.1.1.318

NA


Variants over time by province

Eastern Cape

Limpopo

Mpumalanga

Free State

North West

Northern Cape

Western Cape

Gauteng

KwaZulu−Natal

Oct2020

Nov2020

Dec2020

Jan2021

Feb2021

Mar2021

Apr2021

May2021

Jun2021

month

Variants

20H (Beta, V2)

20I (Alpha, V1)

21A (Delta)

21B (Kappa)

21D (Eta)

B.1.1.318

Other lineages

South Africa variants by province


Detection of Delta in KZN from community

surveillance

Across six districts and in > 30 random selected sites of KwaZulu-Natal, Harry Gwala (n=16), Zululand (n=15), iLembe (n=14), eTheweni (n=12), King Cetshwayo (n=1) and Ugu (n=1)


Delta also detected and increasing

prevalence in the Western Cape

Delta was detected in 3/3 samples in the Garden route in late May


Very limited data in Gauteng

NICD responsibility, but KRISP has now received samples this Thursday (2

days ago) and will have results by Monday/Tuesday


Onset of Illness among the First 425 Confirmed Cases of Novel

Coronavirus (2019-nCoV)–Infected Pneumonia (NCIP) in

Wuhan, China.

Delta mutation profile – spike protein

Source: Johns Hopkins University

Two mutations in receptor-binding domain (L452R & T478K)

Substitution (T19R) and deletion (157-158del) in N-terminal

domain antigenic supersite

Mutation adjacent to S1/S2 furin cleavage site (P681R)

https://covdb.stanford.edu/page/mutation-viewer/#sec_delta




Wuhan, China.

Delta global distribution


First sampled in India October 2020

Now detected in 85 countries, including several in Africa,

and rapidly becoming dominant in many countrieshttps://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports




Wuhan, China.

Summary of Delta variant


Transmissibility

Highly transmissible – more than

all other variants, including Beta

Disease severity

No clear evidence yet

Vaccines

No evidence of vaccine escape

High levels of protection against

severe disease

Risk of reinfection

Reduction in neutralization with

serum from people infected with

Beta variant




Wuhan, China.

Evidence of increased transmissibility


Campbell F, et al. Eurosurveillance 2021

Allen H, et al. Public Health England preprint

Public Health England Technical Briefings

• Preliminary estimates from genomic data and

epidemiological studies suggest Delta may be

significantly more transmissible than other variants of

concern, including Beta (30-60% more transmissible)

• These data imply that Delta could be approximately

twice as transmissible as the earlier non-VOC/VOI

viruses




Wuhan, China.

Clinical presentation


• Some evidence from UK that symptom profile could

be different – most prominent current symptoms are

headache, sore throat, runny nose and sneezing

• More work needed to confirm if this is a consistent

finding with the Delta variant or reflects clinical profile

of infections in certain age groups and/or in

partially/fully vaccinated individuals

https://covid.joinzoe.com/post/new-top-5-covid-symptoms




Wuhan, China.

Disease severity


• Early evidence from the UK suggests there may be an

increased risk of hospitalisation within 14 days of a

positive test, compared to contemporaneous cases

with Alpha variant (risk approximately double)

• No evidence currently from the UK of increased case

fatality ratio with Delta variant, but more follow-up of

cases required

Public Health England Technical Briefings




Wuhan, China.

Vaccine effectivenessUK data – symptomatic disease


Compared to Alpha, there was a modest reduction in

effectiveness against symptomatic disease after a single dose,

but very little difference after two doses

Lopez Bernal J, et al. medRxiv 2021

Vaccine Vaccine effectiveness single

dose

Vaccine effectiveness two

doses

Alpha Delta Alpha Delta

Astra Zeneca 51% (47-55) 33% (19-44) 66% (54-75) 60% (29-77)

Pfizer 49% (43-55) 33% (8-51) 93% (90-96) 88% (78-93)




Wuhan, China.

Vaccine effectivenessUK data – hospitalisation


These findings suggest high levels of protection (>70%) against

hospitalisation with the Delta variant with one or two doses of

either vaccine – levels of protection similar to the Alpha variant

Stowe J, et al. PHE preprint 2021

Vaccine Vaccine effectiveness single

dose

Vaccine effectiveness two

doses

Alpha Delta Alpha Delta

Astra Zeneca 76% (61-85) 71% (51-83) 86% (53-96) 92% (75-97)

Pfizer 83% (62-93) 94% (46-99) 95% (78-99) 96% (86-99)


Summary

• Delta is now rapidly becoming the dominant SARS-CoV-2 variant in

many countries around the world, including SA

• There is now good evidence that Delta is more transmissible than

previously circulating viruses and other variants of concern/interest

• There is some reduction in neutralization with convalescent serum

collected post-Beta infection, raising concerns about potential for re-

infection in SA

• Vaccine effectiveness data from UK suggest good protection against

symptomatic disease, and very high levels of protection against

hospitalization, after two doses of Pfizer or Astra Zeneca vaccine and

seems effective agains J&J




Wuhan, China.

Summary of Delta variant


Transmissibility

Highly transmissible – more than

all other variants, including Beta

Disease severity

No clear evidence yet

Vaccines

No evidence of vaccine escape

High levels of protection against

severe disease

Risk of reinfection

Reduction in neutralization with

serum from people infected with

Beta variant


Network for Genomic Surveillance in South

Africa (NGS-SA)

Supported by the DSI and the SA MRC

Msomi N, Mlisana K, et al. Lancet Microbe 2020




Wuhan, China.

Impact on antibody neutralization & risk

of reinfectionSource: Johns Hopkins University

Liu C, et al. Cell 2021

Non-VOC/VOI sera

Beta sera

• Reduced neutralization of Delta by

convalescent serum from people

infected early in epidemic, but not

as marked as the reduction

observed with Beta

• However, significant reduction in

neutralization of Delta by

convalescent serum from people

infected with Beta variant

• Raises concern that people with

prior Beta infection could be

susceptible to reinfection with Delta




Wuhan, China.

Impact on neutralization by vaccines


Liu C, et al. Cell 2021

Pfizer vaccine

Astra Zeneca vaccine

• Reduced neutralization of Delta by

serum from people post-Pfizer

and Astra Zeneca vaccine,

compared to early circulating

strain

• However, reduction in

neutralization of Delta less

pronounced than for Beta (for both

vaccines)

• No neutralization data yet for

Johnson & Johnson vaccine

update on delta and other variants in south africa

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