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| 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 AccessDecreased susceptibility of Plasmodium falciparum to both dihydroartemisinin and lumefantrine in northern Uganda
In this work, susceptibilities to two key antimalarials, dihydroartemisinin and lumefantrine, were associated with multiple genetic polymorphisms in Plasmodium falciparum, and were lower in northern Uganda, where resistance-mediating mutations have emerged, compared to eastern Uganda.
- Patrick K. Tumwebaze
- , Melissa D. Conrad
- & Philip J. Rosenthal
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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 AccessA population-based matched cohort study of early pregnancy outcomes following COVID-19 vaccination and SARS-CoV-2 infection
Data on the safety of COVD-19 vaccines in early pregnancy are limited. Here, the authors assess the rates of miscarriage and ectopic pregnancy following vaccination using electronic health record data from Scotland, and find no evidence of increased risks.
- Clara Calvert
- , Jade Carruthers
- & Rachael Wood
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Article
| Open AccessHospitalisation and mortality risk of SARS-COV-2 variant omicron sub-lineage BA.2 compared to BA.1 in England
In this cohort study, the authors investigate the risk of severe outcomes following infection from Omicron BA.1 and BA.2 sub-lineages. Using whole genome sequencing and electronic health record data for ~980,000 BA.1 and ~250,000 BA.2 cases in England, they find a slightly lower risk of death and hospitalisation associated with BA.2.
- H. H. Webster
- , T. Nyberg
- & S. Thelwall
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Article
| Open AccessOutcomes among confirmed cases and a matched comparison group in the Long-COVID in Scotland study
In this population-based cohort study from Scotland, the authors investigate the prevalence of symptoms in the post-acute phase of COVID-19 infection compared to matched uninfected controls. They identify persistent symptoms associated with infection and identify factors associated with failure to recover.
- Claire E. Hastie
- , David J. Lowe
- & Jill P. Pell
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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 AccessClinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages compared to BA.1 and Delta in South Africa
South Africa experienced a resurgence in COVID-19 in 2022 driven by Omicron subvariants BA.4 and BA.5. Here, the authors investigate the severity of infections caused by these subvariants, and find no difference in the risk of severe outcomes when compared to Omicron BA.1, whilst all Omicron subvariants were less severe than Delta.
- Nicole Wolter
- , Waasila Jassat
- & Cheryl Cohen
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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 AccessIncreased household transmission and immune escape of the SARS-CoV-2 Omicron compared to Delta variants
In this study the authors investigate household transmission of SARS-CoV-2 in Norway. They find that the secondary attack rate was higher for Omicron than Delta, but that among three-dose vaccinated contacts the secondary attack rate was lower for both variants compared to contacts with two doses.
- Neda Jalali
- , Hilde K. Brustad
- & Birgitte Freiesleben de Blasio
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Article
| Open AccessEffect of booster vaccination against Delta and Omicron SARS-CoV-2 variants in Iceland
Iceland has used four different SARS-CoV-2 vaccines in various combinations. Here, the authors describe differences in the immune responses elicited by different initial/booster vaccine combinations, and then use population-level data to assess the effects of booster doses against Delta and Omicron infection.
- Gudmundur L. Norddahl
- , Pall Melsted
- & Kari Stefansson
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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 AccessDerivation and validation of an epigenetic frailty risk score in population-based cohorts of older adults
Frailty is associated with an increased risk for negative health outcomes in older populations, and being able to predict frailty could facilitate prevention measures. By performing an epigenome-wide screen, the authors derived a DNA methylation based measure for frailty which can predict both prevalence and longer-term incidence of frailty.
- Xiangwei Li
- , Thomas Delerue
- & Hermann Brenner
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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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Article
| 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 AccessModelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era
This mathematical modelling study projects the dynamics of SARS-CoV-2 in England until the end of 2022 assuming that the Omicron BA.2 sublineage remains dominant. They show that booster vaccination was highly effective in mitigating severe outcomes and that future dynamics will depend greatly on assumptions about waning immunity.
- Rosanna C. Barnard
- , Nicholas G. Davies
- & W. John Edmunds
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Article
| Open AccessSARS-CoV-2 antibodies and breakthrough infections in the Virus Watch cohort
Here the authors provide data from a sub-cohort of the Virus Watch study (19,556 adults) who completed at-home capillary blood sampling on a monthly basis and describe an association between anti-spike antibody levels and risk of SARS-CoV-2 infection.
- Robert W. Aldridge
- , Alexei Yavlinsky
- & Andrew Hayward
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| 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 AccessRegional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions
The dynamics of SARS-CoV-2 transmission in the Middle East have been relatively under-studied. Here, the authors integrate genomic and travel data and show that introductions to the region were initially driven by intercontinental air travel, after which regional land travel became a more important driver.
- Edyth Parker
- , Catelyn Anderson
- & Issa Abu-Dayyeh
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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 AccessProtection of Omicron sub-lineage infection against reinfection with another Omicron sub-lineage
The level of immunity induced by infection with different SARS-CoV-2 Omicron sub-lineages against infection with other sub-lineages is not known. Here, the authors use data from Qatar and show that infection with BA.1 induces strong protection against infection with BA.2, and vice versa, for several weeks.
- Hiam Chemaitelly
- , Houssein H. Ayoub
- & Laith J. Abu-Raddad
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Article
| Open AccessA suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples
Clinical diagnosis of Treponema pallidum subspecies pallidum (TPA), the causative agent of syphilis, depends upon serological testing, which has reduced sensitivity for some stages of the disease. Accompanying methods to complement serological testing also have distinct limitations. In this work, authors develop an assay that combines PCR with CRISPR-LwCas13a, and demonstrate sensitivity and specificity on clinically confirmed syphilis samples.
- Wentao Chen
- , Hao Luo
- & Heping Zheng
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Article
| Open AccessSystematic evidence and gap map of research linking food security and nutrition to mental health
There is a broad range of research available on the relationship between food security and mental health. Here the authors carry out a systematic mapping of evidence on food security and nutrition related to mental health and identifies trends in themes, setting, and study design over the 20 year period studied.
- Thalia M. Sparling
- , Megan Deeney
- & Suneetha Kadiyala
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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 AccessEffectiveness of REGEN-COV antibody combination in preventing severe COVID-19 outcomes
REGEN-COV is a SARS-CoV-2 combined monoclonal antibody treatment which has been shown to be effective in randomised controlled trials. Here, the authors assess its real-world effectiveness using data from Israel during the Delta wave and find that it reduced the risk of hospitalisation, severe disease and death.
- Samah Hayek
- , Yatir Ben-shlomo
- & Alon Peretz
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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 AccessA nationwide questionnaire study of post-acute symptoms and health problems after SARS-CoV-2 infection in Denmark
The health impacts associated with SARS-CoV-2 infection are still not well understood. Here, the authors report findings from a survey of ~150,000 people in Denmark, and identify elevated risks associated with testing positive for SARS-CoV-2 for a range of acute and post-acute symptoms and new diagnoses.
- Anna Irene Vedel Sørensen
- , Lampros Spiliopoulos
- & Anders Hviid