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Cited by 707SARS-CoV-2 and COVID-19 ResearchCOVID-19 epidemiological studiesCOVID-19 Clinical Research Studies

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Open access
Tegally, Houriiyah, Moir, Monika, Everatt, Josie, Giovanetti, Marta, Scheepers, Cathrine, Wilkinson, Eduan, Subramoney, Kathleen, Makatini, Zinhle +88 more·2022·Nature Medicine
DOI 10.1038/s41591-022-01911-2PMC PMC9499863

Published version of a preprint

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Abstract

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69–70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69–70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08–0.09) and 0.10 (95% CI: 0.09–0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

AI snapshot

Written from the paper’s full text.

TL;DR

Two new SARS-CoV-2 Omicron lineages, BA.4 and BA.5, were identified in South Africa and drove a fifth infection wave after rapidly replacing BA.2. They share an identical spike protein and showed estimated daily growth advantages over BA.2 of 0.08 for BA.4 and 0.10 for BA.5.

Key findings

  • BA.4 and BA.5 have identical spike proteins, most similar to BA.2 but with additional spike mutations 69–70 deletion, L452R, F486V and wild-type amino acid at Q493; they differ outside spike. They reached more than 50% of sequenced cases in South Africa by the first week of April 2022 and approximately 90% of sequenced cases in Gauteng and KwaZulu-Natal by the week starting 18 April 2022.
  • Estimated growth advantages over BA.2 in South Africa were 0.08 per day (95% CI: 0.08–0.09) for BA.4 and 0.10 per day (95% CI: 0.09–0.11) for BA.5.
  • Among 198 samples with paired valid qPCR and sequence, 77 had S-gene target failure (SGTF); of these, 66 were BA.4 or BA.5, nine were BA.1 and two were BA.2. No BA.4 or BA.5 genomes were S-gene target positive on qPCR.
  • The BA.4/BA.5 wave peaked at ~24% test positivity, lower than the BA.1 wave (~34%), with much lower hospital admissions and deaths than earlier waves in South Africa.

Methods

  • Analyzed 15,225 SARS-CoV-2 sequences from South Africa collected 1 November 2021 to 19 May 2022 through the Network for Genomics Surveillance in South Africa, using phylogenetic, phylogeographic and lineage classification methods.
  • Estimated lineage growth advantage with a multinomial logistic regression model; monitored SGTF using the TaqPath COVID-19 qPCR assay and validated SGTF against genome lineage assignment in 296 unselected samples, of which 198 had paired valid qPCR and sequence results.
  • Used RASCL and natural selection analysis pipelines to assess selection on BA.4 and BA.5 genes; no statistical method was used to predetermine sample size.

Limitations

  • The paper states that estimated growth advantage could be biased by stochastic effects such as superspreading in a low-incidence setting at the start of a wave, potentially overestimating the advantage.
  • The paper states that reliable estimates of population immunity against BA.1 in South Africa were not yet available, making precise estimates of transmissibility or immune evasion difficult; origin uncertainty remains, phylogenetic inference is limited by low sampling coverage (<1% of confirmed cases), and lack of an ancestor complicates placements.
  • Evident from the text: SGTF as a proxy for BA.4/BA.5 may be less useful where BA.1 prevalence is high, and the phenotypic effects of the spike mutations are inferred from prior literature rather than measured directly in this study.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/s41591-022-01911-2

Cites

48 of 48 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 20 cited sources checked · 0 supported · 0 flagged

  • Findingnone given

    The displacement of BA.1 by BA.2 in South Africa was not associated with a substantial resurgence in cases, hospital admissions or deaths.

    “Despite being associated with a modest prolongation of the fourth wave, the displacement of BA.1 by BA.2 in South Africa was not associated with a substantial resurgence in cases, hospital admissions or deaths.”
    Quote in the paperNot a substantial claim
  • Findingown data

    BA.5 is estimated to have originated in early January 2022 (95% HPD: 10 December 2021 to 6 February 2022).

    “BA.4 and BA.5 are estimated to have originated in mid-December 2021 (95% highest posterior density (HPD): 25 November 2021 to 1 January 2022) and early January 2022 (HPD: 10 December 2021 to 6 February 2022), respectively (Fig. 1a).”
    Quote in the paperSubstantial claim
  • Findingown data

    The most recent common ancestor of BA.4 and BA.5 is estimated to have originated in mid-November 2021 (95% HPD: 29 September 2021 to 6 December 2021).

    “The most recent common ancestor of BA.4 and BA.5 is estimated to have originated in mid-November 2021 (HPD: 29 September 2021 to 6 December 2021) (Fig. 1a), coinciding with the emergence of the other lineages—for example, BA.2 in early November 2021 (HPD: 9 October 2021 to 29 November 2021).”
    Quote in the paperSubstantial claim
  • Findingown data

    Before the emergence of BA.4 and BA.5, F486V in the receptor-binding domain (RBD) of spike had been observed in only 54 of 10 million publicly available genome sequences in GISAID.

    “Before the emergence of BA.4 and BA.5, F486V in the receptor-binding domain (RBD) of spike had been observed in only 54 of 10 million publicly available genome sequences in GISAID (https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?aaMutations=S%3AF486V&).”
    Quote in the paperSubstantial claim
  • Findingnone given

    Relative to BA.2, BA.5 has additional reversions at ORF6:D61 and nucleotide positions 26,858 and 27,259.

    “Relative to BA.2, BA.5 has additional reversions at ORF6:D61 and nucleotide positions 26,858 and 27,259.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. 22
  • May combine two claims. 19

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    BA.4 and BA.5 have a nuc:G12160A synonymous mutation in NSP8 that was present in Epsilon (B.1.429) and has arisen in BA.2 in some locations.

    “In addition, BA.4 and BA.5 have a nuc:G12160A synonymous mutation in NSP8 that was present in Epsilon (B.1.429) and has arisen in BA.2 in some locations (Extended Data Fig. 2).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    BA.4 and BA.5 have identical mutational patterns in the 5′ genome region (from ORF1ab to Envelope) yet exhibit genetic divergence in the 3′ region (from M to the 3′ genome end).

    “BA.4 and BA.5 have identical mutational patterns in the 5′ genome region (from ORF1ab to Envelope) yet exhibit genetic divergence in the 3′ region (from M to the 3′ genome end).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Outside of spike, BA.4 has additional mutations at ORF7b:L11F and N:P151S and a triple amino acid deletion in NSP1:141-143 deletion.

    “Outside of spike, BA.4 has additional mutations at ORF7b:L11F and N:P151S and a triple amino acid deletion in NSP1:141–143 deletion, whereas BA.5 has the M:D3N mutation.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Two new Omicron lineages, BA.4 and BA.5, were identified and were responsible for a fifth wave of SARS-CoV-2 infections in South Africa.

    “We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: BA.1 caused most of the infections in South Africa's fourth epidemic wave.

  • May combine two claims.

    Findingreasoning

    The BA.4/BA.5 wave had much lower hospital admissions and deaths than previously recorded during waves of infection in South Africa, because of high population immunity.

    “This wave was characterized by a peak in test positivity rate of ~24%, lower than during the Omicron BA.1 wave (~34%), and, because of high population immunity, much lower hospital admissions and deaths than previously recorded during waves of infection in South Africa.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Findingnone given

    Botswana's fourth wave was driven by BA.1, followed by BA.2 lasting about 3.5 months, and the country's fifth wave is occurring approximately 2 months after the fourth wave.

    “To note, Botswana’s fourth wave was driven by BA.1, followed by BA.2 lasting about 3.5 months, and the country’s fifth wave is occurring approximately 2 months after the fourth wave.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    BA.4 and BA.5 also show a growth advantage against non-Omicron lineages, although these are minimally circulating in the discussed timeframe.

    “The BA.4 and BA.5 lineages also show a growth advantage against non-Omicron lineages, although these are minimally circulating in the discussed timeframe (Extended Data Table 2).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    Botswana was experiencing a rapid rise in cases driven by BA.4 and BA.5, with 19 of 24 health districts experiencing resurgence in cases.

    “At the time of writing this report, Botswana was experiencing a rapid rise in cases driven by BA.4 and BA.5, with 19 of 24 health districts experiencing resurgence in cases.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The data suggest geographic heterogeneity in the distribution of BA.4 and BA.5, with growth predominantly of BA.4 in Gauteng and BA.5 in KwaZulu-Natal.

    “The data suggest geographic heterogeneity in the distribution of these two new lineages, with growth predominantly of BA.4 in Gauteng and BA.5 in KwaZulu-Natal (Extended Data Fig. 4).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Although Bayesian phylogenetic methods suggest that BA.4 and BA.5 are independent lineages that originated around the same time as BA.1-BA.3, maximum likelihood estimations suggest that they could have descended from BA.2.

    “Although the Bayesian phylogenetic methods employed here suggest that BA.4 and BA.5 are independent lineages that originated around the same time as BA.1–BA.3, maximum likelihood estimations suggest that they could have descended from BA.2.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    Two new Omicron lineages (BA.4 and BA.5) were identified, which are associated with a resurgence in infections in South Africa approximately 4 months on from the start of the Omicron wave.

    “In conclusion, we have identified two new Omicron lineages (BA.4 and BA.5), which are associated with a resurgence in infections in South Africa approximately 4 months on from the start of the Omicron wave.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Findingnone given

    Recorded death metrics were further decoupled from cases and hospitalizations compared to the BA.1 wave.

    “It is worth noting that recorded death metrics were further decoupled from cases and hospitalizations compared to the BA.1 wave.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Findingnone given

    Internationally, by the end of May 2022, BA.4 and BA.5 had also been detected and were rising in prevalence in several countries: Botswana (estimated prevalence 60%), Europe (Portugal, Spain and Austria) and the United States.

    “Internationally, by the end of May 2022, BA.4 and BA.5 had also been detected and were rising in prevalence in several countries: in neighboring Botswana (estimated prevalence 60%), in Europe (Portugal, Spain and Austria) and in the United States.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Recent data from public laboratories in South Africa suggest that the proportion of positive PCR tests with SGTF has been increasing since early March, suggesting that BA.4 and BA.5 may be responsible for a growing share of recently confirmed cases.

    “Recent data from public laboratories in South Africa suggest that the proportion of positive polymerase chain reaction (PCR) tests with SGTF has been increasing since early March, suggesting that BA.4 and BA.5 may be responsible for a growing share of recently confirmed cases (Fig. 2a).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In Gauteng and KwaZulu-Natal, BA.4 and BA.5 rapidly replaced BA.2 and were responsible for approximately 90% of sequenced cases by the week starting 18 April 2022.

    “In the two most populous provinces in South Africa—Gauteng and KwaZulu-Natal—BA.4 and BA.5 rapidly replaced BA.2 and were responsible for approximately 90% of sequenced cases by the week starting 18 April 2022 (Extended Data Fig. 4).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The fifth wave in South Africa, driven by BA.4 and BA.5, occurred around 4 months after the fourth wave, driven by BA.1.

    “The fifth wave in South Africa, driven by BA.4 and BA.5, occurred around 4 months after the fourth wave, driven by BA.1.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    SGTF was successfully used to track the early spread of BA.1, later also enabling discrimination between BA.1 and BA.2 infections, because BA.2 viruses generally lack the S:69-70 deletion.

    “SGTF was successfully used to track the early spread of BA.1 (which also demonstrates SGTF), later also enabling discrimination between BA.1 and BA.2 infections, because BA.2 viruses generally lack the S:69–70 deletion15.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [15] Scott, L. et al. Track Omicron’s spread with molecular data. Science 374, 1454–1455 (2021). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationreasoning

    The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

    “The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    When binding to hACE2, spike amino acid F486 interacts with hACE2 residues L79, M82 and Y83, which collectively comprise a hotspot for ACE2 differences between mammalian species.

    “When binding to hACE2, spike amino acid F486 interacts with hACE2 residues L79, M82 and Y83, which collectively comprise a hotspot for ACE2 differences between mammalian species13.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [13] Lan, J. et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581, 215–220 (2020). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    No statistical method was used to predetermine sample size.

    “No statistical method was used to predetermine sample size.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The effects of these different Omicron lineages may differ by location, depending on the immune landscape and, particularly, the patterns of exposure to BA.1 and BA.2.

    “This would also suggest that the effects of these different Omicron lineages may differ by location, depending on the immune landscape and, particularly, the patterns of exposure to BA.1 and BA.2.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    The continued discovery of genetically diverse Omicron lineages shifts the level of support for hypotheses regarding their origin, from an unsampled location to a discrete reservoir, such as human chronic infections and/or animal reservoirs, potentially contributing to further evolution and dispersal of the virus, although currently the data do not provide any definitive evidence in any direction.

    “The continued discovery of genetically diverse Omicron lineages shifts the level of support for hypotheses regarding their origin, from an unsampled location to a discrete reservoir, such as human chronic infections (or even a network of chronic human infections) and/or animal reservoirs, potentially contributing to further evolution and dispersal of the virus, although, currently, the data do not”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Reliable estimates of the level of population immunity against BA.1 in South Africa are not yet available, making it difficult to precisely estimate transmissibility or immune evasion of the new lineages.

    “Second, reliable estimates of the level of population immunity against BA.1 in South Africa are not yet available, making it difficult to precisely estimate transmissibility or immune evasion of the new lineages.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationreasoning

    The growth advantage of Omicron BA.4 and BA.5 could be mediated by an increase in intrinsic transmissibility relative to other variants, an increase in capacity to infect and be transmitted from previously infected and vaccinated individuals, or both.

    “The growth advantage of Omicron BA.4 and BA.5 could be mediated by (1) an increase in its intrinsic transmissibility relative to other variants; (2) an increase relative to other variants in its capacity to infect, and be transmitted from, previously infected and vaccinated individuals; or (3) both.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Convergence of MCMC chains was checked using Tracer version 1.7.1.

    “Convergence of MCMC chains was checked using Tracer version 1.7.1 (ref. 30).”
    • Also stated in: § Phylogeographic analysis · plain
      “with convergence assessed using Tracer version 1.7.1.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [30] Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    To date, the only reverse zoonoses cases reported from the African region were in African lions and a puma in a private zoo in Johannesburg, South Africa.

    “To date, the only reverse zoonoses cases reported from the African region were in African lions and a puma in a private zoo in Johannesburg, South Africa19.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [19] Koeppel, K. N. et al. SARS-CoV-2 reverse zoonoses to pumas and lions, South Africa. Viruses 14, 120 (2022). source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    As part of the Network for Genomics Surveillance in South Africa (NGS-SA), seven sequencing hubs receive randomly selected samples for sequencing every week according to approved protocols at each site.

    “As part of the Network for Genomics Surveillance in South Africa (NGS-SA)23, seven sequencing hubs receive randomly selected samples for sequencing every week according to approved protocols at each site.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [23] Msomi, N., Mlisana, K. & de Oliveira, T. & Network for Genomic Surveillance in South Africa writing group. A genomics network established to respond rapidly to public health threats in South Africa. Lancet Microbe 1, e229–e230 (2020). source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    These estimates are based on unselected sampling for genomic surveillance (samples not selected based on SGTF or genotyping).

    “These estimates are based on unselected sampling for genomic surveillance (samples not selected based on SGTF or genotyping).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Premisenone given

    Estimation of the time of the most recent common ancestor (TMRCA) and dispersal dynamics of the sampled viruses is best achieved using Bayesian phylogenetic methods.

    “Given that the estimation of time of the most recent common ancestor (TMRCA) and dispersal dynamics of the sampled viruses is best achieved using Bayesian phylogenetic methods, we then estimated time-calibrated phylogenies using the Bayesian software package BEAST version 1.10.4 (ref. 28).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Data exclusion was not applicable to this study.

    “Data exclusion, randomization and blinding to allocation during experiments and outcome assessment were not applicable to this study.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    After the emergence of Omicron, the World Organisation for Animal Health released a statement calling for enhanced surveillance in animals to identify the origin of new variants.

    “After the emergence of Omicron, the World Organisation for Animal Health released a statement calling for enhanced surveillance in animals to identify the origin of new variants20.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [20] World Organisation for Animal Health. Statement from the Advisory Group on SARS-CoV-2 Evolution in Animals concerning the origins of Omicron variant. https://www.oie.int/en/document/statement-from-the-advisory-group-on-sars-cov-2-evolution-in-animals-concerning-the-origins-of-omicron-variant/ (2022).

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The estimated time to most recent common ancestor for both BA.4 and BA.5 (mid-November 2021, similar to that for BA.1 and BA.2) argues against the first option because that suggests both lineages would have been circulating throughout the period dominated by BA.1 and then BA.2 without exhibiting a transmission advantage.

    “The estimated time to most recent common ancestor for both BA.4 and BA.5 (mid-November 2021, similar to that for BA.1 and BA.2) argues against the first option because that suggests both lineages would have been circulating throughout the period dominated by BA.1 and then BA.2 without exhibiting a transmission advantage.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Randomization was not applicable to this study.

    “Data exclusion, randomization and blinding to allocation during experiments and outcome assessment were not applicable to this study.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Blinding to allocation during experiments and outcome assessment was not applicable to this study.

    “Data exclusion, randomization and blinding to allocation during experiments and outcome assessment were not applicable to this study.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The estimated growth advantage of the BA.4 and BA.5 lineages could be biased due to stochastic effects (such as superspreading) in a low-incidence setting at the start of a wave, which can lead to overestimates of the growth advantage.

    “First, the estimated growth advantage of the BA.4 and BA.5 lineages could be biased due to stochastic effects (such as superspreading) in a low-incidence setting at the start of a wave, which can lead to overestimates of the growth advantage.”
    Quote in the paperNot a substantial claim
35 of 35

  • The paper relies on this without support.

    The 452 residue is in immediate proximity to the interaction interface of the hACE2 receptor.

    “The 452 residue is in immediate proximity to the interaction interface of the hACE2 receptor.”

  • The paper relies on this without support.

    BA.1 caused most of the infections in South Africa's fourth epidemic wave.

    “BA.1 caused most of the infections in South Africa’s fourth epidemic wave.”

  • The paper relies on this without support.

    The NHLS has a single laboratory information system connecting laboratory testing platforms to a corporate data warehouse, where data can be mined in near real time.

    “The NHLS has a single laboratory information system connecting laboratory testing platforms to a corporate data warehouse, where data can be mined in near real time.”

  • The paper relies on this without support.

    The TaqPath COVID-19 assay accounts for around 20% of NHLS PCR tests performed, with around half of those performed in Gauteng.

    “The TaqPath COVID-19 assay (Thermo Fisher Scientific) accounts for around 20% of NHLS PCR tests performed, with around half of those performed in Gauteng.”
4 of 4

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • BA.2 dominated in South Africa by late January and globally by March.

    “Subvariant BA.2 dominated in South Africa by late January and globally by March [11,12].”

    From Assessing COVID-19 vaccine effectiveness against Omicron subvariants: Report from a meeting of the World Health Organization (2023) · cites this paper as [11]

    The Main section says BA.2 became the dominant South African lineage as the fourth wave receded in mid-January 2022, supporting dominance there by late January. It does not say BA.2 dominated globally by March; its worldwide discussion refers only to some countries and gives no March date. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • BA.2 growth-advantage confidence interval has reversed endpoints

    Minor

    The reported 95% confidence interval runs from 0.07 to 0.06: its stated lower endpoint is greater than its upper endpoint. The interval therefore cannot be interpreted as written.

1 of 1

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Khan, K. et al. Omicron sub-lineages BA.4/BA.5 escape BA.1 infection elicited neutralizing immunity. Preprint at https://www.medrxiv.org/content/10.1101/2022.04.29.22274477v1 (2022). · DOI

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Authors
Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G., Baxter, C., Althaus, C. L., Anyaneji, U. J., Kekana, D., Viana, R., Giandhari, J., Lessells, R. J., Maponga, T., Maruapula, D., Choga, W., Matshaba, M., Mbulawa, M. B., Msomi, N., NGS-SA consortium, Bester, A. P., Claassen, M., Doolabh, D., Mudau, I., Mbhele, N., Engelbrecht, S., Goedhals, D., Hardie, D., Hsiao, N.-Y., Iranzadeh, A., Ismail, A., Joseph, R., Maharaj, A., Mahlangu, B., Mahlakwane, K., Davis, A., Marais, G., Mlisana, K., Mnguni, A., Mohale, T., Motsatsi, G., Mwangi, P., Ntuli, N., Nyaga, M., Olubayo, L., Radibe, B., Ramphal, Y., Ramphal, U., Strasheim, W., Tebeila, N., van Wyk, S., Wilson, S., Lucaci, A. G., Weaver, S., Maharaj, A., Pillay, Y., Davids, M., Mendes, A., Mayaphi, S., Naidoo, Y., Pillay, S., Sanko, T. J., San, J. E., Scott, L., Singh, L., Magini, N. A., Smith-Lawrence, P., Stevens, W., Dor, G., Tshiabuila, D., Wolter, N., Preiser, W., Treurnicht, F. K., Venter, M., Chiloane, G., McIntyre, C., O’Toole, A., Ruis, C., Peacock, T. P., Roemer, C., Kosakovsky Pond, S. L., Williamson, C., Pybus, O. G., Bhiman, J. N., Glass, A., Martin, D. P., Jackson, B., Rambaut, A., Laguda-Akingba, O., Gaseitsiwe, S., von Gottberg, A., & de Oliveira, T.
Affiliations
  • Stellenbosch University (ZA)
  • National Health Laboratory Service (ZA)
  • Universidade Federal de Minas Gerais (BR)
  • University of the Witwatersrand (ZA)
  • Harvard University (US)
  • University of Bern (CH)
  • University of KwaZulu-Natal (ZA)
  • Lancet Laboratories (ZA)
  • Ministry of Health (BW)
  • University of Cape Town (ZA)
  • University of the Free State (ZA)
  • Johannesburg Hospital (ZA)
  • Temple University (US)
  • University of Pretoria (ZA)
  • University of Edinburgh (GB)
  • University of Cambridge (GB)
  • Imperial College London (GB)
  • University of Basel (CH)
  • University of Oxford (GB)
ORCID
Venue
Nature Medicine
Publisher
Springer Science and Business Media LLC
Published
2022-06-27
Volume
28
Issue
9
Pages
1785-1790
ISSN
  • 1078-8956 (ISSN-L)
  • 1546-170X
DOI
10.1038/s41591-022-01911-2
PMC
PMC9499863
OpenAlex
W4283704819
Semantic Scholar
e708146ef3ab87e2f7381416caf7255675d8898b
Cited by
707
References
48
Citations by year
2026: 37 · 2025: 62 · 2024: 142 · 2023: 259 · 2022: 196 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1
FWCI
80.66
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Medicine (publishedVersion, cc-by)
  • medRxiv (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • UpSpace Institutional Repository (University of Pretoria) (submittedVersion)
  • Arca - Repositório Institucional da Fiocruz (submittedVersion, other-oa)
  • Bern Open Repository and Information System (University of Bern) (submittedVersion, cc-by)
  • TUScholarShare (Temple University) (submittedVersion, cc-by)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
  • LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
Funders
  • U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (U01 AI151698)
  • U.S. Department of Health & Human Services | National Institutes of Health (U54 TW012041)
  • South African Medical Research Council
  • Bill and Melinda Gates Foundation (INV-018978)
  • Wellcome Trust (221003/Z/20/Z)
  • U.S. Department of Health & Human Services | NIH | Center for Information Technology (U54 TW012041)
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
  • Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
Keywords
Omicron variant, SARS-CoV-2 lineages, spike protein mutations, S-gene target failure, L452R, growth advantage, COVID-19 waves, South Africa, viral evolution
MeSH terms
COVID-19, SARS-CoV-2, Amino Acids, Animals, Humans, South Africa, Spike Glycoprotein, Coronavirus

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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