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| Open AccessVariant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England
In this study, the authors assess changing symptom profiles associated with different SARS-CoV-2 variants from May 2020 to March 2022 in England. Using data from the REACT-1 study, they find that Omicron infection is more often associated with cold and influenza-like symptoms, and less with loss of taste and smell.
- Matthew Whitaker
- , Joshua Elliott
- & Paul Elliott
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Article
| Open AccessAssociations of hurricane exposure and forecasting with impaired birth outcomes
Early forecasts give people in a storm’s path time to prepare, but less is known about the cost to society when forecasts are incorrect. In this observational study, the authors examine over 700,000 births in the path of Hurricane Irene and find exposure was associated with impaired birth outcomes.
- Jacob Hochard
- , Yuanhao Li
- & Nino Abashidze
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| Open AccessViral load dynamics of SARS-CoV-2 Delta and Omicron variants following multiple vaccine doses and previous infection
COVID vaccination can reduce virus levels in breakthrough infections, which in turn may reduce transmission of the virus. By using qRT-PCR cycle threshold as a surrogate of virus levels, the authors here show that this positive effect of vaccination wanes relatively quickly for Omicron breakthrough infection.
- Yonatan Woodbridge
- , Sharon Amit
- & Naama M. Kopelman
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Article
| Open AccessTracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border
In March 2022, Aotearoa New Zealand re-opened its border allowing quarantine-free travel for many travellers. Here, the authors describe circulating Omicron sub-variants before and after the reopening of the border and show that the rate of viral introductions grew roughly linearly with the increase in daily international travel.
- Jordan Douglas
- , David Winter
- & Jemma L. Geoghegan
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Matters Arising
| Open AccessReply to: Intergenerational nutrition benefits of India’s national school feeding program: Reality or a bridge too far?
- Suman Chakrabarti
- , Samuel Scott
- & Daniel Gilligan
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Matters Arising
| Open AccessIntergenerational nutrition benefits of India’s national school feeding program: Reality or a bridge too far?
- Harshpal Singh Sachdev
- , Clive Osmond
- & Tinku Thomas
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Article
| Open AccessGlobal mortality of snakebite envenoming between 1990 and 2019
Snakebite envenoming is a leading cause of mortality among neglected tropical diseases. Here, the authors analyze a global data repository and estimate that snakebite envenoming caused over 63,000 deaths in 2019, primarily concentrated in South Asia and Sub-Saharan Africa.
- Nicholas L. S. Roberts
- , Emily K. Johnson
- & Kanyin Liane Ong
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Article
| Open AccessDetection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France
Monitoring of co-infections of SARS-CoV-2 variants is important to evaluate their clinical impact and the risk of emergence of recombinants. Here, the authors develop and validate a methodological pipeline to detect co-infections and apply it to samples from France in early 2022, when Delta and Omicron were co-circulating.
- Antonin Bal
- , Bruno Simon
- & Laurence Josset
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Article
| Open AccessContact tracing reveals community transmission of COVID-19 in New York City
In this study, the authors analyse contact tracing records for ~650,000 suspected or confirmed COVID-19 cases in New York City during the second epidemic wave. They reconstruct transmission networks and find that vaccination and zone-based control policies likely contributed to control of the epidemic.
- Sen Pei
- , Sasikiran Kandula
- & Jeffrey Shaman
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Article
| Open AccessPost-acute sequelae of SARS-CoV-2 with clinical condition definitions and comparison in a matched cohort
In this study, the authors use electronic health record data from the US to characterise post-acute sequelae of SARS-CoV-2 infection (PASC). They identify 17 common PASC conditions and find an overall ~12% increase in risk of PASC conditions in the post-acute period among people with a SARS-CoV-2 positive test compared to matched test-negative controls.
- Michael A. Horberg
- , Eric Watson
- & Richard Moore
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Article
| Open AccessTrends in non-COVID-19 hospitalizations prior to and during the COVID-19 pandemic period, United States, 2017–2021
In this study, the authors investigate the impacts of the COVID-19 pandemic on healthcare utilisation in the US. They show that, following an immediate decline, hospitalisations for some conditions returned to pre-pandemic norms by the end of 2020, but for others, including respiratory conditions, this had not occurred by June 2021.
- Kelsie Cassell
- , Casey M. Zipfel
- & Daniel M. Weinberger
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Article
| Open AccessEffectiveness of an inactivated Covid-19 vaccine with homologous and heterologous boosters against Omicron in Brazil
This study investigates the effectiveness of COVID-19 vaccine boosters following a primary series of CoronaVac vaccination. Using data from Brazil during the Omicron wave, the authors show that boosters provided protection against severe disease, with higher effectiveness from a BNT162b2 than CoronaVac booster.
- Otavio T. Ranzani
- , Matt D. T. Hitchings
- & Julio Croda
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Article
| Open AccessImpact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants
Increasing reliance on antigen tests for SARS-CoV-2 screening may risk selection for variants not detected by these tests. Here, the authors identify a variant of this type circulating in Italy, estimate the potential impact of failure to detect the variant, and model testing strategies to mitigate the risk.
- Claudia Del Vecchio
- , Bethan Cracknell Daniels
- & Andrea Crisanti
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Article
| Open AccessThe design and evaluation of hybrid controlled trials that leverage external data and randomization
Patient-level external control data from prior clinical studies or electronic health records can be used in the design and analysis of clinical trials. Here the authors report a hybrid trial design combining the use of external control data and randomization to test experimental treatments, using small cell lung cancer and glioblastoma datasets as examples.
- Steffen Ventz
- , Sean Khozin
- & Lorenzo Trippa
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Article
| Open AccessHousehold transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark
In this study, the authors use household data from Denmark to investigate the transmissibility of the BA.1 and BA.2 Omicron SARS-CoV-2 subvariants. They find that the secondary attack rate was higher for BA.2, but that it had higher infectiousness only when cases were not vaccinated.
- Frederik Plesner Lyngse
- , Carsten Thure Kirkeby
- & Laust Hvas Mortensen
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Article
| Open AccessUsing multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data
SARS-CoV-2 genome sequencing data can be used to infer epidemiological parameters, but the impact of the strategy used to select samples on these estimates is rarely considered. Here, the authors produce estimates using different sampling strategies and compare results to those based on case reporting data.
- Rhys P. D. Inward
- , Kris V. Parag
- & Nuno R. Faria
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Article
| Open AccessHousehold transmission of the SARS-CoV-2 Omicron variant in Denmark
In this study, the authors compare the transmission dynamics of the Delta and Omicron SARS-CoV-2 variants using household data from Denmark. They find that Omicron has a higher secondary attack rate, and that the odds of infection with Omicron was higher than with Delta, particularly for vaccinated individuals.
- Frederik Plesner Lyngse
- , Laust Hvas Mortensen
- & Carsten Thure Kirkeby
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Article
| Open AccessTracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA
In this study, the authors develop a method for estimation of SARS-CoV-2 community transmission rates based on a sentinel population of people seeking outpatient testing with recent symptom onset. This method has fewer operational delays than methods based on hospital data, and may be subject to fewer biases.
- Reese Richardson
- , Emile Jorgensen
- & Jaline Gerardin
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Article
| Open AccessThe impact of repeated rapid test strategies on the effectiveness of at-home antiviral treatments for SARS-CoV-2
Antiviral treatments for SARS-CoV-2 infection are only beneficial when used early in infection, so early case detection is important. Here, the authors assess the frequency of testing needed to achieve population-level benefits and demonstrate the importance of high coverage and short delays from test to treatment.
- Tigist F. Menkir
- & Christl A. Donnelly
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Article
| Open AccessGenomic surveillance of SARS-CoV-2 Omicron variants on a university campus
This study presents results from a SARS-CoV-2 genomic surveillance study at a university campus in which ~2,000 samples were sequenced over five months. The authors document the replacement of Delta with Omicron as the dominant variant, and describe clinical characteristics and transmission dynamics.
- Ana A. Weil
- , Kyle G. Luiten
- & Helen Y. Chu
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| Open AccessInterrupted-time-series analysis of the immediate impact of COVID-19 mitigation measures on preterm birth in China
The broader impacts of COVID-19 mitigation measures may include changes in the incidence of preterm birth. Here, the authors use data from ~11.7 million pregnancies in China and find evidence of a small decline in preterm birth rates immediately following the implementation of COVID-19 mitigation measures.
- Yanxia Xie
- , Yi Mu
- & Jun Zhu
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Article
| Open AccessReproducibility of real-world evidence studies using clinical practice data to inform regulatory and coverage decisions
Analyses of real-world evidence from digital clinical practice data provide important insights for healthcare decision makers. Here, authors test reproducibility of 150 peer-reviewed studies, reporting strong reproducibility, which could be further improved through more complete reporting in future original studies
- Shirley V. Wang
- , Sushama Kattinakere Sreedhara
- & Deborah Zarin
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Article
| Open AccessA prospective observational study of post-COVID-19 chronic fatigue syndrome following the first pandemic wave in Germany and biomarkers associated with symptom severity
Some patients experience long-lasting symptoms after coronavirus disease (COVID-19). Here the authors report the clinical and laboratory parameters in patients with post-COVID-19 syndrome from a prospective observational cohort study.
- Claudia Kedor
- , Helma Freitag
- & Carmen Scheibenbogen
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Comment
| Open AccessCall for a unified approach to Monkeypox infection in pregnancy: Lessons from the COVID-19 pandemic
In the current monkeypox outbreak, vaccination and treatment of pregnant women are recommended only if the benefits outweigh risks, but the extremely sparse data available limit evidence-based recommendations. We must facilitate a unified consensus approach to rapidly collect robust data. Two years into the COVID-19 pandemic, monkeypox has emerged as yet another challenge to the mother-fetus dyad, potentially placing both at risk, if exposed.
- Asma Khalil
- , Athina Samara
- & Shamez Ladhani
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Article
| Open AccessInvestigating disparity in access to Australian clinical genetic health services for Aboriginal and Torres Strait Islander people
Globally it is recognised that Indigenous populations should be able to access the benefits of genomics and precision medicine. Here, authors show that there are disparities in access to clinical genetic health services for Aboriginal and/or Torres Strait Islander people in Australia.
- Joanne Luke
- , Philippa Dalach
- & Margaret Kelaher
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Article
| Open AccessComparison of the 2021 COVID-19 roadmap projections against public health data in England
The ’Roadmap’ for relaxation of COVID-19 restrictions in England in 2021 was informed by mathematical modelling. Here, the authors perform a retrospective assessment of the accuracy of modelling predictions and identify the main sources of uncertainty that led to observed values deviating from projections.
- Matt J. Keeling
- , Louise Dyson
- & Samuel Moore
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Article
| Open AccessTrends in COVID-19 hospital outcomes in England before and after vaccine introduction, a cohort study
This study investigates trends in mortality and length of stay for people hospitalised with COVID-19 in England until September 2021. It shows that risks were higher for unvaccinated people and those with multiple comorbidities, and that busier hospitals had higher mortality rates at the start of the pandemic but this effect lessened over time.
- Peter D. Kirwan
- , Andre Charlett
- & Anne M. Presanis
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Article
| Open AccessSecond-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland
Here, Simpson et al. analyze data from 3.6 million COVID-19 vaccine second doses (ChAdOx1 and BNT162b2) in Scotland for risk of thrombocytopenic, thromboembolic and hemorrhagic events. Borderline increased risks of immune thrombocytopenic purpura and cerebral venous sinus thrombosis were found for the ChAdOx1 vaccine. These events were rare and usually short-lived.
- Colin R. Simpson
- , Steven Kerr
- & Aziz Sheikh
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Article
| Open AccessVaccine effectiveness of CoronaVac against COVID-19 among children in Brazil during the Omicron period
There is limited evidence of the effectiveness of the CoronaVac vaccine for children against the Omicron SARS-CoV-2 variant. Here, the authors use data from Brazil for children aged 6–11 years and estimate effectiveness of 40% against infection and 59% against severe disease at least two weeks after the second dose.
- Pilar T. V. Florentino
- , Flávia J. O. Alves
- & Enny S. Paixão
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Article
| Open AccessEmpirical evidence on the efficiency of backward contact tracing in COVID-19
Backward contact tracing aims to identify individuals who were infected by the same person as infected an index case, and has been shown to be effective in modelling studies of SARS-COV-2. Here, the authors present empirical data of the effectiveness of backward contact tracing from a program amongst university students in Belgium.
- Joren Raymenants
- , Caspar Geenen
- & Emmanuel Andre
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Article
| Open AccessProtection of COVID-19 vaccination and previous infection against Omicron BA.1, BA.2 and Delta SARS-CoV-2 infections
The protection of COVID-19 vaccines against emerging variants needs to be monitored. Here, the authors use community testing data from the Netherlands and find that protection against infection by Omicron subvariants BA.1 and 2 is low and that booster vaccines considerably but temporarily increase protection.
- Stijn P. Andeweg
- , Brechje de Gier
- & Mirjam J. Knol
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Article
| Open AccessSARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings
Air surveillance offers a potential means of monitoring airborne pathogens without the need for individual sampling. Here, the authors perform continuous air sampling in 15 community settings in the US for 29 weeks and demonstrate its feasibility for routine detection of SARS-CoV-2 and other respiratory pathogens.
- Mitchell D. Ramuta
- , Christina M. Newman
- & Shelby L. O’Connor
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Comment
| Open AccessScience in the time of COVID-19: Reflections on the UK Events Research Programme
We reflect on the extent to which the UK Events Research Programme adhered to four principles of design and evaluation in assessing risk of transmission from attending such mass events as football matches and festivals, and lessons learned.
- Theresa M. Marteau
- , Michael J. Parker
- & W. John Edmunds
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Article
| Open AccessDynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England
The REACT-1 study measures the community prevalence of SARS-CoV-2 in England through repeated cross-sectional surveys. Here, the authors present data from REACT-1 that document the increase in infection prevalence, particularly among children, associated with the Omicron variant in January 2022.
- Paul Elliott
- , Oliver Eales
- & Christl A. Donnelly
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Article
| Open AccessLevels of SARS-CoV-2 antibodies among fully vaccinated individuals with Delta or Omicron variant breakthrough infections
The SARS-CoV-2 Omicron variant is associated with high rates of vaccine breakthrough infections, but the immunological basis for this is not well characterised. Here, the authors show that increased anti-Spike IgG antibody levels are associated with a reduced risk of infection with the Delta variant, but not with Omicron.
- Nina Breinholt Stærke
- , Joanne Reekie
- & Ole Schmeltz Søgaard
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Article
| Open AccessDynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England
This study presents data from the REACT-1 SARS-CoV-2 community sampling study in England from November 2021 to March 2022. They show that the Omicron variant peaked in January with a prevalence of ~7% and that the BA.2 sublineage had a 1.5x higher reproduction number compared to other Omicron sublineages.
- Oliver Eales
- , Leonardo de Oliveira Martins
- & Marc Chadeau-Hyam
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Article
| Open AccessAn analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence
Wastewater surveillance could provide a means of monitoring SARS-CoV-2 prevalence that does not rely on testing individuals. Here, the authors report results from England’s national wastewater surveillance program, use it to estimate prevalence, and compare estimates with those from population-based prevalence surveys.
- Mario Morvan
- , Anna Lo Jacomo
- & Leon Danon
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Article
| Open AccessStress-testing the resilience of the Austrian healthcare system using agent-based simulation
As mass quarantines, absences due to sickness, or other shocks thin out patient-physician networks, the system might be pushed to a tipping point where it loses its ability to deliver care. Here, the authors propose a data-driven framework to quantify regional resilience to such shocks via an agent-based model.
- Michaela Kaleta
- , Jana Lasser
- & Peter Klimek
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Article
| Open AccessGenomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand
Aotearoa New Zealand pursued a COVID-19 elimination strategy until October 2021 when it moved to a suppression strategy. In this genomic surveillance study, the authors describe spread of the virus during the transition between these strategies, with evidence of substantial undetected community transmission.
- Lauren Jelley
- , Jordan Douglas
- & Jemma L. Geoghegan
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Article
| Open AccessThe effect of COVID certificates on vaccine uptake, health outcomes, and the economy
Many countries introduced COVID certificates that were required to access public venues. Here, the authors analyse data from France, Germany, and Italy, and estimate that these policies led to increased vaccine uptake of 6-13 percentage points with subsequent beneficial impacts on health and economic outcomes.
- Miquel Oliu-Barton
- , Bary S. R. Pradelski
- & Guntram B. Wolff
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Article
| Open AccessPopulation genomics of ancient and modern Trichuris trichiura
The whipworm Trichuris trichiura is a soil-transmitted helminth that causes the neglected tropical disease trichuriasis in humans. Here, the authors produce whole genome sequences of modern and ancient samples from humans and non-human primates to characterise the genomic diversity and evolution of this pathogen.
- Stephen R. Doyle
- , Martin Jensen Søe
- & Christian Moliin Outzen Kapel
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Article
| Open AccessInferring the epidemiological benefit of indoor vector control interventions against malaria from mosquito data
Estimating the effectiveness of malaria vector control interventions has typically relied on resource-intensive cluster randomised trials. Here, the authors estimate changes in malaria prevalence using entomological data from experimental hut trials, which may provide an alternative route to approval of interventions in some situations.
- Ellie Sherrard-Smith
- , Corine Ngufor
- & Thomas S. Churcher
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Article
| Open AccessRevisiting COVID-19 vaccine hesitancy around the world using data from 23 countries in 2021
Vaccine hesitancy is a public health challenge. Here the authors examine COVID-19 vaccine hesitancy in June 2021 using a survey including individuals from 23 countries, and report differences compared to a year earlier.
- Jeffrey V. Lazarus
- , Katarzyna Wyka
- & Ayman El-Mohandes
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Article
| Open AccessEffect of vaccination on household transmission of SARS-CoV-2 Delta variant of concern
COVID-19 vaccines may reduce the susceptibility of an individual to infection and/or the infectiousness of breakthrough infections. Here, the authors use data from Denmark and estimate that vaccine effectiveness was 61% for susceptibility and 31% for infectiousness during a period of Delta variant dominance.
- Frederik Plesner Lyngse
- , Kåre Mølbak
- & Carsten Thure Kirkeby
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Article
| Open AccessCOVID-19 disease severity in US Veterans infected during Omicron and Delta variant predominant periods
Infection with the SARS-CoV-2 Omicron variant appears to cause milder disease in the general population than infection with Delta. Here the authors use data from the US Department of Veterans Affairs and demonstrate that this also applies to infection in an at-risk population of older age and with more co-morbidities.
- Florian B. Mayr
- , Victor B. Talisa
- & Adeel A. Butt
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Article
| Open AccessAge and sex-specific risks of myocarditis and pericarditis following Covid-19 messenger RNA vaccines
There have been reports of myocarditis and pericarditis following mRNA COVID-9 vaccination. Here, the authors use nationwide data from France and find increased risks of these outcomes in the first week following vaccination, for both the first and second dose, and present age- and sex-specific rates.
- Stéphane Le Vu
- , Marion Bertrand
- & Mahmoud Zureik
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Article
| Open AccessEffective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children
Dewald et al. combine a non-invasive sampling approach (Lolli-Test) with an RT qPCR-pool testing strategy to screen for SARS-CoV-2 infections in children and use the method for surveillance and infection control in > 4000 school and daycare settings.
- Felix Dewald
- , Isabelle Suárez
- & Florian Klein
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Article
| Open AccessContribution of low population immunity to the severe Omicron BA.2 outbreak in Hong Kong
Hong Kong experienced a severe wave of SARS-CoV-2 in early 2022. Here, the authors use genomic and serosurveillance data and show that this wave was dominated by the Omicron BA.2 sublineage, and that low protective immunity, particularly in older age groups, contributed to its severity.
- Lin-Lei Chen
- , Syed Muhammad Umer Abdullah
- & Kelvin Kai-Wang To
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Comment
| Open AccessOpportunities to tackle structural racism and ethnicity-based discrimination in recovering and rebuilding from the COVID-19 pandemic
The impact of COVID-19 has been disproportionately felt by populations experiencing structural racial- and ethnicity-based discrimination. Here, the authors describe opportunities for COVID-19 response and recovery efforts to help build more equal and resilient societies.
- Natalia Linos
- , Mary T. Bassett
- & Theadora Swift Koller