On Nov 25, 2021, about 23 months since the first reported case of COVID-19 and after a global estimated 260 million cases and 5·2 million deaths,1WHOWHO coronavirus (COVID-19) dashboard.https://covid19.who.int/Date: 2021Date accessed: November 29, 2021Google Scholar a new SARS-CoV-2 variant of concern (VoC), omicron,2WHOUpdate on omicron. Nov 28, 2021.https://www.who.int/news/item/28-11-2021-update-on-omicronDate accessed: November 30, 2021Google Scholar was reported. Omicron emerged in a COVID-19-weary world in which anger and frustration with the pandemic are rife amid widespread negative impacts on social, mental, and economic wellbeing. Although previous VoCs emerged in a world in which natural immunity from COVID-19 infections was common, this fifth VoC has emerged at a time when vaccine immunity is increasing in the world. The emergence of the alpha, beta, and delta SARS-CoV-2 VoCs were associated with new waves of infections, sometimes across the entire world.3Fontanet A Autran B Lina B Kieny MP Abdool Karim SS Sridhar D SARS-CoV-2 variants and ending the COVID-19 pandemic.Lancet. 2021; 397: 952-954Summary Full Text Full Text PDF PubMed Scopus (387) Google Scholar For example, the increased transmissibility of the delta VoC was associated with, among others, a higher viral load,4Luo CH Morris CP Sachithanandham J et al.Infection with the SARS-CoV-2 delta variant is associated with higher infectious virus loads compared to the alpha variant in both unvaccinated and vaccinated individuals.medRxiv. 2021; (published online Aug 20.) (preprint).https://doi.org/10.1101/2021.08.15.21262077Google Scholar longer duration of infectiousness,5Wang Y Chen R Hu F et al.Transmission, viral kinetics and clinical characteristics of the emergent SARS-CoV-2 Delta VOC in Guangzhou, China.eClinicalMedicine. 2021; 40101129Summary Full Text Full Text PDF PubMed Scopus (151) Google Scholar and high rates of reinfection, because of its ability to escape from natural immunity,6Townsend JP Hassler HB Wang Z et al.The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study.Lancet Microbe. 2021; 2: e666-e675Summary Full Text Full Text PDF PubMed Scopus (113) Google Scholar which resulted in the delta VoC rapidly becoming the globally dominant variant. The delta VoC continues to drive new waves of infection and remains the dominant VoC during the fourth wave in many countries. Concerns about lower vaccine efficacy because of new variants have changed our understanding of the COVID-19 endgame, disabusing the world of the notion that global vaccination is by itself adequate for controlling SARS-CoV-2 infection. Indeed, VoCs have highlighted the importance of vaccination in combination with existing public health prevention measures, such as masks, as a pathway to viral endemicity.7The Lancet COVID-19 Commission Task Force on Public Health Measures to Suppress the PandemicSARs-CoV-2 variants: the need for urgent public health action beyond vaccines.https://static1.squarespace.com/static/5ef3652ab722df11fcb2ba5d/t/60a3d54f8b42b505d0d0de4f/1621349714141/NPIs+TF+Policy+Brief+March+2021.pdfDate: 2021Date accessed: November 30, 2021Google Scholar The first sequenced omicron case was reported from Botswana on Nov 11, 2021, and a few days later another sequenced case was reported from Hong Kong in a traveller from South Africa.8GISAIDTracking of variants.https://www.gisaid.org/hcov19-variants/Date: 2021Date accessed: November 30, 2021Google Scholar Several sequences from South Africa followed, after initial identification that the new variant was associated with an S-gene target failure on a specific PCR assay because of a 69–70del deletion, similar to that observed with the alpha variant.9Volz E Mishra S Chand M et al.Assessing transmissibility of SARS-CoV-2 lineage B. 1.1. 7 in England.Nature. 2021; 593: 266-269Crossref PubMed Scopus (689) Google Scholar The earliest known case of omicron in South Africa was a patient diagnosed with COVID-19 on Nov 9, 2021, although it is probable that there were unidentified cases in several countries across the world before then. In South Africa, the mean number of 280 COVID-19 cases per day in the week before the detection of omicron increased to 800 cases per day in the following week, partly attributed to increased surveillance.10Department of HealthGovernment of South AfricaCOVID-19. Dec 2, 2021.https://sacoronavirus.co.za/Google Scholar COVID-19 cases are increasing rapidly in the Gauteng province of South Africa; the early doubling time in the fourth wave is higher than that of the previous three waves (figure, appendix).10Department of HealthGovernment of South AfricaCOVID-19. Dec 2, 2021.https://sacoronavirus.co.za/Google Scholar The principal concerns about omicron include whether it is more infectious or severe than other VoCs and whether it can circumvent vaccine protection. Although immunological and clinical data are not yet available to provide definitive evidence, we can extrapolate from what is known about the mutations of omicron to provide preliminary indications on transmissibility, severity, and immune escape. Omicron has some deletions and more than 30 mutations, several of which (eg, 69–70del, T95I, G142D/143–145del, K417N, T478K, N501Y, N655Y, N679K, and P681H) overlap with those in the alpha, beta, gamma, or delta VoCs.8GISAIDTracking of variants.https://www.gisaid.org/hcov19-variants/Date: 2021Date accessed: November 30, 2021Google Scholar These deletions and mutations are known to lead to increased transmissibility, higher viral binding affinity, and higher antibody escape.11Greaney AJ Starr TN Gilchuk P et al.Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition.Cell Host Microbe. 2021; 29: 44-57Summary Full Text Full Text PDF PubMed Scopus (634) Google Scholar, 12Harvey WT Carabelli AM Jackson B et al.SARS-CoV-2 variants, spike mutations and immune escape.Nat Rev Microbiol. 2021; 19: 409-424Crossref PubMed Scopus (2016) Google Scholar Some of the other omicron mutations with known effects confer increased transmissibility and affect binding affinity.11Greaney AJ Starr TN Gilchuk P et al.Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition.Cell Host Microbe. 2021; 29: 44-57Summary Full Text Full Text PDF PubMed Scopus (634) Google Scholar, 12Harvey WT Carabelli AM Jackson B et al.SARS-CoV-2 variants, spike mutations and immune escape.Nat Rev Microbiol. 2021; 19: 409-424Crossref PubMed Scopus (2016) Google Scholar Importantly, the effects of most of the remaining omicron mutations are not known, resulting in a high level of uncertainty about how the full combination of deletions and mutations will affect viral behaviour and susceptibility to natural and vaccine-mediated immunity. The impact of omicron on transmissibility is a concern. If the overlapping omicron mutations maintain their known effects, then higher transmissibility is expected, particularly because of the mutations near the furin cleavage site. Early epidemiological evidence suggests that cases are rising in South Africa and that PCR tests with S-gene target failure are also rising. Although omicron is likely to be highly transmissible, it is not yet clear whether it has greater transmissibility than delta, although preliminary indications suggest that it is spreading rapidly against a backdrop of ongoing delta-variant transmission and high levels of natural immunity to the delta variant. If this trend continues, omicron is anticipated to displace delta as the dominant variant in South Africa. We await knowledge of how this new VoC will impact clinical presentation. At this stage, the available anecdotal data from clinicians at the front lines in South Africa suggest that patients with omicron are younger people with a clinical presentation similar to that of past variants.13National Institute for Communicable DiseasesFrequently asked questions for the B.1.1.529 mutated SARS-CoV-2 lineage in South Africa.https://www.nicd.ac.za/frequently-asked-questions-for-the-b-1-1-529-mutated-sars-cov-2-lineage-in-south-africa/Date: 2021Date accessed: November 30, 2021Google Scholar Although no alarming clinical concerns have been raised thus far, this anecdotal information should be treated with caution given that severe COVID-19 cases typically present several weeks after the initial symptoms associated with mild disease. Immune escape is another concern. In the absence of data on observational vaccine effectiveness and antibody-neutralisation studies on vaccinee sera, preliminary data from the national PCR testing programme could provide some clues. Data on positive PCR tests in people with previous positive tests suggest an increase in cases of reinfection in South Africa. However, the increased use of rapid antigen tests and incomplete capturing of negative results have complicated the interpretation of test positivity rates, which have risen to about four times the previous rate in the past week. Notwithstanding this limitation, the increase in cases of reinfection is in keeping with the immune-escape mutations present in omicron. Although there are conflicting reports on whether COVID-19 vaccines have consistently retained high efficacy for each of the four VoCs preceding omicron, clinical trials have reported lower efficacy for some vaccines in transmission settings in which the beta variant is dominant. Previous variants have lowered vaccine efficacy; for example, the ChAdOx1 vaccine was 70% effective in preventing clinical infections for the D614G variant in the UK, but this efficacy decreased to 10% for the beta variant in South Africa.14Abdool Karim SS de Oliveira T New SARS-CoV-2 variants: clinical, public health, and vaccine implications.N Engl J Med. 2021; 384: 1866-1868Crossref PubMed Scopus (480) Google Scholar However, the efficacy of the BNT162b2 vaccine in preventing clinical infections was retained across both the D614G and beta variants.14Abdool Karim SS de Oliveira T New SARS-CoV-2 variants: clinical, public health, and vaccine implications.N Engl J Med. 2021; 384: 1866-1868Crossref PubMed Scopus (480) Google Scholar Given that omicron has a larger number of mutations than previous VoCs, the potential impact of omicron on the clinical efficacy of COVID-19 vaccines for mild infections is not clear. Thus far, most COVID-19 vaccines have remained effective in preventing severe COVID-19, hospitalisation, and death, for all previous variants, because this efficacy might be more dependent on T-cell immune responses than antibodies. Observational studies from Qatar (n=231 826)15Chemaitelly H Tang P Hasan MR et al.Waning of BNT161b2 vaccine protection against SARS-CoV-2 infection in Qatar.N Engl J Med. 2021; (published online Aug 27.)https://doi.org/10.1056/NEJMoa2114114Crossref Scopus (538) Google Scholar and Kaiser Permanente (n=3 436 957)16Tartof SY Slezak JM Fischer H et al.Effectiveness of mRNA BNT162b2 COVID-19 vaccine up to 6 months in a large integrated health system in the USA: a retrospective cohort study.Lancet. 2021; 398: 1407-1416Summary Full Text Full Text PDF PubMed Scopus (770) Google Scholar reported vaccine efficacy of more than 90% in preventing hospital admissions during delta-variant transmission, even up to 6 months after vaccination. Observational data from the state of New York, USA (n=8 834 604) indicated high vaccine efficacy in preventing severe disease in people older than 65 years, with varying levels of protection conferred by different vaccines—95% for BNT162b2, 97% for mRNA-1273, and 86% for Ad26.COV2.S17Rosenberg ES Dorabawila V Easton D et al.COVID-19 vaccine effectiveness in New York state.N Engl J Med. 2021; (published online Dec 1.)https://doi.org/10.1056/NEJMoa2116063Crossref Scopus (192) Google Scholar—with minimal declines in protection 6 months after vaccination. In terms of diagnostics, the omicron variant is detectable on widely used PCR platforms in South Africa. There is no reason to believe that current COVID-19 treatment protocols and therapeutics would no longer be effective, with the possible exception of monoclonal antibodies, for which data on the omicron variant's susceptibility are not yet available. Importantly, existing public health prevention measures (mask wearing, physical distancing, avoidance of enclosed spaces, outdoor preference, and hand hygiene) that have remained effective against past variants should be just as effective against the omicron variant. Extrapolations based on known mutations and preliminary observations, which should be interpreted with caution, indicate that omicron might spread faster and might escape antibodies more readily than previous variants, thereby increasing cases of reinfection and cases of mild breakthrough infections in people who are vaccinated. On the basis of data from previous VoCs, people who are vaccinated are likely to have a much lower risk of severe disease from omicron infection. A combination prevention approach of vaccination and public health measures is expected to remain an effective strategy. This online publication has been corrected. The corrected version first appeared at thelancet.com on January 6, 2021 This online publication has been corrected. The corrected version first appeared at thelancet.com on January 6, 2021 We declare no competing interests. Download .pdf (.1 MB) Help with pdf files Supplementary appendix Department of ErrorAbdool Karim SS, Abdool Karim Q. Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. Lancet 2021; 398: 2126–28 — In this Comment, reference 5 has been replaced with the correct reference. This correction has been made to the online version as of Jan 6, 2022. Full-Text PDF

Omicron SARS-CoV-2 Variant: a New Chapter in the COVID-19 Pandemic

Infectious viral load (VL) expelled as droplets and aerosols by infected individuals partly determines transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RNA VL measured by qRT–PCR is only a weak proxy for infectiousness. Studies on the kinetics of infectious VL are important to understand the mechanisms behind the different transmissibility of SARS-CoV-2 variants and the effect of vaccination on transmission, which allows guidance of public health measures. In this study, we quantified infectious VL in individuals infected with SARS-CoV-2 during the first five symptomatic days by in vitro culturability assay in unvaccinated or vaccinated individuals infected with pre-variant of concern (pre-VOC) SARS-CoV-2, Delta or Omicron BA.1. Unvaccinated individuals infected with pre-VOC SARS-CoV-2 had lower infectious VL than Delta-infected unvaccinated individuals. Full vaccination (defined as >2 weeks after receipt of the second dose during the primary vaccination series) significantly reduced infectious VL for Delta breakthrough cases compared to unvaccinated individuals. For Omicron ﻿BA.1 breakthrough cases, reduced infectious VL was observed only in boosted but not in fully vaccinated individuals compared to unvaccinated individuals. In addition, infectious VL was lower in fully vaccinated Omicron BA.1﻿-infected individuals compared to fully vaccinated Delta-infected individuals, suggesting that mechanisms other than increased infectious VL contribute to the high infectiousness of SARS-CoV-2 Omicron BA.1﻿. Our findings indicate that vaccines may lower transmission risk and, therefore, have a public health benefit beyond the individual protection from severe disease. The infectious viral load of SARS-CoV-2 Omicron BA.1﻿ is lower than that of Delta in symptomatic breakthrough infections of recipients of two doses of a COVID-19 vaccine, suggesting that the higher transmission of Omicron BA.1﻿ is not linked to higher infectious viral load. 

/pdf/infectious-viral-load-in-unvaccinated-and-vaccinated-1q90885d.pdf

Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2

SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed. 

/pdf/sars-cov-2-viral-load-and-shedding-kinetics-2a6wz4a1.pdf

SARS-CoV-2 viral load and shedding kinetics

We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine effectiveness against infection (VE-I) and death (VE-D) by vaccine type in 780,225 veterans in the Veterans Health Administration, covering 2.7% of the US population. From February to October 2021, VE-I declined for all vaccine types, and the decline was greatest for the Janssen vaccine, resulting in a VE-I of 13.1%. Although breakthrough infection increased risk of death, vaccination remained protective against death in persons who became infected during the Delta variant surge. From July to October 2021, VE-D for age &lt;65 years was 73.0% for Janssen, 81.5% for Moderna, and 84.3% for Pfizer-BioNTech; VE-D for age ≥65 years was 52.2% for Janssen, 75.5% for Moderna, and 70.1% for Pfizer-BioNTech. Findings support continued efforts to increase vaccination, booster campaigns, and multiple additional layers of protection against infection. 

https://www.science.org/cms/asset/607d657e-0d05-4710-933d-2d0b23b77d7b/science.abm0620.v1.pdf

SARS-CoV-2 vaccine protection and deaths among US veterans during 2021

Abstract In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient’s body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence. 

/pdf/drivers-of-adaptive-evolution-during-chronic-sars-cov-2-3e8jy13v.pdf

Drivers of adaptive evolution during chronic SARS-CoV-2 infections

Transmission, viral kinetics and clinical characteristics of the emergent SARS-CoV-2 Delta VOC in Guangzhou, China.

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Transmission, viral kinetics and clinical characteristics of the emergent SARS-CoV-2 Delta VOC in Guangzhou, China.