Differences In Nursing Home Staff COVID-19 Testing Rates And Odds Of Vaccination Across Work Shifts.

COVID-19 vaccination and regular testing of nursing home staff have been critical interventions for mitigating COVID-19 outbreaks in US nursing homes. Although implementation of testing has largely been left to nursing home organizations to coordinate, vaccination occurred through a combination of state, federal, and organization efforts. Little research has focused on structural variation in these processes. We examined whether one structural factor, the primary shift worked by staff, was associated with differences in COVID-19 testing rates and odds of vaccination, using staff-level data from a multistate sample of 294 nursing homes. In facility fixed effects analyses, we found that night-shift staff had the lowest testing rates and lowest odds of vaccination, whereas day-shift staff had the highest testing rates and odds of vaccination. These findings highlight the need to coordinate resources and communication evenly across shifts when implementing large-scale processes in nursing homes and other organizations with shift-based workforces.

The impact of the large-scale circulation anomalies in the northern hemisphere on air quality in Wuhan of China during the Spring Festival in 2020

During the 2020 Chinese Spring Festival extended holidays and the COVID-19 period in Wuhan, the “quasi-zero emissions increase” occurred due to the human activities have a considerably lower impact on air quality. A new scientific question of concern: Why has high of O3 and PM2.5 still been observed? The comparative analysis of the influences of anomalous atmospheric circulation and weather conditions during this special period in 2019–2020 with those in the historical years can be useful. The results in the study were as follows: (1) Even during this “quasi-zero emissions increase” period, the concentrations of O3 and PM2.5 are higher than normal, with O3 being significantly higher in Wuhan. Which is associated with a anomaly large-scale humid/warm water vapor transport in the Northern Hemisphere which is significantly different from that of the same period with historical more-haze years. (2) In this scenario, the large-scale humid/warm water vapor transport brings sustained high-humidity water vapor lifting conditions to north China. The daily cycling change of the sun's zenith angle to support the high-humidity and high-condensation condition are conducive to the elevation of high condensation (fc) and degree of super-saturation (S) going up to the peak of S >10%. Under the condition driven by high fc, it causes the power exponent law to be followed converting NO2 to O3, thereby resulting in an increase in O3 concentration. This additional contribution to O3 concentration is as high as 37% than those from pure chemical process. (3) An objective quantitative reversal method for calculating the monthly threshold in fc is given based on the power exponential conversion law by the observed data. It can be prospectively applied to assess the feedback on the impact of pollution on urban climate.

Factors Affecting SARS-CoV-2 Test Discordance in Skilled Nursing Facilities.

OBJECTIVES: Reverse transcription polymerase chain reaction (PCR) and antigen tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are sometimes discordant. We evaluated the discordance between antigen and PCR tests sampled in skilled nursing facilities (SNFs) to assess the relationship of symptom presence, timing between tests, and the presence of a facility outbreak. DESIGN: Observational study using electronic health record data. SETTING AND PARTICIPANTS: Residents of 306 SNFs in 23 states, operated by 1 company. METHODS: We identified all rapid antigen and PCR tests conducted in study SNFs as of January 10, 2021, and classified whether symptoms were present and whether the facility was in outbreak at time of testing. We calculated the proportions of antigen tests with discordant follow-up PCR results conducted no more than 2 days after the antigen test. RESULTS: Of the 171,280 antigen tests in 34,437 SNF residents, 20,991 (12.3%) were followed by a PCR test within 2 days. A total of 1324 negative antigen tests were followed by a positive PCR result, representing 0.8% of all antigen tests and 6.3% of repeated antigen tests; while 337 positive antigen tests were followed by a negative PCR result, representing 0.2% of all antigen tests and 1.6% of repeated antigen tests. Discordance more often occurred when residents were symptomatic at time of antigen testing, during known facility outbreaks, and when the antigen test was compared with a PCR test done within 2 days vs 1 day. CONCLUSIONS AND IMPLICATIONS: Overall, discordance between SARS-CoV-2 antigen and PCR tests was low. Discordance was more common when the individual was symptomatic at time of antigen testing and during facility outbreaks. This suggests that a testing strategy which couples widespread use of antigen tests with clinical thresholds to conduct follow-up confirmatory PCR testing appears to perform well in SNFs, where timely and accurate SARS-CoV-2 case identification are critical.

A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China.

At the end of 2019, A new type of beta-CoV, SARS-CoV-2 emerged and triggered the COVID-19 pandemic, which spread overwhelmingly around the world in less than a year. However, the origin and direct ancestral viruses of SARS-CoV-2 remain unknown. RaTG13, a novel coronavirus found in bats in China's Yunnan Province, is the closest relative virus of the SARS-CoV-2 identified so far. In this study, a new SARS-CoV-2 related virus, provisionally named PrC31, was discovered in Yunnan province by retrospectively analyse bat next generation sequencing (NGS) data of intestinal samples collected in 2018. PrC31 shared 90.7% and 92.0% nucleotide identities to the genomes of SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment of PrC31 showed that several genomic regions, especially orf1a and orf8 had the highest homology with those corresponding genomic regions of SARS-CoV-2 than any other related viruses. Phylogenetic analysis indicated that PrC31 shared a common ancestor with SARS-CoV-2 in evolutionary history. The differences between the PrC31 and SARS-CoV-2 genomes were mainly manifested in the spike genes. The amino acid homology between the receptor binding domains of PrC31 and SARS-CoV-2 was only 64.2%. Importantly, recombination analysis revealed that PrC31 underwent multiple complex recombination events (including three recombination breakpoints) involving the SARS-CoV and SARS-CoV-2 sub-lineages, indicating that PrC31 evolved from yet-to-be-identified intermediate recombination strains. Combined with previous studies, it is revealed that the beta-CoVs may possess a more complex recombination mechanism than we thought.

Targeting the Conserved Stem Loop 2 Motif in the SARS-CoV-2 Genome.

RNA structural elements occur in numerous single-stranded positive-sense RNA viruses. The stem-loop 2 motif (s2m) is one such element with an unusually high degree of sequence conservation, being found in the 3' untranslated region (UTR) in the genomes of many astroviruses, some picornaviruses and noroviruses, and a variety of coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. The evolutionary conservation and its occurrence in all viral subgenomic transcripts imply a key role for s2m in the viral infection cycle. Our findings indicate that the element, while stably folded, can nonetheless be invaded and remodeled spontaneously by antisense oligonucleotides (ASOs) that initiate pairing in exposed loops and trigger efficient sequence-specific RNA cleavage in reporter assays. ASOs also act to inhibit replication in an astrovirus replicon model system in a sequence-specific, dose-dependent manner and inhibit SARS-CoV-2 replication in cell culture. Our results thus permit us to suggest that the s2m element is readily targeted by ASOs, which show promise as antiviral agents. IMPORTANCE The highly conserved stem-loop 2 motif (s2m) is found in the genomes of many RNA viruses, including SARS-CoV-2. Our findings indicate that the s2m element can be targeted by antisense oligonucleotides. The antiviral potential of this element represents a promising start for further research into targeting conserved elements in RNA viruses.

Short-term impact of nursing home SARS-CoV-2 vaccinations on new infections, hospitalizations, and deaths.

OBJECTIVE: To compare rates of incident SARS-CoV-2 infection and 30-day hospitalization or death among residents with confirmed infection in nursing homes with earlier versus later SARS-CoV-2 vaccine clinics. DESIGN: Matched pairs analysis of nursing homes that had their initial vaccine clinics between December 18, 2020, and January 2, 2021, versus between January 3, 2021, and January 18, 2021. Matched facilities had their initial vaccine clinics between 12 and 16 days apart. SETTING AND PARTICIPANTS: Two hundred and eighty nursing homes in 21 states owned and operated by the largest long-term care provider in the United States. MEASUREMENTS: Incident SARS-CoV-2 infections per 100 at-risk residents per week; hospital transfers and/or deaths per 100 residents with confirmed SARS-CoV-2 infection per day, averaged over a week. RESULTS: The early vaccinated group included 136 facilities with 12,157 residents; the late vaccinated group included 144 facilities with 13,221 residents. After 1 week, early vaccinated facilities had a predicted 2.5 fewer incident SARS-CoV-2 infections per 100 at-risk residents per week (95% CI: 1.2-4.0) compared with what would have been expected based on the experience of the late vaccinated facilities. The rates remained significantly lower for several weeks. Cumulatively over 5 weeks, the predicted reduction in new infections was 5.2 cases per 100 at-risk residents (95% CI: 3.2-7.3). By 5 to 8 weeks post-vaccine clinic, early vaccinated facilities had a predicted 1.1 to 3.8 fewer hospitalizations and/or deaths per 100 infected residents per day, averaged by week than expected based on late vaccinated facilities' experience for a cumulative on average difference of 5 events per 100 infected residents per day. CONCLUSIONS: The SARS-CoV-2 vaccines seem to have accelerated the rate of decline of incident infections, morbidity, and mortality in this large multi-state nursing home population.

SARS-CoV-2 antibody detection in skilled nursing facility residents.

OBJECTIVE: To describe the frequency and timing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody detection in a convenience sample of skilled nursing facility (SNF) residents with and without confirmed SARS-CoV-2 infection. DESIGN: Retrospective analysis of SNF electronic health records. SETTING: Qualitative SARS-CoV-2 antibody test results were available from 81 SNFs in 16 states. PARTICIPANTS: Six hundred and sixty nine SNF residents who underwent both polymerase chain reaction (PCR) and antibody testing for SARS-CoV-2. MEASUREMENTS: Presence of SARS-CoV-2 antibodies following the first positive PCR test for confirmed cases, or first PCR test for non-cases. RESULTS: Among 397 residents with PCR-confirmed infection, antibodies were detected in 4 of 7 (57.1%) tested within 7-14 days of their first positive PCR test; in 44 of 47 (93.6%) tested within 15-30 days; in 182 of 219 (83.1%) tested within 31-60 days; and in 110 of 124 (88.7%) tested after 60 days. Among 272 PCR negative residents, antibodies were detected in 2 of 9 (22.2%) tested within 7-14 days of their first PCR test; in 41 of 81 (50.6%) tested within 15-30 days; in 65 of 148 (43.9%) tested within 31-60 days; and in 9 of 34 (26.5%) tested after 60 days. No significant differences in baseline resident characteristics or symptoms were observed between those with versus without antibodies. CONCLUSIONS: These findings suggest that vulnerable older adults can mount an antibody response to SARS-CoV-2, and that antibodies are most likely to be detected within 15-30 days of diagnosis. That antibodies were detected in a large proportion of residents with no confirmed SARS-CoV-2 infection highlights the complexity of identifying who is infected in real time. Frequent surveillance and diagnostic testing based on low thresholds of clinical suspicion for symptoms and/or exposure will remain critical to inform strategies designed to mitigate outbreaks in SNFs while community SARS-CoV-2 prevalence remains high.

Risk Factors Associated With All-Cause 30-Day Mortality in Nursing Home Residents With COVID-19.

Importance: The coronavirus disease 2019 (COVID-19) pandemic has severely affected nursing homes. Vulnerable nursing home residents are at high risk for adverse outcomes, but improved understanding is needed to identify risk factors for mortality among nursing home residents. Objective: To identify risk factors for 30-day all-cause mortality among US nursing home residents with COVID-19. Design, Setting, and Participants: This cohort study was conducted at 351 US nursing homes among 5256 nursing home residents with COVID-19-related symptoms who had severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection confirmed by polymerase chain reaction testing between March 16 and September 15, 2020. Exposures: Resident-level characteristics, including age, sex, race/ethnicity, symptoms, chronic conditions, and physical and cognitive function. Main Outcomes and Measures: Death due to any cause within 30 days of the first positive SARS-CoV-2 test result. Results: The study included 5256 nursing home residents (3185 women [61%]; median age, 79 years [interquartile range, 69-88 years]; and 3741 White residents [71%], 909 Black residents [17%], and 586 individuals of other races/ethnicities [11%]) with COVID-19. Compared with residents aged 75 to 79 years, the odds of death were 1.46 (95% CI, 1.14-1.86) times higher for residents aged 80 to 84 years, 1.59 (95% CI, 1.25-2.03) times higher for residents aged 85 to 89 years, and 2.14 (95% CI, 1.70-2.69) times higher for residents aged 90 years or older. Women had lower risk for 30-day mortality than men (odds ratio [OR], 0.69 [95% CI, 0.60-0.80]). Two comorbidities were associated with mortality: diabetes (OR, 1.21 [95% CI, 1.05-1.40]) and chronic kidney disease (OR, 1.33 [95%, 1.11-1.61]). Fever (OR, 1.66 [95% CI, 1.41-1.96]), shortness of breath (OR, 2.52 [95% CI, 2.00-3.16]), tachycardia (OR, 1.31 [95% CI, 1.04-1.64]), and hypoxia (OR, 2.05 [95% CI, 1.68-2.50]) were also associated with increased risk of 30-day mortality. Compared with cognitively intact residents, the odds of death among residents with moderate cognitive impairment were 2.09 (95% CI, 1.68-2.59) times higher, and the odds of death among residents with severe cognitive impairment were 2.79 (95% CI, 2.14-3.66) times higher. Compared with residents with no or limited impairment in physical function, the odds of death among residents with moderate impairment were 1.49 (95% CI, 1.18-1.88) times higher, and the odds of death among residents with severe impairment were 1.64 (95% CI, 1.30-2.08) times higher. Conclusions and Relevance: In this cohort study of US nursing home residents with COVID-19, increased age, male sex, and impaired cognitive and physical function were independently associated with mortality. Understanding these risk factors can aid in the development of clinical prediction models of mortality in this population.

Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak.

BACKGROUND: Various models have been applied to predict the trend of the epidemic since the outbreak of COVID-19. METHODS: In this study, we designed a dynamic graph model, not for precisely predicting the number of infected cases, but for a glance of the dynamics under a public epidemic emergency situation and of different contributing factors. RESULTS: We demonstrated the impact of asymptomatic transmission in this outbreak and showed the effectiveness of city lockdown to halt virus spread within a city. We further illustrated that sudden emergence of a large number of cases could overwhelm the city medical system, and external medical aids are critical to not only containing the further spread of the virus but also reducing fatality. CONCLUSION: Our model simulation showed that highly populated modern cities are particularly vulnerable and lessons learned in China could facilitate other countries to plan the proactive and decisive actions. We shall pay close attention to the asymptomatic transmission being suggested by rapidly accumulating evidence as dramatic changes in quarantine protocol are required to contain SARS-CoV-2 from spreading globally. SUPPLEMENTARY MATERIALS: The supplementary materials can be found online with this article at 10.1007/s40484-020-0215-4.