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| Open AccessEvidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics
Amid the COVID-19 pandemic, accurate hospitalization predictions are vital. Here, the authors show that a deep learning model based on statistical mechanics is able to forecast hospitalizations, supporting targeted vaccination efforts.
- Junyi Gao
- , Joerg Heintz
- & Jimeng Sun
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Article
| Open AccessComparative mRNA booster effectiveness against death or hospitalization with COVID-19 pneumonia across at-risk US Veteran populations
mRNA boosters have been shown to be effective against severe COVID-19 illness. In this work, the authors show that in high-risk populations, three doses of mRNA-1273 vaccine instead of BNT162b2 vaccine conferred a small benefit against death or hospitalization with COVID-19 pneumonia.
- J. Daniel Kelly
- , Samuel Leonard
- & Salomeh Keyhani
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Article
| Open AccessLong COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program
The extent to which COVID-19 vaccination protects against long COVID is not well understood. Here, the authors use electronic health record data from the United States and find that, for people who received their vaccination prior to infection, vaccination was associated with lower incidence of long COVID.
- M. Daniel Brannock
- , Robert F. Chew
- & Stuart Katz
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Article
| Open AccessImpaired humoral immunity to BQ.1.1 in convalescent and vaccinated patients
Dewald et al. show a high Spike-IgG seroprevalence (95%) in a multicenter study with 1,411 participants. They determined a substantially reduced serum neutralization against the SARS-CoV-2 VOCs BA.4/5 and BQ.1.1. and explored predictive factors of neutralizing activity.
- Felix Dewald
- , Martin Pirkl
- & Florian Klein
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Article
| Open AccessDeep learning to estimate lung disease mortality from chest radiographs
Risk assessment of lung disease mortality is currently limited. Here, authors show that deep learning can estimate lung disease mortality from a chest x-ray beyond risk factors, which may help to identify individuals at risk in screening and cancer populations.
- Jakob Weiss
- , Vineet K. Raghu
- & Hugo J.W.L. Aerts
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Article
| Open AccessModelling the impact of interventions on imported, introduced and indigenous malaria infections in Zanzibar, Tanzania
Malaria elimination is defined by WHO as the absence of recent indigenous cases in an area. In this study, the authors develop a metapopulation model that identifies indigenous cases and use it to investigate the likelihood of malaria elimination in Zanzibar under different intervention scenarios.
- Aatreyee M. Das
- , Manuel W. Hetzel
- & Nakul Chitnis
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Article
| Open AccessThe impact of introduction of the 10-valent pneumococcal conjugate vaccine on pneumococcal carriage in Nigeria
Nigeria has the highest incidence of pneumococcal disease in Africa and introduced the 10-valent pneumococcal vaccine for infants between 2014 and 2016. Here, the authors conduct repeated cross-sectional surveys to analyse the impact of the vaccination campaign on pneumococcal carriage and serotype distribution.
- Aishatu L. Adamu
- , J. Ojal
- & Ifedayo M. O. Adetifa
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| Open AccessVirus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals
Monitoring the diversity of viruses infecting animals is important for assessing zoonotic risk. Here, the authors use metatranscriptomics to characterise the viromes of small mammals, pangolins, and zoo animals in China to identify potentially zoonotic viruses.
- Xinyuan Cui
- , Kewei Fan
- & Yongyi Shen
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Article
| Open AccessResurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong
Hong Kong experienced a large wave of COVID-19 in early 2022 driven by Omicron BA.2. Here, the authors describe the epidemiological dynamics of this wave and show discordant inferences based on genomic and epidemiological data that underscore the need to improve near real-time epidemic growth estimates.
- Ruopeng Xie
- , Kimberly M. Edwards
- & Vijaykrishna Dhanasekaran
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Article
| Open AccessMachine learning prediction of the degree of food processing
Evidence suggests that increased consumption of ultra-processed food has adverse health implications, however, it remains difficult to classify processed food. Here, the authors introduce FPro, a machine learning-based score predicting the degree of food processing.
- Giulia Menichetti
- , Babak Ravandi
- & Albert-László Barabási
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Article
| Open AccessHealth disparities among older adults following tropical cyclone exposure in Florida
Tropical cyclones pose a significant threat to human health. Here, authors show associations between tropical cyclones and risk of cause-specific hospitalizations, with elevated risks according to neighborhood-level poverty, homeownership and urbanicity.
- K. Burrows
- , G. B. Anderson
- & M. L. Bell
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Article
| Open AccessAccounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S.
SARS-CoV-2 seroprevalence surveys aim to estimate the proportion of the population that has been infected, but their accuracy depends on the characteristics of the test assay used. Here, the authors use statistical models to assess the impact of the use of different assays on estimates of seroprevalence in the United States.
- Bernardo García-Carreras
- , Matt D. T. Hitchings
- & Derek A. T. Cummings
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Article
| Open AccessDrivers of SARS-CoV-2 testing behaviour: a modelling study using nationwide testing data in England
SARS-CoV-2 testing rates have varied during the pandemic but the drivers of changes in testing behaviour are unclear. Here, the authors link national testing data from England to indicators of epidemic trends to describe how testing varies according to level of virus transmission, disease susceptibility/severity, public health measures, and risk perception.
- Younjung Kim
- , Christl A. Donnelly
- & Pierre Nouvellet
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Article
| Open AccessComparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas
The Amazonas region has been the most heavily affected by COVID-19 in Brazil. In this study, the authors conduct phylodynamic analyses to assess SARS-CoV-2 lineage replacement dynamics in the region and infer the impact of population immunity on the spread and severity of the Delta and Omicron variants.
- Ighor Arantes
- , Gonzalo Bello
- & Felipe Gomes Naveca
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| Open AccessEffectiveness of inactivated COVID-19 vaccines among older adults in Shanghai: retrospective cohort study
Inactivated COVID-19 vaccines have been widely used in China, but there is limited real-world evidence for their effectiveness in this setting. Here, the authors estimate effectiveness of inactivated vaccines for people aged 60 or older in Shanghai during a period when Omicron was the dominant circulating variant.
- Zhuoying Huang
- , Shuangfei Xu
- & Weibing Wang
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Article
| Open AccessThe evolution and international spread of extensively drug resistant Shigella sonnei
An increase in shigellosis cases among men who have sex with men in the United Kingdom has been linked to an extensively drug-resistant strain of Shigella sonnei. In this genomic epidemiology study, the authors investigate the genetic basis, evolutionary history, and international dissemination of the outbreak strain.
- Lewis C. E. Mason
- , David R. Greig
- & Kate S. Baker
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Article
| Open AccessData-driven analysis to understand long COVID using electronic health records from the RECOVER initiative
In this study, the authors characterise post-acute sequelae of SARS-CoV-2 (PASC) in two large cohorts based on electronic health records from the USA. They identify a broad range of PASC-related conditions which were only partially replicated across the two cohorts, indicating possible heterogeneity between populations.
- Chengxi Zang
- , Yongkang Zhang
- & Rainu Kaushal
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Article
| Open AccessLong-term measles antibody profiles following different vaccine schedules in China, a longitudinal study
The timing of measles vaccination in infants affects the risk of infection in young children and the duration of protection provided. Here, the authors investigate optimal vaccination timing by characterising antibody kinetics following different vaccine schedules in two cohorts of children in southern China.
- Qianli Wang
- , Wei Wang
- & Hongjie Yu
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Article
| Open AccessRisk of death following COVID-19 vaccination or positive SARS-CoV-2 test in young people in England
Rare but serious cardiac disease side effects have been linked to COVID-19 vaccinations, especially in young people. Here, the authors find very little evidence of an association between vaccination and mortality, except for in females after a non mRNA vaccine, but show an increased risk of death following COVID-19 infection
- Vahé Nafilyan
- , Charlotte R. Bermingham
- & James C. Doidge
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Article
| Open AccessThe genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain
Escherichia albertii is an emerging gastrointestinal pathogen that causes disease in humans and animals, notably birds. In this genomic epidemiology study, the authors investigate characteristics of isolates sampled from humans and birds in Great Britain and find that they tend to cluster separately.
- Rebecca J. Bengtsson
- , Kate S. Baker
- & Becki Lawson
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Article
| Open AccessTransmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemics
Accurately estimating the burden of tuberculosis is challenging due to incomplete registration systems and the relationship with HIV. Here, the authors develop a Bayesian modelling strategy accounting for these factors that estimates age- and country-specific annual risks of infection and the proportion resulting from recent infection.
- Peter J. Dodd
- , Debebe Shaweno
- & Helen Ayles
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| Open AccessPredicting vaccine effectiveness against severe COVID-19 over time and against variants: a meta-analysis
In this study, the authors perform a meta-analysis of COVID-19 vaccine effectiveness studies and compare observed protection against severe disease with model-based estimates of neutralising antibody titres. Their results show that SARS-CoV-2 antibody titres are predictive of protection against severe COVID-19 disease.
- Deborah Cromer
- , Megan Steain
- & Miles P. Davenport
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Article
| Open AccessSpatial immunization to abate disease spreading in transportation hubs
Efficient spatial targeting of interventions could reduce the spread of infections in transportation hubs. Here, the authors assess the optimal locations to target in Heathrow airport using disease transmission models informed by a contact network based on anonymised location data from 200,000 individuals.
- Mattia Mazzoli
- , Riccardo Gallotti
- & José J. Ramasco
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Article
| Open AccessNon-falciparum malaria infection and IgG seroprevalence among children under 15 years in Nigeria, 2018
Nigeria has a high burden of malaria which mostly results from Plasmodium falciparum infection, but other species are also endemic. Here, the authors estimate the prevalence of active infection and previous exposure to P malariae, P ovale, and P vivax in children in Nigeria in 2018 and determine risk factors.
- Camelia Herman
- , Colleen M. Leonard
- & Eric Rogier
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Article
| 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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Article
| 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 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 AccessAssociations of timing of physical activity with all-cause and cause-specific mortality in a prospective cohort study
There is a growing interest in the role of timing of physical activity (PA) in improving health. Here, using a large-scale cohort study, the authors show that moderate-to-vigorous PA at the optimal time of day robustly predicts lower mortality risk and may maximize the beneficial effect of PA.
- Hongliang Feng
- , Lulu Yang
- & Jihui Zhang
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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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| Open AccessA scoping review of the impacts of COVID-19 physical distancing measures on vulnerable population groups
Physical distancing measures introduced to control the spread of COVID-19 had socio-economic trade-offs that may have particularly impacted vulnerable population groups. Here, the authors perform a scoping review and summarise the impacts on different vulnerable groups described in 265 studies.
- Lili Li
- , Araz Taeihagh
- & Si Ying Tan
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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 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 AccessProviding normative information increases intentions to accept a COVID-19 vaccine
The authors show that accurate information about descriptive norms can increase intentions to accept a vaccine for COVID-19. They show that these effects are largely consistent in the 23 included countries and are concentrated among people who were otherwise uncertain about accepting a vaccine.
- Alex Moehring
- , Avinash Collis
- & Dean Eckles
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Article
| 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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| Open AccessCreative arts and digitial interventions as potential tools in prevention and recovery from the mental health consequences of adverse childhood experiences
Adverse childhood experiences (ACEs) can harm mental health across the lifespan and reduce life expectancy. We provide a commentary of evidence on the health impacts, and how creative arts and digital interventions may support prevention and recovery.
- Kamaldeep Bhui
- , Sania Shakoor
- & Michaela Otis
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Article
| 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 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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Article
| 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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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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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 AccessValidation of Food Compass with a healthy diet, cardiometabolic health, and mortality among U.S. adults, 1999–2018
The Food Compass is a nutrient profiling system to characterize the healthfulness of diverse foods, beverages and meals. In a nationally representative cohort of 47,999 U.S. adults, the authors validate a person’s individual Food Compass Score against health outcomes.
- Meghan O’Hearn
- , Joshua Erndt-Marino
- & Dariush Mozaffarian
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Article
| Open AccessGlobal disparities in SARS-CoV-2 genomic surveillance
In this study, the authors provide a global overview of SARS-CoV-2 genome sequencing, and estimate the proportion of cases sequenced and time to genome upload. They identify disparities and highlight the need to strengthen surveillance in lower and middle income countries.
- Anderson F. Brito
- , Elizaveta Semenova
- & Nuno R. Faria
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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 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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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