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| Open AccessIndoor air surveillance and factors associated with respiratory pathogen detection in community settings in Belgium
Surveillance of respiratory pathogens in air may improve understanding of indoor transmission risks but impacts of context-specific factors on pathogen abundance are not well understood. Here, the authors investigate factors associated with 29 respiratory pathogens through surveillance of 21 community settings in Belgium.
- Joren Raymenants
- , Caspar Geenen
- & Emmanuel André
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| Open AccessEffectiveness of mRNA COVID-19 vaccine booster doses against Omicron severe outcomes
This study investigates the protection provided by mRNA COVID-19 vaccine booster doses against Omicron-associated severe disease in adults aged 50 and older. The authors use data from Ontario, Canada, and find that booster doses provide strong protection but that it declined during the period of BA.4/BA.5 predominance.
- Ramandip Grewal
- , Lena Nguyen
- & Jeffrey C. Kwong
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| Open AccessMaternal SARS-CoV-2 vaccination and infant protection against SARS-CoV-2 during the first six months of life
This study investigates the impact of maternal COVID-19 vaccination during pregnancy on infant infection during the first six months of life. Using data from California, USA, the authors find that protection against infection during the period of Delta dominance was high, but that it declined during the Omicron period.
- Ousseny Zerbo
- , G. Thomas Ray
- & Nicola P. Klein
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| Open AccessDetection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA
A variant of group A Streptococcus serotype M1 (UK) has been increasingly reported and can be differentiated from the global variant by its overexpression of the superantigen SpeA. Here, Davies et al probe the mechanism behind enhanced SpeA expression and demonstrate that a SNP in the 5’ leader sequence of ssrA is responsible for this virulence phenotype.
- Mark R. Davies
- , Nadia Keller
- & Mark J. Walker
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| Open AccessEpidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year
The NHS COVID-19 digital contact tracing app was designed to notify people of potential exposure to SARS-CoV-2. Here, the authors summarise the uptake and engagement with the app in its first year, and estimate its epidemiological impact in terms of numbers of cases, hospitalisations, and deaths averted.
- Michelle Kendall
- , Daphne Tsallis
- & Christophe Fraser
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| Open AccessNational surveillance data analysis of COVID-19 vaccine uptake in England by women of reproductive age
Women of reproductive age may have specific concerns relating to perceived impacts on fertility and menstrual cycles that make them hesitant to receive COVID-19 vaccination. In this study, the authors explore COVID-19 vaccine uptake rates in women of reproductive age using linked data for ~13 million women in England.
- Laura A. Magee
- , Erika Molteni
- & Sara White
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| Open AccessOptimal age targeting for pneumococcal vaccination in older adults; a modelling study
Vaccination against invasive pneumococcal disease is recommended for older adults but the optimal age group to target has not been determined and may vary by epidemiological setting. Here, the authors use statistical modelling to estimate the optimal ages for vaccination in Brazil, England, Malawi, and South Africa.
- Deus Thindwa
- , Samuel Clifford
- & Stefan Flasche
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Article
| Open AccessGenetic correlates of vitamin D-binding protein and 25-hydroxyvitamin D in neonatal dried blood spots
In this study the authors measure the concentration of 25-hydroxyvitamin D and vitamin D binding protein (DBP) in 65,589 neonatal dried blood samples. Findings from further analyses include that the genetic correlates of DBP concentration predict the risk of vitamin D deficiency.
- Clara Albiñana
- , Zhihong Zhu
- & John J. McGrath
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| Open AccessThe impacts of SARS-CoV-2 vaccine dose separation and targeting on the COVID-19 epidemic in England
In England, SARS-CoV-2 vaccines were initially targeted to older, more vulnerable people; first vaccine doses were prioritised over second doses, and an interval of twelve weeks was used between doses. Here, the authors assess the impacts of these policy decisions by simulating counterfactual scenarios.
- Matt J. Keeling
- , Samuel Moore
- & Edward M. Hill
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Article
| Open AccessQuantifying the direct and indirect protection provided by insecticide treated bed nets against malaria
Long lasting insecticide treated mosquito nets (LLINs) provide protection from malaria through both direct effects to the user and indirect community-level effects. Here, the authors use mathematical modelling to assess the relative contributions of these effects under different insecticide resistance and LLIN usage scenarios.
- H. Juliette T. Unwin
- , Ellie Sherrard-Smith
- & Azra C. Ghani
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Article
| Open AccessRapid emergence of extensively drug-resistant Shigella sonnei in France
There have been increasing reports of extensively drug-resistant (XDR) Shigella sonnei infections in recent years. In this laboratory surveillance study from France, the authors document the rise of XDR isolates from 2005 to 2021 and perform whole genome sequencing to investigate their genomic diversity and evolutionary history.
- Sophie Lefèvre
- , Elisabeth Njamkepo
- & François-Xavier Weill
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Article
| Open AccessProjected health impact of post-discharge malaria chemoprevention among children with severe malarial anaemia in Africa
Trial data have shown that post-discharge malaria chemoprevention (PDMC) reduces the risk of readmission and death in children previously hospitalised with severe malarial anaemia. Here, the authors use mathematical modelling to estimate the potential epidemiological impacts of PDMC in malaria-endemic countries in Africa.
- Lucy C. Okell
- , Titus K. Kwambai
- & Amani Thomas Mori
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Article
| Open AccessImpact of the Euro 2020 championship on the spread of COVID-19
In this Bayesian inference study, the authors aim to quantify the impact of the men’s 2020 UEFA Euro Football Championship on COVID-19 spread in twelve participating countries. They estimate that 0.84 million cases and 1,700 deaths were attributable to the championship, with most impacts in England and Scotland.
- Jonas Dehning
- , Sebastian B. Mohr
- & Viola Priesemann
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| Open AccessRapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa
Emergence of the Omicron BA.1/2 SARS-CoV-2 subvariants led to a wave of infection South Africa. Here, the authors use serological data from a prospective household study to characterise infection rates in the context of diverse immune histories following vaccination and exposure to different variants.
- Kaiyuan Sun
- , Stefano Tempia
- & Floidy Wafawanaka
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| Open AccessEffectiveness of mRNA-1273 vaccination against SARS-CoV-2 omicron subvariants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5
In this study, the authors estimate the effectiveness of the mRNA-1273 (Moderna) vaccine for Omicron subvariants using data from the USA on ~31,000 cases and ~92,000 matched controls. They find that effectiveness against infection waned rapidly after third and fourth doses, but effectiveness against hospitalization remained high.
- Hung Fu Tseng
- , Bradley K. Ackerson
- & Lei Qian
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Article
| Open AccessA population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection
The risks of major congenital anomalies associated with SARS-CoV-2 vaccination in early pregnancy are not well understood. Here, the authors conduct a population-based cohort study using electronic health records from Scotland and find no evidence of an association, supporting vaccine safety in pregnancy.
- Clara Calvert
- , Jade Carruthers
- & Rachael Wood
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Article
| Open AccessDirect and indirect effects of the COVID-19 pandemic on mortality in Switzerland
COVID-19-releated public health measures may have indirectly impacted mortality rates by causing or averting deaths. Here, the authors use data from Switzerland until April 2022 and estimate that, after accounting for deaths directly related to COVID-19, mortality was lower than expected, indicating some evidence of an overall positive impact of control measures.
- Julien Riou
- , Anthony Hauser
- & Garyfallos Konstantinoudis
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| Open AccessEvaluation of mortality attributable to SARS-CoV-2 vaccine administration using national level data from Qatar
This study assesses the probability that deaths following a COVID-19 vaccination are attributable to the vaccine. The authors review all deaths that occurred within 30 days of vaccine receipt in Qatar until June 2022 and find that deaths attributable to vaccination are extremely rare.
- Adeel A. Butt
- , Mylai D. Guerrero
- & Abdul-Badi Abou-Samra
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Article
| Open AccessParatype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity
The bacterium Salmonella Paratyphi A causes paratyphoid fever. Here, the authors sequence over 800 isolates from South Asia, build a global database representing 37 countries, and develop a genotyping tool that identifies genomic variation and antimicrobial resistance markers for surveillance studies.
- Arif M. Tanmoy
- , Yogesh Hooda
- & Senjuti Saha
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| Open AccessMulti-organ imaging demonstrates the heart-brain-liver axis in UK Biobank participants
While heart disease, dementia and liver disease often co-occur, multi-organ imaging is needed for deeper elucidation of these cross-organ links. Here, the authors use image-derived phenotypes to describe underlying associations between heart, brain and liver health in a large population cohort.
- Celeste McCracken
- , Zahra Raisi-Estabragh
- & Stefan Neubauer
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| Open AccessThe burden of heatwave-related preterm births and associated human capital losses in China
Frequent heatwaves caused by global warming can lead to an increased risk of preterm birth, however, what remains unknown is the extent to which anthropogenic climate change has contributed to such burdens. Here, the authors combine health impact and economic assessment methods to comprehensively evaluate the entire preterm birth burden of heatwave exposure.
- Yali Zhang
- , Shakoor Hajat
- & Cunrui Huang
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Article
| Open AccessBA.2 and BA.5 omicron differ immunologically from both BA.1 omicron and pre-omicron variants
SARS-CoV-2 omicron variant BA.1 has shown increased transmissibility and immune escape, relative to previous SARS-CoV-2 variants. In this study, authors utilise antigenic cartography to characterise the neutralisation profiles of omicron sub-lineages, BA.2 and BA.5, in comparison to BA.1 and pre-omicron variants.
- Annika Rössler
- , Antonia Netzl
- & Janine Kimpel
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| Open AccessInferring time-varying generation time, serial interval, and incubation period distributions for COVID-19
The generation time (interval between successive infections in a transmission chain) is an important parameter for epidemiological modeling. Here, the authors develop a framework for estimating this parameter and how it changes over time and apply it to data from China in the first months of the pandemic.
- Dongxuan Chen
- , Yiu-Chung Lau
- & Sheikh Taslim Ali
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| Open AccessEffectiveness of ChAdOx1-S COVID-19 booster vaccination against the Omicron and Delta variants in England
Vaccine effectiveness of a ChAdOx1-S booster was estimated in a test-negative case-control study in England. Protection was found to be moderate against mild disease but remained high and comparable to that of an mRNA booster against hospitalisation with Omicron.
- Freja Cordelia Møller Kirsebom
- , Nick Andrews
- & Jamie Lopez Bernal
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| Open AccessAn umbrella review of the evidence linking oral health and systemic noncommunicable diseases
Previous studies have supported a potential bidirectional association between oral diseases and systemic noncommunicable diseases (NCDs) Here the authors perform an umbrella review of meta-analyses for the association between oral health and NCDs, and report that 27 NCDs were associated with oral disease, however, the overall strength of evidence was found to be unfavorable and with methodological inconsistencies.
- João Botelho
- , Paulo Mascarenhas
- & Vanessa Machado
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Article
| Open AccessThe gut microbiota and depressive symptoms across ethnic groups
Here, by studying a multi-ethnic cross-sectional urban cohort (N = 3211, 6 ethnic groups), the authors show that depressive symptom levels are related to the gut microbiota taxonomic characteristics but that these are largely invariant across ethnic groups.
- Jos A. Bosch
- , Max Nieuwdorp
- & Anja Lok
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Article
| Open AccessThe overlapping burden of the three leading causes of disability and death in sub-Saharan African children
In this disease mapping study, the authors estimate disability-adjusted life year rates for three of the major causes of mortality for children under five 43 countries in sub-Saharan Africa. They identify significant heterogeneity at the subnational level, highlighting the need for a targeted intervention approach.
- Robert C. Reiner Jr.
- , Catherine A. Welgan
- & Simon I. Hay
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| Open AccessA population-based serological study of post-COVID syndrome prevalence and risk factors in children and adolescents
The post-acute impacts of COVID-19 in children and adolescents are not well understood. In this population-based study in Geneva, the authors find evidence of COVID-19-related symptom persistence beyond 12 weeks in adolescents, and identify chronic conditions and lower socioeconomic status as risk factors.
- Roxane Dumont
- , Viviane Richard
- & Idris Guessous
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Article
| Open AccessEstimation of stillbirths attributable to ambient fine particles in 137 countries
Gestational exposure to ambient fine particles increases the risk of stillbirth, but the related disease burden is unknown, particularly in low- and middle-income countries (LMICs). Here, the authors combine state-of-the-art estimates on stillbirths, and multiple exposure–response functions to evaluate the burden in 137 countries.
- Tao Xue
- , Mingkun Tong
- & Tong Zhu
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Article
| Open AccessSeroepidemiology of enterovirus A71 infection in prospective cohort studies of children in southern China, 2013-2018
Hand, foot and mouth disease, caused by enterovirus A71 (EV-A71) infection, is common in children in China. Here, the authors estimate EV-A71 incidence and seroprevalence using data from two longitudinal cohorts and find that, despite high infection rates, a large proportion of children under 6 are susceptible.
- Juan Yang
- , Qiaohong Liao
- & Hongjie Yu
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Article
| Open AccessThrombosis and thrombocytopenia after vaccination against and infection with SARS-CoV-2 in the United Kingdom
Population-based studies can provide information on the safety of COVID-19 vaccines. Here the authors report the rates thrombosis and thrombocytopenia after vaccination against and infection with SARS-CoV-2 in the United Kingdom and compare them with the background (expected) rates in the general population.
- Edward Burn
- , Xintong Li
- & Daniel Prieto-Alhambra
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Article
| Open AccessThrombosis and thrombocytopenia after vaccination against and infection with SARS-CoV-2 in Catalonia, Spain
Population-based studies can provide information on the safety of COVID-19 vaccines. Here the authors report the rates of thrombosis and thrombocytopenia after vaccination against and infection with SARS-CoV-2 in Catalonia, Spain and compare them with the background (expected) rates in the general population.
- Edward Burn
- , Elena Roel
- & Talita Duarte-Salles
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| Open AccessEffectiveness of a third BNT162b2 mRNA COVID-19 vaccination during pregnancy: a national observational study in Israel
Data on the effectiveness of a third dose of COVID-19 vaccine in pregnant women are limited. In this observational study, the authors report that a third dose of the BNT162b2 mRNA COVID-19 vaccine during pregnancy enhances protection against maternal adverse COVID-19-related outcomes.
- Joshua Guedalia
- , Michal Lipschuetz
- & Ofer Beharier
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Article
| Open AccessDaylight saving time affects European mortality patterns
How daylight saving time shift (DST) affects mortality dynamics on a large population scale remains unknown. Here, the authors examine the impact of DST on all-cause mortality in 16 European countries for the period 1998-2012.
- Laurent Lévy
- , Jean-Marie Robine
- & François R. Herrmann
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Article
| Open AccessSafety and immunogenicity following a homologous booster dose of CoronaVac in children and adolescents
Few countries have approved SARS-CoV-2 booster doses in children and adolescents due to insufficient evidence about the safety and interval vaccination. Here, the authors assess the safety and immunogenicity of a homologous booster dose of CoronaVac in a cohort of 3–17 year olds.
- Lei Wang
- , Zhiwei Wu
- & Qiang Gao
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Article
| 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 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 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