Longitudinal Surveillance Study Research Articles

Longitudinal genomics reveals carbapenem-resistant Acinetobacter baumannii population changes with emergence of highly resistant ST164 clone

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a persistent nosocomial pathogen that poses a significant threat to global public health, particularly in intensive care units (ICUs). Here we report a three-month longitudinal genomic surveillance study conducted in a Hangzhou ICU in 2021. This followed a three-month study conducted in the same ICU in 2019, and infection prevention and control (IPC) interventions targeting patients, staff and the ICU environment. Most A. baumannii isolated in this ICU in 2021 were CRAB (80.9%; 419/518) with higher-level resistance to carbapenems. This was accompanied by the proportion of global clone 2 (GC2) isolates falling from 99.5% in 2019 to 50.8% (213/419) in 2021. The phylogenetic diversity of GC2 increased, apparently driven by regular introductions of distinct clusters in association with patients. The remaining CRAB (40.2%; 206/419) were a highly clonal population of ST164. Isolates of ST164 carried blaNDM-1 and blaOXA-23 carbapenemase genes, and exhibited higher carbapenem MIC50/MIC90 values than GC2. Comparative analysis of publicly available genomes from 26 countries (five continents) revealed that ST164 has evolved towards carbapenem resistance on multiple independent occasions. Its success in this ICU and global capacity for acquiring resistance determinants indicate that ST164 CRAB is an emerging high-risk lineage of global concern.

Epidemiological characterization of hand, foot, and mouth disease among hospitalized children from 2014 to 2023 in a hospital in Henan Province: Longitudinal surveillance study.

Hand, foot, and mouth disease (HFMD) is an acute infectious illness primarily caused by enteroviruses. The present study aimed to describe the epidemiological characteristics of hospitalized HFMD patients in a hospital in Henan Province (Zhengzhou, China), and to predict the future epidemiological parameters. In this study, we conducted a retrospective analysis of general demographic and clinical data on hospitalized children who were diagnosed with HFMD from 2014 to 2023. We used wavelet analysis to determine the periodicity of the disease. We also conducted an analysis of the impact of the COVID-19 epidemic on the detection ratio of severe illness. Additionally, we employed a Seasonal Difference Autoregressive Moving Average (SARIMA) model to forecast characteristics of future newly hospitalized HFMD children. A total of 19 487 HFMD cases were included in the dataset. Among these cases, 1515 (7.8%) were classified as severe. The peak incidence of HFMD typically fell between May and July, exhibiting pronounced seasonality. The emergence of COVID-19 pandemic changed the ratio of severe illness. In addition, the best-fitted seasonal ARIMA model was identified as (2,0,2)(1,0,1)12. The incidence of severe cases decreased significantly following the introduction of the vaccine to the market (χ2 = 109.9, p < 0.05). The number of hospitalized HFMD cases in Henan Province exhibited a seasonal and declining trend from 2014 to 2023. Non-pharmacological interventions implemented during the COVID-19 pandemic have led to a reduction in the incidence of severe illness.

Coccidioidomycosis seasonality in California: a longitudinal surveillance study of the climate determinants and spatiotemporal variability of seasonal dynamics, 2000–2021

Coccidioidomycosis, an emerging fungal disease in the western USA, exhibits seasonal patterns that are poorly understood, including periods of strong cyclicity, aseasonal intervals, and variation in seasonal timing that have been minimally characterized, and unexplained as to their causal factors. Coccidioidomycosis incidence has increased markedly in recent years, and our limited understanding of intra- and inter-annual seasonality has hindered the identification of important drivers of disease transmission, including climate conditions. In this study, we aim to characterize coccidioidomycosis seasonality in endemic regions of California and to estimate the relationship between drought conditions and coccidioidomycosis seasonal periodicity and timing. We analysed data on all reported incident cases of coccidioidomycosis in California from 2000 to 2021 to characterize seasonal patterns in incidence, and conducted wavelet analyses to assess the dominant periodicity, power, and timing of incidence for 17 counties with consistently high incidence rates. We assessed associations between seasonality parameters and measures of drought in California using a distributed lag nonlinear modelling framework. All counties exhibited annual cyclicity in incidence (i.e., a dominant wavelet periodicity of 12 months), but there was considerable heterogeneity in seasonal strength and timing across regions and years. On average, 12-month periodicity was most pronounced in the Southern San Joaquin Valley and Central Coast. Further, the annual seasonal cycles in the Southern San Joaquin Valley and the Southern Inland regions occurred earlier than those in coastal and northern counties, yet the timing of annual cycles became more aligned among counties by the end of the study period. Drought conditions were associated with a strong attenuation of the annual seasonal cycle, and seasonal peaks became more pronounced in the 1-2 years after a drought ended. We conclude that drought conditions do not increase the risk of coccidioidomycosis onset uniformly across the year, but instead promote increased risk concentrated within a specific calendar period (September to December). The findings have important implications for public health preparedness, and for how future shifts in seasonal climate patterns and extreme events may impact spatial and temporal coccidioidomycosis risk. National Institutes of Health.

Trends and Predictors of Students’ Academic Performances by Levels of Study in University of Health and Allied Sciences in Ghana: A Longitudinal Surveillance Study Among a Cohort of 2020 Graduating Class of Undergraduates at the School of Allied Health Sciences in Ho North Campus

Background: Ascertainment of trends and predictors of academic performances among Allied Health students is critical to United Nation’s Sustainable Development Goals 3, 4 and 8. This article assesses the dynamics and academic risk factors associated with students’ performances at the University of Health and Allied Sciences (UHAS), Ghana. Method: This is a longitudinal cohort study, designed to evaluate retrospectively, the academic records of 180 students of the 2020 graduating class of undergraduates in the School of Allied Health Sciences. The published grades of each student from levels 100 to 400 were collated using a data extraction log that was quality controlled, double-entered and statistically analysed using Microsoft Visual Basic and STATA platforms respectively. The trends and predictors of academic performances by levels were determined using the Cochrane-Armitage test for trends and the Cochran-Martin-Haenszel test for association respectively. Results: The mean rates of scoring grades ‘A’, ‘B+’, ‘B’, ‘C’, ‘D’ and ‘E/F’ among this cohort were 22.2%, 21.2%, 23.3%, 25.8%, 7.9% and 0.5% respectively. The inter-variations in a proportion of grades within the levels were statistically significant (p&lt;0.01). However, the intra-variations in proportional distribution of grades trended insignificantly across the levels (p&gt;0.05). Although, the Spearman’s coefficient depicted a strong negative correlation between grade ‘A’ and levels (r= -0.9); the associations were only between grade ‘A’ and level 200s (OR=1.9; CI: 1.05-1. 33, p&lt;0.001) and between grade ‘A’ and level 300 (OR=1.4;(CI: 1.25-1.59), p&lt;0.001). Conclusion: The cumulative proportion of 43.4% students scoring grade ‘A’ and ‘B +’ reflected above average performances in SAHS. However the distribution of grades on Gaussian curve deviates the Central Limit Theorem. In addition, the observed negative correlation between trends of grade ‘A’ from lower (100) to high (400) levels of studies deviates Bloom’s and SOLO Taxonomies, and Trans-Theoretical Model (TTM) of assessing students’ learning progression. These phenomena have Quality Assurance, Academic Policy and Research implications. Therefore, the use of modify (hybrid) grading System is strongly recommended in SAHS. Also, we strongly recommend an extended study to determine factors that affect the poor performances of levels 100 and 400 students in SAHS.

Prevalence of SARS-CoV-2 antibodies and associated factors in the adult population of Belgium: a general population cohort study between March 2021 and April 2022

BackgroundThis study assessed seroprevalence trends of SARS-CoV-2 antibodies in the Belgian adult population between March 2021 and April 2022, and explored factors associated with seropositivity and seroreversion among the vaccinated and unvaccinated population.MethodsA prospective longitudinal surveillance study was conducted within a random sample of the general population (18 + years) in Belgium, selected from the national register through a multistage sampling design. Participants provided a saliva sample and completed a survey questionnaire on three occasions: at baseline and in two follow-up waves. Outcome variables included (1) seropositivity, defined as the presence of SARS-CoV-2 antibodies, assessed with a semi-quantitative measure of anti-RBD (Receptor Binding Domain) IgG ELISA and (2) seroreversion, defined as passing from a positive to a negative antibody test between two measurements. Trends in SARS-CoV-2 antibody prevalence were assessed using binary logistic regression with contrasts applying post-stratification. Potential determinants of seropositivity were assessed through multilevel logistic regressions.ResultsIn total 6,178 valid observations were obtained from 2,768 individuals. SARS-CoV-2 antibody prevalence increased from 25.1% in the beginning of the study period to 92.3% at the end. Among the vaccinated population, factors significantly associated with higher seropositivity rates were being younger, having a bachelor diploma, living with others, having had a vaccine in the last 3 months and having received a nucleic-acid vaccine or a combination. Lower seropositivity rates were observed among vaccinated people with a neurological disease and transplant patients. Factors significantly associated with higher seropositivity rates among the unvaccinated population were having non-O blood type and being non-smoker. Among vaccinated people, the seroreversion rate was much lower (0.3%) in those who had received their latest vaccine in the last 3 months compared to those who had received their latest vaccine more than 3 months ago (2.7%) (OR 0.13; 95%CI 0.04–0.42).ConclusionsThe rapid increase in antibody seropositivity in the general adult population in Belgium during the study period was driven by the vaccination campaign which ran at full speed during this period. Among vaccinated people, seropositivity varied in function of the time since last vaccine, the type of vaccine, sociodemographic features and health status.

Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage

The origin of novel SARS-CoV-2 spike sequences found in wastewater, without corresponding detection in clinical specimens, remains unclear. We sought to determine the origin of one such cryptic wastewater lineage by tracking and characterising its persistence and genomic evolution over time. We first detected a cryptic lineage, WI-CL-001, in municipal wastewater in Wisconsin, USA, in January, 2022. To determine the source of WI-CL-001, we systematically sampled wastewater from targeted sub-sewershed lines and maintenance holes using compositing autosamplers. Viral concentrations in wastewater samples over time were measured by RT digital PCR. In addition to using metagenomic 12s rRNA sequencing to determine the virus's host species, we also sequenced SARS-CoV-2 spike receptor binding domains, and, where possible, whole viral genomes to identify and characterise the evolution of this lineage. We traced WI-CL-001 to its source at a single commercial building. There we detected the cryptic lineage at concentrations as high as 2·7× 109 genome copies per L. The majority of 12s rRNA sequences detected in wastewater leaving the identified source building were human. Additionally, we generated over 100 viral receptor binding domain and whole-genome sequences from wastewater samples containing the cryptic lineage collected over the 13consecutive months this virus was detectable (January, 2022, to January, 2023). These sequences contained a combination of fixed nucleotide substitutions characteristic of Pango lineage B.1.234, which circulated in humans in Wisconsin at low levels from October, 2020, to February, 2021. Despite this, mutations in the spike gene and elsewhere resembled those subsequently found in omicron variants. We propose that prolonged detection of WI-CL-001 in wastewater indicates persistent shedding of SARS-CoV-2 from a single human initially infected by an ancestral B.1.234 virus. The accumulation of convergent omicron-like mutations in WI-CL-001's ancestral B.1.234 genome probably reflects persistent infection and extensive within-host evolution. People who shed cryptic lineages could be an important source of highly divergent viruses that sporadically emerge and spread. The Rockefeller Foundation, Wisconsin Department of Health Services, Centers for Disease Control and Prevention, National Institute on Drug Abuse, and the Center for Research on Influenza Pathogenesis and Transmission.

Swine influenza A virus infection dynamics and evolution in intensive pig production systems.

Swine influenza A virus (swIAV) is one of the main viral pathogens responsible for respiratory disease in farmed pigs. While outbreaks are often epidemic in nature, increasing reports suggest that continuous, endemic infection of herds is now common. The move towards larger herd sizes and increased intensification in the commercial pig industry may promote endemic infection; however, the impact that intensification has on swIAV infection dynamics and evolution is unclear. We carried out a longitudinal surveillance study for over 18 months on two enzootically infected, intensive, indoor, and multi-site pig production flows. Frequent sampling of all production stages using individual and group sampling methods was performed, followed by virological and immunological testing and whole-genome sequencing. We identified weaned pigs between 4 and 12-weeks old as the main reservoir of swIAV in the production flows, with continuous, year-round infection. Despite the continuous nature of viral circulation, infection levels were not uniform, with increasing exposure at the herd level associated with reduced viral prevalence followed by subsequent rebound infection. A single virus subtype was maintained on each farm for the entire duration of the study. Viral evolution was characterised by long periods of stasis punctuated by periods of rapid change coinciding with increasing exposure within the herd. An accumulation of mutations in the surface glycoproteins consistent with antigenic drift was observed, in addition to amino acid substitutions in the internal gene products as well as reassortment exchange of internal gene segments from newly introduced strains. These data demonstrate that long-term, continuous infection of herds with a single subtype is possible and document the evolutionary mechanisms utilised to achieve this.

Evolution of the burden of diabetes among adults and children in Québec, Canada, from 2001 to 2019: A population-based longitudinal surveillance study

IntroductionMany developed countries, including Canada, have observed reductions in incidence of diabetes. Given the latest improvements in the case definition of diabetes for the younger population in Quebec, Canada, we sought to examine the evolution of diabetes among adults and children in Quebec, between 2001 and 2019. MethodsCrude and age-standardized incidence and prevalence of diabetes among individuals ≥1 year were calculated using data from the Quebec Integrated Chronic Disease Surveillance System (n≈8,351,500 in 2019), using two case definitions for adults and the youth respectively. Age-standardized all-cause hospitalizations and mortality proportions were calculated among the population ≥20 years. ResultsBetween 2001 and 2019, age-standardized incidence decreased by 30%, with a crude incidence of 4.6 per 1,000 in 2019. Incidence rates decreased from age group ≥50 years but increased by 25% for the group of 1-19 years. Age-standardized prevalence increased by 42% (crude prevalence in 2019: 8.1%). Males had higher incidence and prevalence of diabetes, with an incremental gap between sexes increasing with age. All-cause hospitalization and mortality proportions among individuals with diabetes declined by 21% and 29% respectively between 2001 and 2019. Age-standardized hospitalizations and mortality ratios for individuals with/without diabetes remained stable and were 2.7 (99% Confidence Intervals [CI]: 2.7-2.8) and 2.2 (99% CI: 2.1-2.3) in 2019, respectively. ConclusionDespite the reduction of incidence among adults, diabetes incidence increased among the youth and remained high among adults, especially for males. These results highlight the importance of improving earlier preventive care and initiatives for reducing the diabetes burden in Quebec.

Perceptions of lung function surveillance in urban firefighters.

Workplace health and safety (WHS) is an important responsibility falling on both employers and employees and is most effective when the perspectives of all stakeholders are considered. This study aimed to explore the facilitators and barriers to a voluntary workplace lung function surveillance program from the perspective of urban firefighters and describe their perceptions of its value. Using a qualitative, descriptive methodology, firefighters who had participated in a longitudinal lung function surveillance study were invited to participate in semi-structured interviews. Purposeful, maximum variation sampling was used to achieve diversity in those firefighters invited to participate. We used inductive content analysis to identify themes. Interviews with 15 firefighters identified 3 main themes: (i) practical experience of surveillance (administration, communication, workplace culture change, convenience, acceptability, and appeal); (ii) value of surveillance (lung health efficacy and control, social support, workplace management support/motivations, contribution to global firefighter health); and (iii) contribution of surveillance to health (occupational risk, relevance in the context of total health, workability, and fitness and future value). Practical and psychosocial facilitators and barriers to providing lung function surveillance in the fire service were identified. In addition to the personal benefits of detecting adverse lung health and allowing for medical intervention, factors known to positively influence firefighter workplace wellbeing, such as providing peace of mind, feedback on good work practices, motivation to utilize control measures, management commitment to health, and providing data to assist with global knowledge were valued aspects of longitudinal lung function surveillance.

A longitudinal environmental surveillance study for SARS-CoV-2 from the emergency department of a teaching hospital in Hong Kong

Understanding factors associated with SARS-CoV-2 exposure risk in the hospital setting may help improve infection control measures for prevention. To monitor SARS-CoV-2 exposure risk among healthcare workers and to identify risk factors associated with SARS-CoV-2 detection. Surface and air samples were collected longitudinally over 14 months spanning 2020-2022 at the Emergency Department (ED) of a teaching hospital in Hong Kong. SARS-CoV-2 viral RNA was detected by real-time reverse-transcription polymerase chain reaction. Ecological factors associated with SARS-CoV-2 detection were analysed by logistic regression. A sero-epidemiological study was conducted in January to April 2021 to monitor SARS-CoV-2 seroprevalence. A questionnaire was used to collect information on job nature and use of personal protective equipment (PPE) of the participants. SARS-CoV-2 RNA was detected at low frequencies from surfaces (0.7%, n=2562) and air samples (1.6%, n=128). Crowding was identified as the main risk factor, as weekly ED attendance (OR=1.002, p=0.04) and sampling after peak-hours of ED attendance (OR=5.216, p=0.03) were associated with the detection of SARS-CoV-2 viral RNA from surfaces. The low exposure risk was corroborated by the zero seropositive rate among 281 participants by April 2021. Crowding may introduce SARS-CoV-2 into ED through increased attendances. Multiple factors may have contributed to the low contamination of SARS-CoV-2 at the ED, including hospital infection control measures for screening ED attendees, high PPE compliance among healthcare workers, and various public health and social measures implemented to reduce community transmission in Hong Kong where a dynamic zero COVID-19 policy was adopted.

Epidemiological Characteristics of Respiratory Syncytial Virus Infection Among Hospitalized Children With Acute Respiratory Tract Infections From 2014 to 2022 in a Hospital in Hubei Province, China: Longitudinal Surveillance Study.

Longitudinal studies characterizing the epidemic trend of respiratory syncytial virus (RSV) in Hubei Province are scarce. We aimed to depict the dynamics of the RSV epidemic among hospitalized children with acute respiratory tract infections (ARTIs) during 2014 to 2022 in the Maternal and Child Health Hospital of Hubei Province and investigate the influence of the 2-child policy and the COVID-19 pandemic on RSV prevalence. The medical records and testing results of hospitalized children with ARTI from January 2014 to June 2022 were extracted. Nasopharyngeal samples were tested with direct immunofluorescence assay. Detection rates of RSV were categorized according to the diagnosis of patients: (1) overall, (2) upper respiratory tract infection (URTI), and (3) lower respiratory tract infection (LRTI). Poisson regression models were used to investigate the association between RSV detection rate and age, gender, or diagnosis. The detection rates of RSV before and after the implementation of the universal 2-child policy were compared using a Poisson regression model. Multiple comparisons of RSV detection rates were conducted among 3 stages of the COVID-19 pandemic using chi-square tests. Seasonal autoregressive integrated moving average was performed to predict RSV behaviors from February 2020 to June 2020 under the assumption of a non-COVID-19 scenario. Among 75,128 hospitalized children with ARTI, 11.1% (8336/75,128) were RSV-positive. Children aged <1 year had higher detection rates than older children (4204/26,498, 15.9% vs 74/5504, 1.3%; P<.001), and children with LRTI had higher detection rates than children with URTI (7733/53,145, 14.6% vs 603/21,983, 2.7%; P<.001). Among all the children, a clear seasonal pattern of the RSV epidemic was observed before 2021. Most of the highest detection rates were concentrated between December and February. The yearly detection rate of RSV remained at a relatively low level (about 8%) from 2014 to 2017, then increased to 12% and above from 2018. The highest monthly detection rate was in December 2018 (539/1493, 36.1%), and the highest yearly rate was in 2021 (1372/9328, 14.7%). There was a moderate increase in the RSV detection rate after the 2-child policy was implemented (before: 860/10,446, 8.2% vs after: 4920/43,916, 11.2%; P<.001). The largest increase, by 5.83%, occurred in children aged <1 year. The RSV epidemic level decreased sharply in the short term after the COVID-19 outbreak (detection rate before: 1600/17,010, 9.4% vs after: 32/1135, 2.8%; P<.001). The largest decrease, by 12.0%, occurred in children aged <1 year, but a rebounding epidemic occurred after 2020 (680/5744, 11.8%; P<.001). Children have been experiencing increased prevalence of RSV since 2018 based on surveillance from a hospital in Hubei Province with a large sample size. The 2-child policy might have increased the RSV prevalence, and the COVID-19 epidemic had a temporary inhibitory effect on RSV transmission. Vaccines against RSV are urgently needed.

Real-time sewage surveillance for SARS-CoV-2 in Dhaka, Bangladesh versus clinical COVID-19 surveillance: a longitudinal environmental surveillance study (December, 2019–December, 2021)

Clinical surveillance for COVID-19 has typically been challenging in low-income and middle-income settings. From December, 2019, to December, 2021, we implemented environmental surveillance in a converging informal sewage network in Dhaka, Bangladesh, to investigate SARS-CoV-2 transmission across different income levels of the city compared with clinical surveillance. All sewage lines were mapped, and sites were selected with estimated catchment populations of more than 1000 individuals. We analysed 2073 sewage samples, collected weekly from 37 sites, and 648 days of case data from eight wards with varying socioeconomic statuses. We assessed the correlations between the viral load in sewage samples and clinical cases. SARS-CoV-2 was consistently detected across all wards (low, middle, and high income) despite large differences in reported clinical cases and periods of no cases. The majority of COVID-19 cases (26 256 [55·1%] of 47 683) were reported from Ward 19, a high-income area with high levels of clinical testing (123 times the number of tests per 100 000 individuals compared with Ward 9 [middle-income] in November, 2020, and 70 times the number of tests per 100 000 individuals compared with Ward 5 [low-income] in November, 2021), despite containing only 19·4% of the study population (142 413 of 734 755 individuals). Conversely, a similar quantity of SARS-CoV-2 was detected in sewage across different income levels (median difference in high-income vs low-income areas: 0·23 log10 viral copies + 1). The correlation between the mean sewage viral load (log10 viral copies + 1) and the log10 clinical cases increased with time (r = 0·90 in July-December, 2021 and r=0·59 in July-December, 2020). Before major waves of infection, viral load quantity in sewage samples increased 1-2 weeks before the clinical cases. This study demonstrates the utility and importance of environmental surveillance for SARS-CoV-2 in a lower-middle-income country. We show that environmental surveillance provides an early warning of increases in transmission and reveals evidence of persistent circulation in poorer areas where access to clinical testing is limited. Bill & Melinda Gates Foundation.

SARS-Cov-2 Infection and Seroconversion Rates in Healthcare Providers Prior to COVID-19 Vaccine Rollout.

A 6-month longitudinal surveillance study of asymptomatic healthcare providers (HCP) was carried out at a large urban academic medical center in the United States to assess whether their job occupation with higher exposure risks to SARS-CoV-2 would equate with higher risk of contracting COVID-19 at the beginning of the pandemic before COVID-19 vaccines were available. A longitudinal cohort study design was used to collect and analyze immunological and virological monitoring data and self-report survey assessments of personal protective equipment (PPE) availability, adherence to infection control guidelines, and time spent on COVID-19 wards. Among 289 eligible participants, SARS-CoV-2 exposure risk was high with 48-69% participants working in COVID-19 units and more than 30% of them caring for COVID-19 patients. However, the seroconversion rate was low with only 2.1% of participants developing humoral or cellular immunity against SARS-CoV-2. Our study findings suggest that, for this HCP cohort working at a large urban academic medical center, a low incidence of SARS-CoV-2 infection could be maintained under conditions of strict infection prevention protocols and reliable PPE availability.

530. Characterization of the Proteomic Changes via SARS-CoV-2 Infection or Vaccination in the COVID-19 Community Research Partnership (CCRP)

Abstract Background There remain important gaps in knowledge concerning the effects of SARS-CoV-2 infection or vaccination on the human blood proteome. Methods The CCRP is a longitudinal surveillance study with information on SARS-CoV-2 infections, vaccinations and associated humoral immune responses in over 37,000 individuals. We selected a sample of blood spots cards (n=510) from serum antibody studies obtained between October 2020 and April 2021 for mass spectrometry proteomics analysis covering 540 unique plasma proteins. We analyzed the quantified protein differences based on dried blood samples obtained before and after infection or vaccination among previously non-infected individuals (immune naïve) after adjustment for batch effects, age, sex, or prior diagnosis of cancer, cardiovascular or autoimmune disease, or diabetes. The majority of infected individuals were minimally symptomatic. Differentially expressed proteins were considered significant with an FDR adjusted p-value of &amp;lt; 0.05 and log2 fold change (L2FC) &amp;gt;0.2. Results We found 11 and 12 proteins differentially expressed proteins in the naïve/infected and naïve/vaccinated people respectively, of which 10 were shared. Hepatocyte growth factor receptor (HGF) was upregulated (L2FC 0.24; p &amp;lt; 0.001) only in those who were infected while fibrillarin (L2FC -0.24; p&amp;lt; 0.001) and lambda-crystallin homolog (L2FC -0.29, p &amp;lt; 0.001) were downregulated only in the vaccinated samples (Fig 1). The remaining DE protein were associated with a wide array of functions including metabolic, cytostructural, extracellular matrix and DNA regulatory processes. Conclusion We found changes in the proteome both from infection and vaccination. HGF, elevated in the infected, has been associated with endothelial inflammation, upregulation of pro-inflammatory cytokines to reduce lung fibrosis and is known to promote tissue repair. Fibrillarin, downregulated in the vaccinated, has been associated with higher rates of bacterial and viral clearance, inflammation reduction, and increased cell survival. These findings suggest detectable complex inflammation from mild to moderate infections. Further investigation is required to understand the mechanism of action and clinical implication of these findings. Disclosures All Authors: No reported disclosures.

Phenotypic and functional changes of T cell subsets after CoronaVac vaccination

BackgroundThe pandemic coronavirus disease 2019 (COVID-19) is a major global public health concern and several protective vaccines, or preventive/therapeutic approaches have been developed. Sinovac-CoronaVac, an inactivated whole virus vaccine, can protect against severe COVID-19 disease and hospitalization, but less is known whether it elicits long-term T cell responses and provides prolonged protection. MethodsThis is a longitudinal surveillance study of SARS-CoV-2 receptor binding domain (RBD)-specific IgG levels, neutralizing antibody levels (NAb), T cell subsets and activation, and memory B cells of 335 participants who received two doses of CoronaVac. SARS-CoV-2 RBD-specific IgG levels were measured by enzyme-linked immunosorbent assay (ELISA), while NAb were measured against two strains of SARS-CoV-2, the Wuhan and Delta variants. Activated T cells and subsets were identified by flow cytometry. Memory B and T cells were evaluated by enzyme-linked immune absorbent spot (ELISpot). FindingsTwo doses of CoronaVac elicited serum anti-RBD antibody response, elevated B cells with NAb capacity and CD4+ T cell-, but not CD8+ T cell-responses. Among the CD4+ T cells, CoronaVac activated mainly Th2 (CD4+ T) cells. Serum antibody levels significantly declined three months after the second dose. InterpretationCoronaVac mainly activated B cells but T cells, especially Th1 cells, were poorly activated. Activated T cells were mainly Th2 biased, demonstrating development of effector B cells but not long-lasting memory plasma cells. Taken together, these results suggest that protection with CoronaVac is short-lived and that a third booster dose of vaccine may improve protection.

Early SARS-CoV-2 dynamics and immune responses in unvaccinated participants of an intensely sampled longitudinal surveillance study

BackgroundA comprehensive understanding of the SARS-CoV-2 infection dynamics and the ensuing host immune responses is needed to explain the pathogenesis as it relates to viral transmission. Knowledge gaps exist surrounding SARS-CoV-2 in vivo kinetics, particularly in the earliest stages after exposure.MethodsAn ongoing, workplace clinical surveillance study was used to intensely sample a small cohort longitudinally. Nine study participants who developed COVID-19 between November, 2020 and March, 2021 were monitored at high temporal resolution for three months in terms of viral loads as well as associated inflammatory biomarker and antibody responses. CD8 + T cells targeting SARS-CoV-2 in blood samples from study participants were evaluated.ResultsHere we show that the resulting datasets, supported by Bayesian modeling, allowed the underlying kinetic processes to be described, yielding a number of unexpected findings. Early viral replication is rapid (median doubling time, 3.1 h), providing a narrow window between exposure and viral shedding, while the clearance phase is slow and heterogeneous. Host immune responses different widely across participants.ConclusionsResults from our small study give a rare insight into the life-cycle of COVID-19 infection and hold a number of important biological, clinical, and public health implications.

Effects of precipitation, heat, and drought on incidence and expansion of coccidioidomycosis in western USA: a longitudinal surveillance study

Drought is an understudied driver of infectious disease dynamics. Amidst the ongoing southwestern North American megadrought, California (USA) is having the driest multi-decadal period since 800 CE, exacerbated by anthropogenic warming. In this study, we aimed to examine the influence of drought on coccidioidomycosis, an emerging infectious disease in southwestern USA. We analysed California census tract-level surveillance data from 2000 to 2020 using generalised additive models and distributed monthly lags on precipitation and temperature. We then developed an ensemble prediction algorithm of incident cases of coccidioidomycosis per census tract to estimate the counterfactual incidence that would have occurred in the absence of drought. Between April 1, 2000, and March 31, 2020, there were 81 448 reported cases of coccidioidomycosis throughout California. An estimated 1467 excess cases of coccidioidomycosis were observed in California in the 2 years following the drought that occurred between 2007 and 2009, and an excess 2649 drought-attributable cases of coccidioidomycosis were observed in the 2 years following the drought that occurred between 2012 and 2015. These increased numbers of cases more than offset the declines in cases that occurred during drought. An IQR increase in summer temperatures was associated with 2·02 (95% CI 1·84-2·22) times higher incidence in the following autumn (September to November), and an IQR increase in precipitation in the winter was associated with 1·45 (1·36-1·55) times higher incidence in the autumn. The effect of winter precipitation was 36% (25-48) stronger when preceded by two dry, rather than average, winters. Incidence in arid counties was most sensitive to precipitation fluctuations, while incidence in wetter counties was most sensitive to temperature. In California, multi-year cycles of dry conditions followed by a wet winter increases transmission of coccidioidomycosis, especially in historically wetter areas. With anticipated increasing frequency of drought in southwestern USA, continued expansion of coccidioidomycosis, along with more intense seasons, is expected. Our results motivate the need for heightened precautions against coccidioidomycosis in seasons that follow major droughts. National Institutes of Health.

The impact of enterovirus A71 vaccination program on hand, foot, and mouth disease in Guangdong, China: A longitudinal surveillance study

Enterovirus A71 (EV71) vaccination program was introduced in 2016 in China. Based on a longitudinal surveillance dataset from 2012 to 2019 in Guangdong, China, we estimated the impact of the EV71 vaccination program on hand, foot, and mouth disease (HFMD) incidence, by using a counterfactual prediction made from synthetic control approach integrated with a Bayesian time-series model. We observed a relative reduction of 41.4% for EV71-associated HFMD cases during the post-vaccination period of 2017–2019, corresponding to 26,226 cases averted. The reduction of EV71-associated HFMD cases raised with the elevation of EV71 vaccine coverage by year. We found an indirect effect for the children aged 6–14 years who were less likely to be vaccinated. Whereas, the EV71 vaccine may not protect against non-EV71-associated HFMD. This study provides a template for ongoing public health surveillance of EV71 vaccine effectiveness with a counterfactual study design. Our results show strong evidence of the EV71 vaccination program working on reducing EV71-associated HFMD in real-world settings. The finding will benefit policy-making of EV71 vaccination and the prevention of HFMD.

Self-reported mask use among persons with or without SARS CoV-2 vaccination —United States, December 2020–August 2021

Wearing a facemask can help to decrease the transmission of COVID-19. We investigated self-reported mask use among subjects aged 18 years and older participating in the COVID-19 Community Research Partnership (CRP), a prospective longitudinal COVID-19 surveillance study in the mid-Atlantic and southeastern United States. We included those participants who completed ≥5 daily surveys each month from December 1, 2020 through August 31, 2021. Mask use was defined as self-reported use of a face mask or face covering on every interaction with others outside the household within a distance of less than 6 feet. Participants were considered vaccinated if they reported receiving ≥1 COVID-19 vaccine dose. Participants (n = 17,522) were 91% non-Hispanic White, 68% female, median age 57 years, 26% healthcare workers, with 95% self-reported receiving ≥1 COVID-19 vaccine dose through August 2021; mean daily survey response was 85%. Mask use was higher among vaccinated than unvaccinated participants across the study period, regardless of the month of the first dose. Mask use remained relatively stable from December 2020 through April (range 71–80% unvaccinated; 86–93% vaccinated) and declined in both groups beginning in mid-May 2021 to 34% and 42% respectively in June 2021; mask use increased again since July 2021. Mask use by all was lower during weekends and on Christmas and Easter, regardless of vaccination status. Independent predictors of higher mask use were vaccination, age ≥65 years, female sex, racial or ethnic minority group, and healthcare worker occupation, whereas a history of self-reported prior COVID-19 illness was associated with lower use.

Comparison of Vaccine Effectiveness Against the Omicron (B.1.1.529) Variant in Hemodialysis Patients

Comparison of Vaccine Effectiveness Against the Omicron (B.1.1.529) Variant in Hemodialysis Patients