Molecular and Clinical Epidemiology of SARS-CoV-2 Infection Among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey (preprint)

New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOC) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5,007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOC, including Alpha (n =714), Delta (n =1,877), and Omicron (n =1,802). Omicron isolates were further sub-typed as BA.1 (n =899), BA.2 (n =853), and BA.4/BA.5 (n =50); the remaining 614 isolates were classified as “Other”. Approximately 31.5% (1,577/5,007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p <0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p <0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p <0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.

Understanding the Scientific Topics in the Chinese Government's Communication about COVID-19: An LDA Approach

The communication of scientific topics can play a key role in the fight against misinformation and has become an important component of governments' communication regarding COVID-19. This study reviewed the Chinese government's COVID-19 information sources and identified the patterns of science communication models within them. A corpus of science-related content was collected and coded from 1521 news briefings announced by the Chinese government. An LDA (latent Dirichlet allocation) topic model, correlation analysis, and ANOVA were used to analyze the framing of the scientific topics and their social environmental characteristics. The major findings showed the following: (1) The frames in the Chinese government's communication of scientific topics about COVID-19 had three purposes-to disseminate knowledge about prevention and control, epidemiological investigations, and the public's personal health;to make the public understand scientific R&D in Chinese medicine, enterprises, vaccines, treatment options, and medical resources;and to involve citizens, communities, and enterprises in scientific decision making. (2) The frames were correlated with the public and media concerns. (3) The frames varied with the different levels of officials, different types of government agencies, different income regional governments, and different severity levels of the epidemic. (4) The topics concerning sustainability science were more correlated with public and media concern. In addition, we propose several suggestions for building sustainable communication approaches during the pandemic.

The Spatiotemporal Characteristics and Climatic Factors of COVID-19 in Wuhan, China

COVID-19 is threatening the whole world. This paper aims to explore the correlation between climatic factors and the morbidity of COVID-19 in Wuhan, China, mainly by using a geographic detector and GWR model. It was found that the response of the morbidity of COVID-19 to meteorological factors in Wuhan is different at different stages. On the whole, the morbidity of COVID-19 has a strong spatial aggregation, mainly concentrated in the central area of Wuhan City. There is a positive correlation between wind speed and the spread of COVID-19, while temperature has a negative correlation. There is a positive correlation between air pressure and the number of COVID-19 cases. Rainfall is not significantly correlated with the spread of COVID-19. It is concluded that wind speed, relative humidity, temperature, and air pressure are important meteorological factors affecting the spread of COVID-19 in Wuhan. Any two variables have greater interaction with the spatial distribution of the incidence rate of COVID-19 than any one factor alone. Those findings not only provide a new insight for the key intervention measures and the optimal allocation of health care resources accordingly but also lay a theoretical foundation for disease prevention, disease intervention and health services.

Post-vaccination SARS-COV-2 among healthcare workers in New Jersey: a genomic epidemiological study (preprint)

ABSTRACT Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called Variants of Concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated healthcare professionals (HCP). Our post-vaccination COVID-19 symptoms-based surveillance program among HCPs in a 17-hospital network, identified all vaccinated HCP who tested positive for COVID-19 after routine screening or after self-reporting. From 01/01/2021 to 04/30/2021, 23,687 HCP received either mRNA-1273 or BNT162b2 mRNA vaccine. All available post-vaccination SARS-CoV-2 samples and a random collection from non-vaccinated patients during the similar timeframe were subjected to VOC screening and whole genome sequencing (WGS). 62% (23,697/37,500) of HCPs received at least one vaccine dose, with 95% (22,458) fully vaccinated. We detected 138 (0.58%, 138/23,697) COVID-19 cases, 105 among partially vaccinated and 33 (0.15%, 33/22,458) among fully vaccinated. Five partially vaccinated required hospitalization, four with supplemental oxygen. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; concurrent non-vaccinated samples was 37% (523/1404) and 20% (284/1394), respectively. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). WGS analysis from vaccinated and non-vaccinated individuals indicated highly congruent phylogenies. We did not detect an increased frequency of any RBD/NTD polymorphism between groups (P>0.05). Our results support robust protection by vaccination, particularly among recipients of both doses. Despite VOCs accounting for over 40% of SARS-CoV-2 from fully vaccinated individuals, the genomic diversity appears to proportionally represent those among non-vaccinated populations. IMPORTANCE A number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants, with high transmission potential and immune evasion properties, the so-called Variants of Concern (VOC), continues to be a major concern. Whether these VOCs alter the efficacy of the administered vaccines is of great concern, and a critical question to study. We describe the initial genomic epidemiology of SARS-CoV-2 recovered from vaccinated healthcare professionals and probe specifically for VOC enrichment. Our findings support the high-level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the non-vaccinated population. Thus, we do not find evidence of VOC enrichment among vaccinated groups. Overall, the genomic diversity of SARS-CoV-2 recovered post-vaccination appears to proportionally represent the observed viral diversity within the community.

A Novel Diagnostic Test to Screen SARS-CoV-2 Variants Containing E484K and N501Y Mutations (preprint)

Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility. While the concerning variants are fast spreading in various geographical areas, identification and monitoring of these variants is lagging far behind, due in large part to the slow speed and insufficient capacity of viral sequencing. In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report. Using this tool, we screened a total of 435 clinical NS samples collected from COVID patients at 8 hospitals within the Hackensack Meridian Health network in New Jersey. While B.1.351 and P.1 variants were absent from the current study, our data revealed a dramatic increase in the frequency of E484K over time, underscoring the need for continuous epidemiological monitoring.

An Observational Study of COVID-19 from A Large Healthcare System in Northern New Jersey: Diagnosis, Clinical Characteristics, and Outcomes (preprint)

BackgroundNew Jersey was an early epicenter for the COVID-19 pandemic in the United States, yet information on hospitalized COVID-19 patients from this area is scarce. This study aimed to provide data on demographics and clinical features of a hospitalized patient population who were confirmed with infection by our in-house (CDI) real-time reverse-transcription polymerase chain reaction (RT-PCR) test. MethodsWe included consecutive patients who were admitted to Hackensack Meridian Health system hospitals with laboratory-confirmed diagnoses of COVID-19 at Hackensack University Medical Center by the CDI virus test between March 12, 2020, and April 8, 2020. Clinical data and viral testing results were collected and analyzed for characteristics associated with outcomes, as well as the correlation with viral load. ResultsA total of 722 patients were included in the study, with a median age of 63 (interquartile range (IQR), 51-75) and 272 (37.7%) females. Mortality of this case series was 25.8%, with a statistically significant linear increase observed from age 40 to [≥]80 by 10-year intervals. Viral load, as indicated by the cycle of threshold (Ct) values from the RT-PCR test, was significantly higher in the oldest patient group ([≥]80), and inversely correlated with survival. ConclusionsThis is the first report to describe the clinical characteristics and outcomes in a large hospitalized COVID-19 patient series from New Jersey. Findings from this study are valuable to the ongoing response of both nationwide healthcare networks and the medical research community. SummaryWe describe the diagnosis, clinical characteristics, and outcomes of a large hospitalized patient population in northern New Jersey during the early stages of the COVID-19 pandemic.

Physical Activity, Screen Time, and Emotional Well-Being during the 2019 Novel Coronavirus Outbreak in China

We aimed to evaluate the effects of the COVID-19 lock down on lifestyle in China during the initial stage of the pandemic. A questionnaire was distributed to Chinese adults living in 31 provinces of China via the internet using a snowball sampling strategy. Information on 7-day physical activity recall, screen time, and emotional state were collected between January 24 and February 2, 2020. ANOVA, χ²test, and Spearman"s correlation coefficients were used for statistical analysis. 12,107 participants aged 18-80 years were included. During the initial phase of the COVID-19 outbreak, nearly 60% of Chinese adults had inadequate physical activity (95% CI 56.6%-58.3%), which was more than twice the global prevalence (27.5%, 25.0%-32.2%). Their mean screen time was more than 4 hours per day while staying at home (261.3 ±189.8 min per day), and the longest screen time was found in young adults (305.6 ±217.5 min per day). We found a positive and significant correlation between provincial proportions of confirmed COVID-19 cases and negative affect scores (r = 0.501, p = 0.004). Individuals with vigorous physical activity appeared to have a better emotional state and less screen time than those with light physical activity. During this nationwide lockdown, more than half of Chinese adults temporarily adopted a sedentary lifestyle with insufficient physical activity, more screen time, and poor emotional state, which may carry considerable health risks. Promotion of home-based self-exercise can potentially help improve health and wellness.