Confronting the Delta Variant of SARS-CoV-2, Summer 2021

Wastewater-Based Surveillance of Respiratory Syncytial Virus Reveals a Temporal Disconnect in Disease Trajectory across an Active International Land Border

Conventional metrics for tracking infectious diseases, including case and outbreak data and syndromic surveillance, can be resource-intensive, misleading, and comparatively slow with prolonged data collection, analysis and authentication. This study examined the 2022-2023 Respiratory Syncytial Virus (RSV) season in a contiguous metropolitan area connected by an active international land border, affording an opportunity for comparison of the respiratory virus season spanning two independent public health jurisdictions. Time-lagged cross correlation and qualitative examination of the wastewater signals showed that the peak of the Detroit (MI, USA) RSV season predated the peak in Windsor (ON, Canada) by approximately 5 weeks. A strong positive relationship was observed between RSV N-gene concentrations in wastewater and hospitalization rates in Windsor-Essex (Kendall's τ = 0.539, p ≤ 0.001, Spearman's ρ = 0.713, p ≤ 0.001) as well as Detroit (Kendall's τ = 0.739, p ≤ 0.001, Spearman's ρ = 0.888, p ≤ 0.001). This study demonstrated that wastewater surveillance can reveal regional differences in infection dynamics between communities and can provide an independent measure of the prevalence of RSV, an underreported disease. These findings support the use of wastewater surveillance as a cost-effective tool in monitoring of RSV to enhance existing surveillance systems and to better inform public health disease mitigation strategies.

Delivery Hospitalization Cardiac and Respiratory Complications during SARS-CoV-2 Delta Variant Dominance

In 2021, the severe acute respiratory syndrome coronavirus 2 Delta variant rapidly proliferated and became dominant. Some but not all research evidence supports that Delta was associated with increased maternal risk. The purpose of this study was to determine whether Delta was associated with risk for cardiac and respiratory complications in a national sample. Of an estimated 3,495,188 delivery hospitalizations in 2021, 1.8% of pre-Delta deliveries (n = 29,580; January-June) and 2.1% of Delta-period deliveries (n = 37,545; July-December) had a coronavirus disease 2019 (COVID-19) diagnosis. The Delta period was associated with increased adjusted odds of respiratory complications (adjusted odds ratio [aOR] = 1.54, 95% CI: 1.41, 1.69) and cardiac severe maternal morbidity (SMM; aOR = 1.54, 95% CI: 1.40, 1.69). Among deliveries with a COVID-19 diagnosis, the Delta period was associated with a higher incidence of respiratory complications (8.4 vs. 3.7%) and cardiac SMM (8.4 vs. 3.5%; p < 0.01 for both). These findings corroborate prior clinical studies suggesting that the Delta strain was associated with an increased maternal population-level clinical burden. · The Delta strain was associated with an increased maternal population-level clinical burden.. · The Delta period was associated with an increased risk for cardiac and respiratory complications.. · Among deliveries with a COVID-19 diagnosis, the Delta period was associated with increased risk..

Extracorporeal Membrane Oxygenation for COVID-19 During the Delta and Omicron Waves in North America

Clinical outcomes for patients with severe acute respiratory failure caused by different variants of the coronavirus disease 2019 (COVID-19) supported with extracorporeal membrane oxygenation (ECMO) are incompletely understood. Clinical characteristics, pre-ECMO management, and hospital mortality at 90 days for adults with COVID-19 who received venovenous ECMO (VV-ECMO) at North American centers during waves predominated by Delta (August 16 to December 12, 2021) and Omicron (January 31 to May 31, 2022) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants were compared in a competing risks framework. One thousand seven hundred and sixty-six patients (1,580 Delta, 186 Omicron) received VV-ECMO for COVID-19 during the Delta- and Omicron-predominant waves in North American centers. In the unadjusted competing risks model, no significant difference was observed in risk of hospital mortality at 90 days between patients during the Delta- versus Omicron-predominant wave (subhazard ratio [sHR], 0.94; 95% confidence interval [CI], 0.74-1.19), but patients supported with VV-ECMO during the Omicron-predominant wave had a significantly lower adjusted risk of hospital mortality at 90 days (subhazard ratio, 0.71; 95% CI, 0.51-0.99). Patients receiving VV-ECMO during the Omicron-predominant wave had a similar unadjusted risk of hospital mortality at 90 days, but a significantly lower adjusted risk of hospital mortality at 90 days than those receiving VV-ECMO during the Delta-predominant wave.

Effect of Inactivated Vaccines Against SARS-CoV-2 on Immunogenicity Outcome

OBJECTIVES

The purpose of this study was to measure and examine the levels of IgG, IgM, and Spike antibody induced by inactivated vaccines, including CoronaVac and BBIBP-CorV.

METHODS

Two groups of healthy adults over 18 years old (50 participants per group), who had previously received 1 dose of either BBIBP-CorV or CoronaVac and receiving either a homologous booster of BBIBP-CorV or a heterologous booster of CoronaVac. Serum IgG, IgM, and Spike antibody levels against SARS-COV-2 were measured using magnetic particle chemiluminescence immunoassay and the ELISA method.

RESULTS

The results showed that both spike antibody and IgG/IgM antibodies elicited by a CoronaVac booster following 1 dose of BBIBP-CorV were significantly higher than those elicited by either a homologous BBIBP-CorV booster or a heterologous BBIBP-CorV booster. The Spike antibody against SARS-COV-2 induced by the heterologous CoronaVac booster reached 200.3, which is substantially greater than that induced by the homologous BBIBP-CorV booster (127.5 pg/mL). Conversely, the Spike antibody against SARS-COV-2 induced by the heterologous BBIBP-CorV booster reached 53.93 pg/mL, which is substantially greater than that induced by the homologous CoronaVac booster (9.60 pg/mL).

CONCLUSIONS

In summary, CoronaVac is immunogenic as a booster dose following 1 dose of BBIBP-CorV and is immunogenically superior to both the homologous booster and the heterologous BBIBP-CorV booster.

Chronological and Geographical Variations in the Incidence and Acceptance of COVID-19-Positive Donors and Outcomes Among Abdominal Transplant Patients

INTRODUCTION

Given the importance of understanding COVID-19-positive donor incidence and acceptance, we characterize chronological and geographic variations in COVID-19 incidence relative to COVID-19-positive donor acceptance.

METHODS

Data on deceased donors and recipients of liver and kidney transplants were obtained from the UNOS database between 2020 and 2023. Hierarchical cluster analysis was used to assess trends in COVID-19-positive donor incidence. Posttransplant graft and patient survival were assessed using Kaplan-Meier curves.

RESULTS

From among 38 429 deceased donors, 1517 were COVID-19 positive. Fewer kidneys (72.4% vs. 76.5%, p < 0.001) and livers (56.4% vs. 62.0%, p < 0.001) were used from COVID-19-positive donors versus COVID-19-negative donors. Areas characterized by steadily increased COVID-19 donor incidence exhibit the highest transplantation acceptance rates (92.33%), followed by intermediate (84.62%) and rapidly increased (80.00%) COVID-19 incidence areas (p = 0.016). Posttransplant graft and patient survival was comparable among recipients, irrespective of donor COVID-19 status.

CONCLUSIONS

Regions experiencing heightened rates of COVID-19-positive donors are associated with decreased acceptance of liver and kidney transplantation. Similar graft and patient survival is noted among recipients, irrespective of donor COVID-19 status. These findings emphasize the need for adaptive practices and unified medical consensus in navigating a dynamic pandemic.

Middle-Aged and Older Adult Employment and the Perceived Risk of Running Out of Money During COVID-19: A Dynamic Panel Data Analysis

BACKGROUND AND OBJECTIVES

The coronavirus disease of 2019 (COVID-19) adversely affected the health of middle-aged and older adults and altered their economic outlook. Several national polls revealed older adults felt stress about money and many reported difficulties in paying expenses during 2021. Although such descriptive reports have raised awareness, peer-reviewed studies utilizing panel data can offer additional insight. As such, the purpose of this study was to contribute to this growing literature by examining the demographic, economic, and health factors associated with employment and the perceived risk of running out of money for middle-aged and older adults during the pandemic.

RESEARCH DESIGN AND METHODS

This study utilized the April-May 2020, April-May 2021, and March 2022 waves of the Understanding America Study. Next, a dynamic panel data model was formulated to account for reverse causality and unobserved heterogeneity with a sample of 2,302 adults between the ages of 50 and 74.

RESULTS

Employment (-2.77, p < .05) was negatively associated with the perceived risk of running out of money. Male, higher education levels, currently married, and health insurance status also exhibited a negative association. Meanwhile, a positive association was found for non-White (6.79, p < .01).

DISCUSSION AND IMPLICATIONS

Financial well-being is an important consideration in later life and what role employment played during the COVID-19 pandemic is a worthwhile examination. A better understanding of which factors may be associated with the perceived risk of running out of money during the pandemic can be useful when devising policies which address financial security for middle-aged and older adults.

The Behaviour of IL-6 and Its Soluble Receptor Complex during Different Waves of the COVID-19 Pandemic

In late December 2019, SARS-CoV-2 was identified as the cause of a new pneumonia (COVID-19), leading to a global pandemic declared by the WHO on 11 March 2020, with significant human, economic, and social costs. Although most COVID-19 cases are asymptomatic or mild, 14% progress to severe disease, and 5% develop critical illness with complications such as interstitial pneumonia, acute respiratory distress syndrome (ARDS), and multiple organ dysfunction syndrome (MODS). SARS-CoV-2 primarily targets the respiratory system but can affect multiple organs due to the widespread presence of angiotensin-converting enzyme 2 (ACE2) receptors, which the virus uses to enter cells. This broad distribution of ACE2 receptors means that SARS-CoV-2 infection can lead to cardiovascular, gastrointestinal, renal, hepatic, central nervous system, and ocular damage. The virus triggers the innate and adaptive immune systems, resulting in a massive cytokine release, known as a "cytokine storm", which is linked to tissue damage and poor outcomes in severe lung disease. Interleukin-6 (IL-6) is particularly important in this cytokine release, with elevated levels serving as a marker of severe COVID-19. IL-6 is a multifunctional cytokine with both anti-inflammatory and pro-inflammatory properties, acting through two main pathways: classical signalling and trans-signalling. Classical signalling involves IL-6 binding to its membrane-bound receptor IL-6R and then to the gp130 protein, while trans-signalling occurs when IL-6 binds to the soluble form of IL-6R (sIL-6R) and then to membrane-bound gp130 on cells that do not express IL-6R. The soluble form of gp130 (sgp130) can inhibit IL-6 trans-signalling by binding to sIL-6R, thereby preventing it from interacting with membrane-bound gp130. Given the central role of IL-6 in COVID-19 inflammation and its association with severe disease, we aimed to analyse the behaviour of IL-6 and its soluble receptor complex during different waves of the pandemic. This analysis could help determine whether IL-6 levels can serve as prognostic markers of disease severity.

SARS-CoV-2 Delta variant remains viable in environmental biofilms found in meat packaging plants

To determine why SARS-CoV-2 appears to thrive specifically well in meat packaging plants, we used SARS-CoV-2 Delta variant and meat packaging plant drain samples to develop mixed-species biofilms on materials commonly found within meat packaging plants (stainless steel (SS), PVC, and ceramic tile). Our data provides evidence that SARS-CoV-2 Delta variant remained viable on all the surfaces tested with and without an environmental biofilm after the virus was inoculated with the biofilm for 5 days at 7°C. We observed that SARS-CoV-2 Delta variant was able to remain infectious with each of the environmental biofilms by conducting plaque assay and qPCR experiments, however, we detected a significant reduction in viability post-exposure to Plant B biofilm on SS, PVC, and on ceramic tile chips, and to Plant C biofilm on SS and PVC chips. The numbers of viable SARS-CoV-2 Delta viral particles was 1.81-4.57-fold high than the viral inoculum incubated with the Plant B and Plant C environmental biofilm on SS, and PVC chips. We did not detect a significant difference in viability when SARS-CoV-2 Delta variant was incubated with the biofilm obtained from Plant A on any of the materials tested and SARS-CoV-2 Delta variant had higher plaque numbers when inoculated with Plant C biofilm on tile chips, with a 2.75-fold difference compared to SARS-CoV-2 Delta variant on tile chips by itself. In addition, we detected an increase in the biofilm biovolume in response to SARS-CoV-2 Delta variant which is also a concern for food safety due to the potential for foodborne pathogens to respond likewise when they come into contact with the virus. These results indicate a complex virus-environmental biofilm interaction which correlates to the different bacteria found in each biofilm. Our results also indicate that there is the potential for biofilms to protect SARS-CoV-2 from disinfecting agents and remaining prevalent in meat packaging plants.

Temporal assessment of SARS-CoV-2 detection in wastewater and its epidemiological implications in COVID-19 case dynamics

This research evaluated the relationship between daily new Coronavirus Disease 2019 (COVID-19) cases and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) concentrations in wastewater, followed by effects of differential SARS-CoV-2 shedding loads across various COVID-19 outbreaks. Linear regression analyses were utilized to examine the lead time of the SARS-CoV-2 signal in wastewater relative to new COVID-19 clinical cases. During the Delta wave, no lead time was evident, highlighting limited predictive capability of wastewater monitoring during this phase. However, significant lead times were observed during the Omicron wave, potentially attributed to testing capacity overload and subsequent case reporting delays or changes in shedding patterns. During the Post-Omicron wave (Febuary 23 to May 19, 2022), no lead time was discernible, whereas following the lifting of the COVID-19 state of emergency (May 30, 2022 to May 30, 2023), the correlation coefficient increased and demonstrated the potential of wastewater surveillance as an early warning system. Subsequently, we explored the virus shedding in wastewater through feces, operationalized as the ratio of SARS-CoV-2 concentrations to daily new COVID-19 cases. This ratio varied significantly across the Delta, Omicron, other variants and post-state-emergency phases, with the Kruskal-Wallis H test confirming a significant difference in medians across these stages (P < 0.0001). Despite its promise, wastewater surveillance of COVID-19 disease prevalence presents several challenges, including virus shedding variability, data interpretation complexity, the impact of environmental factors on viral degradation, and the lack of standardized testing procedures. Overall, our findings offer insights into the correlation between COVID-19 cases and wastewater viral concentrations, potential variation in SARS-CoV-2 shedding in wastewater across different pandemic phases, and underscore the promise and limitations of wastewater surveillance as an early warning system for disease prevalence trends.

Lessons we learned during the past four challenging years in the COVID-19 era: pharmacotherapy, long COVID complications, and vaccine development

About four years have passed since the detection of the first cases of COVID-19 in China. During this lethal pandemic, millions of people have lost their lives around the world. Since the first waves of COVID-19 infection, various pharmacotherapeutic agents have been examined in the management of COVID-19. Despite all these efforts in pharmacotherapy, drug repurposing, and design and development of new drugs, multiple organ involvement and various complications occurred during COVID-19. Some of these complications became chronic and long-lasting which led to the "long COVID" syndrome appearance. Therefore, the best way to eradicate this pandemic is prophylaxis through mass vaccination. In this regard, various vaccine platforms including inactivated vaccines, nucleic acid-based vaccines (mRNA and DNA vaccines), adenovirus-vectored vaccines, and protein-based subunit vaccines have been designed and developed to prevent or reduce COVID-19 infection, hospitalization, and mortality rates. In this focused review, at first, the most commonly reported clinical presentations of COVID-19 during these four years have been summarized. In addition, different therapeutic regimens and their latest status in COVID-19 management have been listed. Furthermore, the "long COVID" and related signs, symptoms, and complications have been mentioned. At the end, the effectiveness of available COVID-19 vaccines with different platforms against early SARS-CoV-2 variants and currently circulating variants of interest (VOI) and the necessity of booster vaccine shots have been summarized and discussed in more detail.

Regional variations in vaccination against COVID-19 in Germany

Vaccination willingness against COVID-19 is generally perceived as low. Moreover, there is large heterogeneity across and within countries. As a whole, Germany has average vaccination rates compared to other industrialized countries. However, vaccination rates in the 16 different German federal states differ by more than 20 percentage points. We describe variation in vaccination rates on the level of the 400 German counties using data on all vaccinations carried out until December 2022. Around 52-72% of that variation can be explained by regional differences in demographic characteristics, housing, education and political party preferences. We find indications that the remaining part may be due to differences in soft factors such as risk aversion, trust in the German government, trust in science, and beliefs in conspiracy theories regarding the origins of the Corona virus. We conclude that improving the trust in science and the fight against conspiracy theories may possibly be effective tools to improve vaccination rates and effectively fight pandemics.

A potential antiviral against COVID-19 obtained from Byrsonima coccolobifolia leaves extract

In this study, we specifically focused on the crude methanolic leaf extract of Byrsonima coccolobifolia, investigating its antifungal potential against human pathogenic fungi and its antiviral activity against COVID-19. Through the use of high-performance liquid chromatography coupled with electrospray ionization ion trap tandem mass spectrometry, direct infusion electrospray ionization ion trap tandem mass spectrometry, and chromatographic dereplication procedures, we identified galloyl quinic acid derivatives, catechin derivatives, proanthocyanidins, and flavonoid glycosides. The broth dilution assay revealed that the methanolic leaf extract of B. coccolobifolia exhibits antifungal activity against Cryptococcus neoformans (IC50 = 4 μg/mL). Additionally, docking studies were conducted to elucidate the interactions between the identified compounds and the central residues at the binding site of biological targets associated with COVID-19. Furthermore, the extract demonstrated an in vitro half-maximum effective concentration (EC50 = 7 μg/mL) and exhibited significant selectivity (>90%) toward SARS-CoV-2.

Public opinion on global COVID-19 vaccine procurement and distribution policies: A nationally representative survey in Aotearoa New Zealand 2022

The World Health Organisation and many health experts have regarded vaccine nationalism, a "my country first" approach to vaccines procurement, as a critical pandemic response failure. However, few studies have considered public opinion in this regard. This study gauged public support for vaccine nationalism and vaccine internationalism in a representative survey in New Zealand (N = 1,135). Support for vaccine internationalism (M (mean rating) = 3.64 on 5-point scales) was significantly stronger than for vaccine nationalism (M = 3.24). Additionally, support for openly sharing COVID-19 vaccine manufacturing knowledge and technology (M = 4.17 on 5-point scales) was significantly stronger than support for safeguarding vaccine manufacturers' intellectual property (M = 2.66). The public also supported a utilitarian approach that would see distributions based on need (M = 3.76 on 5-point scales) over an equal proportional international distribution (M = 3.16). Akin to the few preceding studies, the present observations suggest that the public is likely to be more supportive of pandemic responses that are globally equitable and long-term orientated. Our findings have substantial implications for pandemic preparedness as the congruence or lack thereof of public vaccine-related values with government policies can affect public trust, which, in turn, can affect public cooperation. It may pay for governments to invest in proactive public engagement efforts before and during a pandemic to discuss critical ethical issues and inequities in global vaccine procurement and distributions.

Impact of public health policy and mobility change on transmission potential of severe acute respiratory syndrome coronavirus 2 in Rhode Island, March 2020 - November 2021

To study the SARS-CoV-2 transmission potential in Rhode Island (RI) and its association with policy changes and mobility changes, the time-varying reproduction number, Rt, was estimated. The daily incident case counts (16 March 2020, through 30 November 2021) were bootstrapped within a 15-day sliding window and multiplied by Poisson-distributed multipliers (λ = 4, sensitivity analysis: 11) to generate 1000 estimated infection counts, to which EpiEstim was applied to generate Rt time series. The median Rt percentage change when policies changed was estimated. The time lag correlations were assessed between the 7-day moving average of the relative changes in Google mobility data in the first 90 days, and Rt and estimated infection count, respectively. There were three major pandemic waves in RI in 2020-2021: spring 2020, winter 2020-2021 and fall-winter 2021. The median Rt fluctuated within the range of 0.5-2 from April 2020 to November 2021. Mask mandate (18 April 2020) was associated with a decrease in Rt (-25.99%, 95% CrI: -37.42%, -14.30%). Termination of mask mandates on 6 July 2021 was associated with an increase in Rt (36.74%, 95% CrI: 27.20%, 49.13%). Positive correlations were found between changes in grocery and pharmacy, Rt retail and recreation, transit, and workplace visits, for both Rt and estimated infection count, respectively. Negative correlations were found between changes in residential area visits for both Rt and estimated infection count, respectively. Public health policies enacted in RI were associated with changes in the pandemic trajectory. This ecological study provides further evidence of how non-pharmaceutical interventions and vaccination slowed COVID-19 transmission in RI.

Trajectory of COVID-19 response and management strategy in China: scientific rationale driven strategy adjustments

The pneumonia caused by novel coronavirus SARS-CoV-2 infection in early December 2019, which was later named coronavirus disease 2019 (COVID-19) by the World Health Organization (WHO), rapidly spread across the world. China has made extraordinary efforts to this unprecedented pandemic, put its response and control at a very high level of infectious disease management (Category B but with measures for Category A), given top priority to the people and their lives, and balanced the pandemic control and socio-economic development. After more than three years' fighting against this disease, China downgraded the management of COVID-19 to Category B infectious disease on January 8, 2023 and the WHO declared the end of public health emergency on May 5, 2023. However, the ending of pandemic does not mean that the disease is no longer a health threat. Experiences against COVID-19 from China and the whole world should be learned to prepare well for the future public health emergencies. This article gives a systematic review of the trajectory of COVID-19 development in China, summarizes the critical policy arrangements and provides evidence for the adjustment during policy making process, so as to share experiences with international community and contribute to the global health for all humanity.

Comparison of Omicron and Delta Variants of SARS-CoV-2: A Systematic Review of Current Evidence

INTRODUCTION

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) caused the outbreak of coronavirus disease 2019 (COVID-19) in late 2019 in Wuhan, China. In early 2020, the disease spread rapidly around the world. Since the pandemic, SARS-CoV-2 has evolved dramatically into a wide variety of variants endowed with devastating properties. As of March 6, 2022, five SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, Delta, and Omicron strains have been identified. Due to the crucial importance of understanding the differences between the Omicron and Delta variants, this systematic review was conducted.

METHODS

This systematic review investigated new variants of Omicron SARS-CoV-2 based on current studies. Online databases were searched for English articles as of January 03, 2023. Selection of publications was a two-step process of title/abstract and full-text assessment against eligibility criteria. The relevant data from the included articles were systematically collected and organized in a designed table for analysis. To ensure the quality of the review, the PRISMA checklist and Newcastle- Ottawa Scale (NOS) of quality assessment were utilized.

RESULTS

The data extracted from 58 articles were analyzed, including 10003 pieces of evidence. Lower risk of hospitalization, ICU admission, and mortality after vaccination were reported in the Omicron variant compared to the Delta variant. Additionally, the Delta variant led to more severe clinical symptoms in comparison to the Omicron variant.

CONCLUSION

The Omicron variant of SARS-CoV-2 results in less severe disease outcomes as compared to Delta. Nevertheless, it remains crucial to maintain ongoing monitoring, implement containment measures, and adapt vaccination protocols to effectively address the evolving variants.

Explaining the challenges of resources management and its underlying factors in COVID-19 era in Iran: a qualitative study

BACKGROUND

Identifying factors affecting health costs can contribute to formulating the best policies for controlling and managing health costs. To this end, the present study aimed to analyze resource wastage and identify the factors underlying it in COVID-19 management in Iran's health sector.

METHOD

This qualitative content analysis study was conducted in Iran's health sector. The participants were 23 senior, middle, and operational managers in the health sector. The data were collected through semistructured interviews with the managers. The participants were selected using purposive, quota, and snowball sampling techniques. The interviews continued until the data were saturated. The collected data were analyzed using MAXQDA software (version 10).

RESULTS

Following the data analysis, the factors affecting the wastage of health resources were divided into 4 themes and 13 main themes. Vaccines, diagnostic kits, medicines, and human resources were the main factors underlying resource wastage. The identified main themes were open and unused vials, nonuse of distributed vaccines and their expiration, excess supply and decreased demand for vaccines, expiration of diagnostic and laboratory kits and their quantitative and qualitative defects, and the large number of tests. Inefficiency and the expiration of COVID-19 drugs, poor drug supply and consumption chain management, inaccuracy in inventory control and expiration dates, disorganization and inconsistency in the distribution of healthcare staff, low productivity of the staff, and failure to match the staff's skills with assigned tasks in selected centers were identified as the most important causes of resource wastage.

CONCLUSION

Given the limited health funds and the increased healthcare costs, effective preparation and planning and making reasonable decisions for unexpected events can minimize unnecessary costs and resource wastage, which requires some revisions in attitudes toward COVID-19 management in the healthcare sector.

Dynamic zero-COVID policy and healthcare utilization patterns in China during the Shanghai COVID-19 Omicron outbreak

BACKGROUND

In April 2022, an outbreak of the SARS-CoV-2 virus Omicron variant in Shanghai precipitated an extensive lockdown. We assessed changes in healthcare utilization during this outbreak and investigated the relationship between the stringency of mitigation strategies and disruptions in healthcare utilization.

METHODS

Using provincial-level data from routine health information systems covering all hospitals across Mainland China, we conducted an interrupted time series analysis to examine changes in healthcare utilization during the Shanghai outbreak. Linear regression was used to evaluate the direction and magnitude of the association between the relative changes in the move-out movement index, a proxy for the stringency in population-level mitigation strategies, and the estimated relative changes in healthcare utilization.

RESULTS

Overall, there were 22.9 billion outpatient visits and 1.2 billion discharged inpatients during the study period from January 2016 to May 2022, including 9.1 billion (39.7%) and 0.46 billion (38.2%) in the post-COVID-19 period (January 2020-May 2022), respectively. From March through May 2022, the outbreak resulted in an accumulative loss of 23.5 million (47%) outpatient visits and 0.6 million (55%) discharged inpatients in Shanghai, and a loss of 150.3 million (14%) outpatient visits and 3.6 million (7%) discharged inpatients in other regions. We find that for every 10-percentage point reduction in the relative change of move-out index, a 2.7 (95% CI: 2.0-3.4) percentage point decline in the relative change of outpatient visits, and a 4.3 (95% CI: 3.5-5.2) percentage points decline in the relative change of inpatient discharges.

CONCLUSIONS

The Shanghai COVID-19 Omicron outbreak associates with a substantial reduction in outpatient visits and inpatient discharges within Shanghai and other regions in China. The stringency of the COVID-19 lockdown policies associates with more profound reductions in healthcare utilization.

The lead time and geographical variations of Baidu Search Index in the early warning of COVID-19

Internet search data was a useful tool in the pre-warning of COVID-19. However, the lead time and indicators may change over time and space with the new variants appear and massive nucleic acid testing. Since Omicron appeared in late 2021, we collected the daily number of cases and Baidu Search Index (BSI) of seven search terms from 1 January to 30 April, 2022 in 12 provinces/prefectures to explore the variation in China. Two search peaks of "COVID-19 epidemic", "Novel Coronavirus" and "COVID-19" can be observed. One in January, which showed 3 days lead time in Henan and Tianjin. Another on early March, which occurred 0-28 days ahead of the local epidemic but the lead time had spatial variation. It was 4 weeks in Shanghai, 2 weeks in Henan and 5-8 days in Jilin Province, Jilin and Changchun Prefecture. But it was only 1-3 days in Tianjin, Quanzhou Prefecture, Fujian Province and 0 day in Shenzhen, Shandong Province, Qingdao and Yanbian Prefecture. The BSI was high correlated (rs:0.70-0.93) to the number of cases with consistent epidemiological change trend. The lead time of BSI had spatial and temporal variation and was close related to the strength of nucleic acid testing. The case detection ability should be strengthened when perceiving BSI increase.

Vaccine hesitancy promotes emergence of new SARS-CoV-2 variants

The successive emergence of SARS-CoV-2 mutations has led to an unprecedented increase in COVID-19 incidence worldwide. Currently, vaccination is considered to be the best available solution to control the ongoing COVID-19 pandemic. However, public opposition to vaccination persists in many countries, which can lead to increased COVID-19 caseloads and hence greater opportunities for vaccine-evasive mutant strains to arise. To determine the extent that public opinion regarding vaccination can induce or hamper the emergence of new variants, we develop a model that couples a compartmental disease transmission framework featuring two strains of SARS-CoV-2 with game theoretical dynamics on whether or not to vaccinate. We combine semi-stochastic and deterministic simulations to explore the effect of mutation probability, perceived cost of receiving vaccines, and perceived risks of infection on the emergence and spread of mutant SARS-CoV-2 strains. We find that decreasing the perceived costs of being vaccinated and increasing the perceived risks of infection (that is, decreasing vaccine hesitation) will decrease the possibility of vaccine-resistant mutant strains becoming established by about fourfold for intermediate mutation rates. Conversely, we find increasing vaccine hesitation to cause both higher probability of mutant strains emerging and more wild-type cases after the mutant strain has appeared. We also find that once a new variant has emerged, perceived risk of being infected by the original variant plays a much larger role than perceptions of the new variant in determining future outbreak characteristics. Furthermore, we find that rapid vaccination under non-pharmaceutical interventions is a highly effective strategy for preventing new variant emergence, due to interaction effects between non-pharmaceutical interventions and public support for vaccination. Our findings indicate that policies that combine combating vaccine-related misinformation with non-pharmaceutical interventions (such as reducing social contact) will be the most effective for avoiding the establishment of harmful new variants.

A novel COVID-19 program, delivering vaccines throughout rural and remote Australia

Background

The Royal Flying Doctor Service of Australia (RFDS) established a unique SARS-CoV-2 vaccination program for vaccinating Australians that live in rural and remote areas. This paper describes the preparation and response phases of the RFDS response.

Methods

This study includes vaccinations conducted by the RFDS from 01 January 2021 until 31 December 2021 when vaccines were mandatory for work and social activities. Prior to each clinic, we conducted community consultation to determine site requirements, patient characteristics, expected vaccination numbers, and community transmission rates.

Findings

Ninety-five organizations requested support. The majority (n = 60; 63.2%) came from Aboriginal Community Controlled Health Organizations. Following consultation, 360 communities were approved for support. Actual vaccinations exceeded expectations (n = 70,827 vs. 49,407), with a concordance correlation coefficient of 0.88 (95% CI, 0.83, 0.93). Areas that reported healthcare workforce shortages during the preparation phase had the highest population proportion difference between expected and actual vaccinations. Areas that reported high vaccine hesitancy during the preparation phase had fewer than expected vaccines. There was a noticeable increase in vaccination rates in line with community outbreaks and positive polymerase chain reaction cases [r (41) = 0.35, p = 0.021]. Engagement with community leaders prior to clinic deployment was essential to provide a tailored response based on community expectations.

Risk Factors of Adverse Maternal Outcome among SARS-CoV-2 Infected Critically Ill Pregnant Women in Serbia

BACKGROUND AND OBJECTIVES

During the COVID-19 pandemic, Serbia has faced devastating losses related to increased mortality rates among men and women of all ages. With 14 registered cases of maternal death in 2021, it became obvious that pregnant women are faced with a serious threat that jeopardises their life as well as the life of their unborn child. Studying the consequences of the COVID-19 pandemic on maternal outcomes is vivifying and stimulating for many professionals and decision-makers, and knowing the contextual characteristics can facilitate the application of literature findings in practice. Therefore, the aim of this study was to present findings of maternal mortality in Serbia associated with SARS-CoV-2 infected and critically ill pregnant women.

METHODS

Clinical status and pregnancy-related features were analysed for a series of 192 critically ill pregnant women with confirmed SARS-CoV-2 infection. According to the treatment outcome, pregnant women were divided in two study groups: a group of survivors and a group of deceased patients.

RESULTS

A lethal outcome was recorded in seven cases. Pregnant women in the deceased group were presenting at admission more commonly with X-ray-confirmed pneumonia, a body temperature of >38 °C, cough, dyspnea, and fatigue. They were more likely to have a progression of the disease, to be admitted to intensive care unit, and be dependent from mechanical ventilation, as well as to have nosocomial infection, pulmonary embolism, and postpartum haemorrhage. On average, they were in their early third trimester of pregnancy, presenting more commonly with gestational hypertension and preeclampsia.

CONCLUSIONS

Initial clinical manifestations of SARS-CoV-2 infection, such as dyspnea, cough, fatigue, and fever, could be a potent factors in risk stratification and outcome prediction. Prolonged hospitalization, ICU admission, and associated risk of hospital-acquired infections require strict microbiological surveillance and should be a constant reminder of rational antibiotics use. Understanding and identification of risk factors associated with poor maternal outcomes among pregnant women infected with SARS-CoV-2 should warn medical professionals of potentially unwanted outcomes and can be used for organising an individualised treatment for a pregnant patient's specific needs, including a guide to necessary consultations with medical specialists in various fields.

Associations of Combustible Cigarette, Electronic Cigarette, and Dual Use With COVID Infection and Severity in the U.S.: A Cross-sectional Analysis of the 2021 National Health Information Survey

Given the potential respiratory health risks, the association of COVID infection and the use of combustible cigarettes, electronic nicotine delivery systems (ENDS), and concurrent dual use is a priority for public health. Many published reports have not accounted for known covarying factors. This study sought to calculate adjusted odds ratios for self-reported COVID infection and disease severity as a function of smoking and ENDS use, while accounting for factors known to influence COVID infection and disease severity (i.e., age, sex, race and ethnicity, socioeconomic status and educational attainment, rural or urban environment, self-reported diabetes, COPD, coronary heart disease, and obesity status). Data from the 2021 U.S. National Health Interview Survey, a cross-sectional questionnaire design, were used to calculate both unadjusted and adjusted odds ratios for self-reported COVID infection and severity of symptoms. Results indicate that combustible cigarette use is associated with a lower likelihood of self-reported COVID infection relative to non-use of tobacco products (AOR = .64; 95% CI [.55, .74]), whereas ENDS use is associated with a higher likelihood of self-reported COVID infection (AOR = 1.30; 95% CI [1.04, 1.63]). There was no significant difference in COVID infection among dual users (ENDS and combustible use) when compared with non-users. Adjusting for covarying factors did not substantially change the results. There were no significant differences in COVID disease severity between those of varying smoking status. Future research should examine the relationship between smoking status and COVID infection and disease severity utilizing longitudinal study designs and non-self-report measures of smoking status (e.g., the biomarker cotinine), COVID infection (e.g., positive tests), and disease severity (e.g., hospitalizations, ventilator assistance, mortality, and ongoing symptoms of long COVID).

Understanding the challenges to COVID-19 vaccines and treatment options, herd immunity and probability of reinfection

Unlike pandemics in the past, the outbreak of coronavirus disease 2019 (COVID-19), which rapidly spread worldwide, was met with a different approach to control and measures implemented across affected countries. The lack of understanding of the fundamental nature of the outbreak continues to make COVID-19 challenging to manage for both healthcare practitioners and the scientific community. Challenges to vaccine development and evaluation, current therapeutic options, convalescent plasma therapy, herd immunity, and the emergence of reinfection and new variants remain the major obstacles to combating COVID-19. This review discusses these challenges in the management of COVID-19 at length and highlights the mechanisms needed to provide better understanding of this pandemic.

Impact of Health Workers' Choice of COVID-19 Vaccine Booster on Immunization Levels in Istanbul, Turkey

BACKGROUND

There are limited data regarding short- and medium-term IgG antibody levels after the CoronaVac and BNT162b2 vaccines. This study aimed to investigate the antibody responses of health workers who initially received two doses of CoronaVac one month apart followed by a booster dose of either CoronaVac or BNT162b2, as well as determine whether either vaccine provided superior results.

METHODS

This research represents the second phase of a mixed-methods vaccine cohort study and was conducted between July 2021 and February 2022. The participants (n = 117) were interviewed in person and blood samples were collected before and at 1 and 6 months after the booster vaccination.

RESULTS

BNT162b2 was found to have greater immunogenic potential than CoronaVac (p < 0.001). Health workers without chronic disease exhibited statistically significant increases in antibody levels after both vaccines (p < 0.001), whereas only BNT162b2 caused a significant increase in antibody levels in participants with chronic disease (p < 0.001). Samples obtained before and at 1 and 6 months after the booster vaccination revealed no age- or sex-based differences in IgG-inducing potential for either vaccine (p > 0.05). Antibody levels were comparable in both vaccine groups before the booster regardless of COVID-19 history (p > 0.05); however, antibody levels were significantly higher after the BNT162b2 booster at 1 month (<0.001) and at 6 months, except among participants who had a positive history of COVID-19 infection (p < 0.001).

CONCLUSIONS

Our results suggest that even a single booster dose of BNT162b2 after initial vaccination with CoronaVac provides a protective advantage against COVID-19, especially for risk groups such as health workers and those with chronic diseases.

Factor Analysis in Distinguishing Coronavirus Disease 2019 From Other Influenza-like Illness Using a Validated Patient-Reported Outcome Instrument FLU-PRO Plus: A Prospective Real-world Cohort Study

BACKGROUND/OBJECTIVE

InFLUenza Patient-reported Outcome (FLU-PRO Plus) is a 34-item patient-reported outcome instrument designed to capture the intensity and frequency of viral respiratory symptoms. This study evaluates whether FLU-PRO Plus responses could discriminate between symptoms of coronavirus disease 2019 (COVID-19) and influenza-like illness (ILI) with no COVID diagnosis, as well as forecast disease progression.

METHODS

FLU-PRO Plus was administered daily for 14 days. Exploratory factor analysis was used to reduce the FLU-PRO Plus responses on the first day to 3 factors interpreted as "symptom clusters." The 3 clusters were used to predict COVID-19 versus ILI diagnosis in logistic regression. Correlation between the clusters and quality of life (QoL) measures was used to assess concurrent validity. The timing of self-reported return to usual health in the 14-day period was estimated as a function of the clusters within COVID-19 and ILI groups.

RESULTS

Three hundred fourteen patients completed day 1 FLU-PRO Plus, of which 65% had a COVID-19 diagnosis. Exploratory factor analysis identified 3 symptom clusters: (1)general Body, (2) tracheal/bronchial, and (3) nasopharyngeal. Higher nasopharyngeal scores were associated with higher odds of COVID-19 compared with ILI diagnosis [adjusted odds ratio = 1.61 (1.21, 2.12)]. Higher tracheal/bronchial scores were associated with lower odds of COVID-19 [0.58 (0.44, 0.77)]. The 3 symptom clusters were correlated with multiple QoL measures ( r = 0.14-0.56). Higher scores on the general body and tracheal/bronchial symptom clusters were associated with prolonged time to return to usual health [adjusted hazard ratios: 0.76 (0.64, 0.91), 0.80 (0.67, 0.96)].

CONCLUSION

Three symptom clusters identified from FLU-PRO Plus responses successfully discriminated patients with COVID-19 from non-COVID ILI and were associated with QoL and predicted symptom duration.

HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2

Accurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their spread. Here we introduce HaploCoV, a novel software framework that enables the exploration of SARS-CoV-2 genomic diversity through space and time, to identify novel emerging viral variants and prioritize variants of potential epidemiological interest in a rapid and unsupervised manner. HaploCoV can integrate with any classification/nomenclature and incorporates an effective scoring system for the prioritization of SARS-CoV-2 variants. By performing retrospective analyses of more than 11.5 M genome sequences we show that HaploCoV demonstrates high levels of accuracy and reproducibility and identifies the large majority of epidemiologically relevant viral variants - as flagged by international health authorities - automatically and with rapid turn-around times.Our results highlight the importance of the application of strategies based on the systematic analysis and integration of regional data for rapid identification of novel, emerging variants of SARS-CoV-2. We believe that the approach outlined in this study will contribute to relevant advances to current and future genomic surveillance methods.

Update on the effectiveness of COVID-19 vaccines on different variants of SARS-CoV-2

It has been more than three years since the first emergence of coronavirus disease 2019 (COVID-19) and millions of lives have been taken to date. Like most pandemics caused by viral infections, massive public vaccination is the most promising approach to cease COVID-19 infection. In this regard, several vaccine platforms including inactivated virus, nucleic acid-based (mRNA and DNA vaccines), adenovirus-based, and protein-based vaccines have been designed and developed for COVID-19 prevention and many of them have received FDA or WHO approval. Fortunately, after global vaccination, the transmission rate, disease severity, and mortality rate of COVID-19 infection have diminished significantly. However, a rapid increase in COVID-19 cases due to the omicron variant in vaccinated countries has raised concerns about the effectiveness of these vaccines. In this review, articles published between January 2020 and January 2023 were reviewed using PubMed, Google Scholar, and Web of Science search engines with appropriate related keywords. The related papers were selected and discussed in detail. The current review mainly focuses on the effectiveness and safety of COVID-19 vaccines against SARS-CoV-2 variants. Along with discussing the available and approved vaccines, characteristics of different variants of COVID-19 have also been discussed in brief. Finally, the currently circulating COVID-19 variant i.e Omicron, along with the effectiveness of available COVID-19 vaccines against these new variants are discussed in detail. In conclusion, based on the available data, administration of newly developed bivalent mRNA COVID-19 vaccines, as booster shots, would be crucial to prevent further circulation of the newly developed variants.

Comparative admission rates and infection severity of COVID-19 among unvaccinated and vaccinated patients

Vaccination efforts have limited the burden of the pandemic caused by the coronavirus disease 2019 (COVID-19) with substantial evidence showing reduced hospitalization rates among vaccinated populations. However, few studies have explored correlations between vaccination status and inpatient COVID-19 outcomes. This observational case-control study involved a retrospective chart review of adult patients hospitalized for COVID-19 infection at a medium-sized hospital in Central Michigan between May 1, 2021 and September 30, 2021. Unadjusted analyses involved t-tests and chi-square tests followed by adjusted analyses using binary logistic and linear regression models. Of the 192 screened patients, 171 subjects met the inclusion criteria. Vaccinated patients were significantly older (71.09 vs 57.45, p < 0.001), more likely to identify as white (89.4% vs 66.9%, p = 0.026), and had a lower baseline 10-year survival rate predicted by the Charlson Comorbidity Index (42% vs 69%, p < 0.001) compared to unvaccinated patients. Common symptoms between both groups included shortness of breath (50%), malaise (23%-37%), cough (28%-32%), and fever or chills (25%). Upon matching, adjusted analysis showed significantly higher rates of remdesivir administration to unvaccinated patients (41.3% vs 13.3%, odds ratio (OR): 4.63, 90% confidence interval (CI): 1.98-11.31). Despite higher intensive care unit admission rates among unvaccinated patients (39.1% vs 23.9%, OR: 1.83, 90% CI: 0.74-4.64), this difference did not reach statistical significance. Accordingly, immunization status strongly correlates with patient demographics and differences in inpatient treatment. Larger studies are needed to further assess the vaccine's impact on inpatient outcomes outside of our community.

adaPop: Bayesian inference of dependent population dynamics in coalescent models

The coalescent is a powerful statistical framework that allows us to infer past population dynamics leveraging the ancestral relationships reconstructed from sampled molecular sequence data. In many biomedical applications, such as in the study of infectious diseases, cell development, and tumorgenesis, several distinct populations share evolutionary history and therefore become dependent. The inference of such dependence is a highly important, yet a challenging problem. With advances in sequencing technologies, we are well positioned to exploit the wealth of high-resolution biological data for tackling this problem. Here, we present adaPop, a probabilistic model to estimate past population dynamics of dependent populations and to quantify their degree of dependence. An essential feature of our approach is the ability to track the time-varying association between the populations while making minimal assumptions on their functional shapes via Markov random field priors. We provide nonparametric estimators, extensions of our base model that integrate multiple data sources, and fast scalable inference algorithms. We test our method using simulated data under various dependent population histories and demonstrate the utility of our model in shedding light on evolutionary histories of different variants of SARS-CoV-2.

Development and Validation of a Clinical Risk Score to Predict Hospitalization Within 30 Days of Coronavirus Disease 2019 Diagnosis

INTRODUCTION

Early identification of patients with coronavirus disease 2019 (COVID-19) who are at risk for hospitalization may help to mitigate disease burden by allowing healthcare systems to conduct sufficient resource and logistical planning in the event of case surges. We sought to develop and validate a clinical risk score that uses readily accessible information at testing to predict individualized 30-day hospitalization risk following COVID-19 diagnosis.

METHODS

We assembled a retrospective cohort of U.S. Veterans Health Administration patients (age ≥ 18 years) diagnosed with COVID-19 between March 1, 2020, and December 31, 2020. We screened patient characteristics using Least Absolute Shrinkage and Selection Operator logistic regression and constructed the risk score using characteristics identified as most predictive for hospitalization. Patients diagnosed before November 1, 2020, comprised the development cohort, while those diagnosed on or after November 1, 2020, comprised the validation cohort. We assessed risk score discrimination by calculating the area under the receiver operating characteristic (AUROC) curve and calibration using the Hosmer-Lemeshow (HL) goodness-of-fit test. This study was approved by the Veteran's Institutional Review Board of Northern New England at the White River Junction Veterans Affairs Medical Center (Reference no.:1473972-1).

RESULTS

The development and validation cohorts comprised 11,473 and 12,970 patients, of whom 4,465 (38.9%) and 3,669 (28.3%) were hospitalized, respectively. The independent predictors for hospitalization included in the risk score were increasing age, male sex, non-white race, Hispanic ethnicity, homelessness, nursing home/long-term care residence, unemployed or retired status, fever, fatigue, diarrhea, nausea, cough, diabetes, chronic kidney disease, hypertension, and chronic obstructive pulmonary disease. Model discrimination and calibration was good for the development (AUROC = 0.80; HL P-value = .05) and validation (AUROC = 0.80; HL P-value = .31) cohorts.

CONCLUSIONS

The prediction tool developed in this study demonstrated that it could identify patients with COVID-19 who are at risk for hospitalization. This could potentially inform clinicians and policymakers of patients who may benefit most from early treatment interventions and help healthcare systems anticipate capacity surges.

Persuading the "Movable Middle": Characteristics of effective messages to promote routine and COVID-19 vaccinations for adults and children - The impact of COVID-19 on beliefs and attitudes

PURPOSE

We sought to 1) explore trusted sources for vaccine information, 2) describe persuasive characteristics of trusted messages promoting routine and COVID-19 vaccines for children and adults and 3) explore how the pandemic has impacted attitudes and beliefs about routine vaccinations. We conducted a mixed method cross-sectional study between May 3-June 14, 2021 including a survey and six focus groups among a sub-set of survey respondents. A total of 1,553 survey respondents (from which n = 33 participated in the focus groups) including adults without children under age nineteen years (n = 582) and parents with children under age nineteen years (n = 971).

RESULTS

Primary care providers, family, and credible sources, characterized as known and well-established entities, were top sources of vaccine information. Neutrality, honesty, and having a trusted source to rely on in sorting through volumes of sometimes conflicting information were highly valued. Trustworthy qualities about sources included: 1) expertise, 2) fact-based, 3) unbiased, and 4) having an established process for sharing information. Because of the evolving nature of the pandemic, attitudes and beliefs about COVID-19 vaccine and sources of COVID-19 information differed from typical views about routine vaccines. Of 1,327 (85.4 %) survey respondents, 12.7 % and 9.4 % of adults and parents cited that the pandemic impacted their attitudes and beliefs. Among these respondents, 8 % of adults and 3 % of parents cited more favorable attitudes and beliefs about getting vaccinated with routine vaccines because of the pandemic.

CONCLUSION

Vaccine attitudes and beliefs which inform intent to vaccinate can change and differ among different vaccines. Messaging should be tailored to resonate with parents and adults to improve vaccine uptake.

Clinical outcomes of the SARS-cov-2 omicron and delta variant: systematic review and meta-analysis of 33 studies covering 6,037,144 COVID-19 positive patients

BACKGROUND

Although the SARS-CoV-2 Omicron variant is considered to induce less severe disease, there have been no consistent results on the extent of the decrease in severity.

OBJECTIVES

To compare the clinical outcomes of COVID-19 positive patients with Omicron and Delta variant infection.

DATA SOURCES

Searches were implemented up to 8 November 2022 in PubMed, Web of Science, BioRvix, and MedRvix.

STUDY ELIGIBILITY CRITERIA

Eligible studies were cohort studies reporting the clinical outcomes of COVID-19 positive patients with omicron and delta variant infection, including hospitalization, ICU admission, receiving invasive mechanical ventilation (IMV), and death.

PARTICIPANTS

COVID-19 positive patients with Omicron and Delta variant infection. Assessment of risk of bias: Risk of bias was assessed employing the Newcastle-Ottawa Scale (NOS). Methods of data synthesis: Random-effect models were employed to pool the Odds ratios (ORs) and 95% confidence intervals (CIs) to compare the risk of clinical outcome. I² was employed to evaluate heterogeneity between studies.

RESULTS

A total of 33 studies with 6,037,144 COVID-19 positive patients were included in this meta-analysis. In the general population of COVID-19 positive, compared to Delta, Omicron variant infection resulted in a decreased risk of hospitalization (10.24% Vs 4.14%, OR=2.91, 95%CI=2.35-3.60), ICU admission (3.67% Vs 0.48%, OR=3.64, 95%CI=2.63-5.04), receiving IMV (3.93% Vs 0.34%, OR=3.11, 95%CI=1.76-5.50), and death (2.40% Vs 0.46%, OR=2.97, 95%CI=2.17-4.08). In the hospitalized patients with COVID-19 positive, compared to Delta, Omicron variant infection resulted in a decreased risk of ICU admission (20.70% Vs 12.90%, OR=1.63, 95%CI=1.32-2.02), receiving IMV (10.90% Vs 5.80%, OR=1.65, 95%CI=1.28-2.14), and death (10.72% Vs 7.10%, OR=1.44, 95%CI=1.22-1.71).

DISCUSSION

Compared to Delta, the severity of Omicron variant infection decreased.

Trend and Co-occurrence Network of COVID-19 Symptoms From Large-Scale Social Media Data: Infoveillance Study

BACKGROUND

For an emergent pandemic, such as COVID-19, the statistics of symptoms based on hospital data may be biased or delayed due to the high proportion of asymptomatic or mild-symptom infections that are not recorded in hospitals. Meanwhile, the difficulty in accessing large-scale clinical data also limits many researchers from conducting timely research.

OBJECTIVE

Given the wide coverage and promptness of social media, this study aimed to present an efficient workflow to track and visualize the dynamic characteristics and co-occurrence of symptoms for the COVID-19 pandemic from large-scale and long-term social media data.

METHODS

This retrospective study included 471,553,966 COVID-19-related tweets from February 1, 2020, to April 30, 2022. We curated a hierarchical symptom lexicon for social media containing 10 affected organs/systems, 257 symptoms, and 1808 synonyms. The dynamic characteristics of COVID-19 symptoms over time were analyzed from the perspectives of weekly new cases, overall distribution, and temporal prevalence of reported symptoms. The symptom evolutions between virus strains (Delta and Omicron) were investigated by comparing the symptom prevalence during their dominant periods. A co-occurrence symptom network was developed and visualized to investigate inner relationships among symptoms and affected body systems.

RESULTS

This study identified 201 COVID-19 symptoms and grouped them into 10 affected body systems. There was a significant correlation between the weekly quantity of self-reported symptoms and new COVID-19 infections (Pearson correlation coefficient=0.8528; P<.001). We also observed a 1-week leading trend (Pearson correlation coefficient=0.8802; P<.001) between them. The frequency of symptoms showed dynamic changes as the pandemic progressed, from typical respiratory symptoms in the early stage to more musculoskeletal and nervous symptoms in the later stages. We identified the difference in symptoms between the Delta and Omicron periods. There were fewer severe symptoms (coma and dyspnea), more flu-like symptoms (throat pain and nasal congestion), and fewer typical COVID symptoms (anosmia and taste altered) in the Omicron period than in the Delta period (all P<.001). Network analysis revealed co-occurrences among symptoms and systems corresponding to specific disease progressions, including palpitations (cardiovascular) and dyspnea (respiratory), and alopecia (musculoskeletal) and impotence (reproductive).

CONCLUSIONS

This study identified more and milder COVID-19 symptoms than clinical research and characterized the dynamic symptom evolution based on 400 million tweets over 27 months. The symptom network revealed potential comorbidity risk and prognostic disease progression. These findings demonstrate that the cooperation of social media and a well-designed workflow can depict a holistic picture of pandemic symptoms to complement clinical studies.

If you build it, will they come? Is test site availability a root cause of geographic disparities in COVID-19 testing?

OBJECTIVES

The purpose of this study was to examine the relationship between test site availability and testing rate within the context of social determinants of health.

STUDY DESIGN

A retrospective ecological investigation was conducted using statewide COVID-19 testing data between March 2020 and December 2021.

METHODS

Ordinary least squares and geographically weighted regression were used to estimate state and ZIP code level associations between testing rate and testing sites per capita, adjusting for neighbourhood-level confounders.

RESULTS

The findings indicate that site availability is positively associated with the ZIP code level testing rate and that this association is amplified in communities of greater economic deprivation. In addition, economic deprivation is a key factor for consideration when examining ethnic differences in testing in medically underserved states.

CONCLUSION

The study findings could be used to guide the delivery of testing facilities in resource-constrained states.

Estimated SARS-CoV-2 antibody seroprevalence trends and relationship to reported case prevalence from a repeated, cross-sectional study in the 50 states and the District of Columbia, United States-October 25, 2020-February 26, 2022

Background

Sero-surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can reveal trends and differences in subgroups and capture undetected or unreported infections that are not included in case-based surveillance systems.

Methods

Cross-sectional, convenience samples of remnant sera from clinical laboratories from 51 U.S. jurisdictions were assayed for infection-induced SARS-CoV-2 antibodies biweekly from October 25, 2020, to July 11, 2021, and monthly from September 6, 2021, to February 26, 2022. Test results were analyzed for trends in infection-induced, nucleocapsid-protein seroprevalence using mixed effects models that adjusted for demographic variables and assay type.

Findings

Analyses of 1,469,792 serum specimens revealed U.S. infection-induced SARS-CoV-2 seroprevalence increased from 8.0% (95% confidence interval (CI): 7.9%-8.1%) in November 2020 to 58.2% (CI: 57.4%-58.9%) in February 2022. The U.S. ratio of the change in estimated seroprevalence to the change in reported case prevalence was 2.8 (CI: 2.8-2.9) during winter 2020-2021, 2.3 (CI: 2.0-2.5) during summer 2021, and 3.1 (CI: 3.0-3.3) during winter 2021-2022. Change in seroprevalence to change in case prevalence ratios ranged from 2.6 (CI: 2.3-2.8) to 3.5 (CI: 3.3-3.7) by region in winter 2021-2022.

Interpretation

Ratios of the change in seroprevalence to the change in case prevalence suggest a high proportion of infections were not detected by case-based surveillance during periods of increased transmission. The largest increases in the seroprevalence to case prevalence ratios coincided with the spread of the B.1.1.529 (Omicron) variant and with increased accessibility of home testing. Ratios varied by region and season with the highest ratios in the midwestern and southern United States during winter 2021-2022. Our results demonstrate that reported case counts did not fully capture differing underlying infection rates and demonstrate the value of sero-surveillance in understanding the full burden of infection. Levels of infection-induced antibody seroprevalence, particularly spikes during periods of increased transmission, are important to contextualize vaccine effectiveness data as the susceptibility to infection of the U.S. population changes.

Funding

This work was supported by the Centers for Disease Control and Prevention, Atlanta, Georgia.

Vaccination or NPI? A conjoint analysis of German citizens' preferences in the context of the COVID-19 pandemic

This research uses discrete choice-based conjoint analysis that elicits the preference structure of German citizens when it comes to their timely intention to vaccinate. The focus is on the trade-offs between pharmaceuticals (vaccine) and "non-pharmaceutical interventions" (NPIs) such as lock-downs and social distancing measures, as well as the value of voluntary versus mandatory compliance to the citizens. Our results highlight three critical insights: (a) value of waiting: at 70% effective vaccine, 1/3 of citizens still would prefer to be vaccinated in the next 6 months rather than immediately; (b) costs of NPI constraints: an effective vaccine may come as a solution to compensate for the costs induced by invasive NPI imposed for an extended period; (c) freedom of choice: voluntary compliance is preferred by citizens over imposed measures whether it relates to vaccination choice, lock-down measures, or work location choice during the pandemic. Backing up those findings in monetary value, a quick shot of a 100% effective vaccination is estimated to be worth in the range of 11,400€. Still, the value of the shot quickly falls to no value when effectiveness drops below 50. At the same time, the cost of imposing protective rules lies in the range of 1500-2500€, depending on the rule analyzed. In comparison, the burden of extra complete lock-down and social distancing is about 775€ per citizen per month. As most current vaccines are being proven to have high efficacy, a strategy that selects the most effective vaccine candidates while emphasizing how the vaccine may stop the pain of lasting lock-downs will be appropriate to nudge the population towards vaccination. Control measures that are too restrictive may be welfare-deteriorating, but enough NPI measures must be recommended as long as vaccination adoption is not sufficiently large.

Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape

The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.

Clinical characteristics and mortality risk among critically ill patients with COVID-19 owing to the B.1.617.2 (Delta) variant in Vietnam: A retrospective observational study

BACKGROUND

SARS-CoV-2 Delta variant caused a large number of COVID-19 cases in many countries, including Vietnam. Understanding mortality risk factors is crucial for the clinical management of severe COVID-19.

METHODS

We conducted a retrospective study at an intensive care center in Ho Chi Minh City that urgently built by Bach Mai Hospital during the COVID-19 outbreak in Vietnam, when the Delta variant predominated. Participants were laboratory-confirmed patients with SARS-CoV-2 infection, admitted in August 2021. Data on patients' demographic and clinical characteristics, radiographic and laboratory findings, treatment, and clinical time course were compared between survivors and non-survivors. Risk factors to mortality were assessed using logistic regression.

RESULTS

Among 504 eligible COVID-19 patients, case fatality was 52.2%. Unvaccinated patients accounted for 61.2% of non-survivors and 43.6% of survivors (p < 0.001). The time from onset to hospital admission was 8 days in non-survivors and 7 days in survivors (p = 0.004). Among non-survivors, 90.2% developed acute respiratory distress syndrome (ARDS). Oxygen therapy was administered for all patients, but antiviral agent was given to 51.7% of non-survivors. 54.2% of non-survivors tested positive for the bacterial infection using blood culture. The risk factors for mortality were diabetes mellitus, respiration rate, oxygen saturation, vaccination status, time from onset to admission, and older age.

CONCLUSIONS

Critical patients with COVID-19 owing to the Delta variant in Vietnam had delayed hospital admission, leading to ARDS and death. Early availability of vaccines and preventing bacterial infections are crucial for reducing mortality of COVID-19, especially in low- and middle-income countries.

Incentivizing COVID-19 vaccination among racial/ethnic minority adults in the United States: $209 per dose could convince the hesitant

BACKGROUND

More than two years into the coronavirus disease (COVID-19) pandemic, it remains unclear whether financial incentives can reduce vaccine hesitancy and improve uptake among key unvaccinated populations. This study estimated the willingness of racial/ethnic minority adults in the United States to accept financial incentives for COVID-19 vaccination and the minimum amount needed to vaccinate a sufficiently high percentage of this population.

METHODS

From August through September 2021, we conducted an online survey of 367 Black/African American and Hispanic patients, age ≥ 18 years, from 8 community health centers in Rhode Island. Contingent valuation questions assessed respondents' willingness-to-accept (WTA) incentives for COVID-19 vaccination using random-starting-points and iterative incentive offers of $5 to $50 per dose. Ordered logistic regression models examined associations between respondent characteristics and WTA. Predictive probabilities were modeled using both within-survey range and out-of-survey range incentive offer amounts and compared against vaccination thresholds needed to reach herd immunity.

RESULTS

Less than 30% of unvaccinated survey respondents were WTA an incentive of $50/dose for vaccination. Models using out-of-survey incentive offer amounts greater than $50 suggested that 85% of respondents would agree $140/dose (95% CI: $43-$236) could convince other people to accept vaccination, while $209/dose (95% CI: -$91-$509) would be needed for 85% of respondents to accept vaccination themselves.

CONCLUSIONS

Findings from this analysis may inform the design of incentive schemes aiming to reduce racial/ethnic disparities in vaccine and booster uptake, which will continue to be important as new variants of SARS-CoV-2 emerge.

Frailty Reduces Vaccine Effectiveness Against SARS-CoV-2 Infection: A Test-Negative Case Control Study Using National VA Data

OBJECTIVES

To assess the variation of vaccine effectiveness against SARS-CoV-2 infection during the Delta wave according to frailty status among U.S. veterans.

DESIGN

Test-negative case-control study of SARS-CoV-2 mRNA vaccine effectiveness.

SETTING

Veterans Health Administration (VHA) medical centers.

PARTICIPANTS

Veterans 19 years and older who had at least one COVID-19/Flu like symptoms and received a SARS-CoV-2 PCR or antigen test at VHA medical centers between July 25 to September 30, 2021.

INTERVENTION

mRNA vaccination.

MEASUREMENTS

New SARS-CoV-2 infection. Vaccine effectiveness was defined as 1-odds of vaccination in cases/odds of vaccination in controls, where cases were patients who had a COVID-19 test and tested positive for SARS-CoV-2, and controls were those who tested negative. Frailty was measured using the VA frailty index, categorized as robust (0-<0.1), pre-frail (≥0.1-<0.21) and frail (≥0.21).

RESULTS

A total of 58,604 patients (age:58.9±17.0, median:61, IQR:45-72; 87.5%men; 68.1%white; 1.3%African American, 8.3%Hispanic) were included in the study. Of these, 27,733 (47.3%) were robust, 16,276 (27.8%) were prefrail, and 14,595 (24.9%) were frail. mRNA vaccine effectiveness against the Delta variant symptomatic infection was lower in patients with frailty, 62.8 %(95%CI:59.8-65.7), versus prefrail 73.9%(95%CI:72.0-75.7), and robust, 77.0 %(95%CI:75.7-78.3).

CONCLUSIONS

This test-negative case control study showed that mRNA vaccine effectiveness against infection declined in veterans with frailty. Frailty status is a factor to consider when designing, developing, and evaluating COVID-19 vaccines.

Excess deaths from COVID-19 among Medicare beneficiaries with psychiatric diagnoses: Community versus nursing home

BACKGROUND

Psychiatric illness may pose an additional risk of death for older adults during the COVID-19 pandemic. Older adults in the community versus institutions might be influenced by the pandemic differently. This study examines excess deaths during the COVID-19 pandemic among Medicare beneficiaries with and without psychiatric diagnoses (depression, anxiety, bipolar disorder, and schizophrenia) in the community versus nursing homes.

METHODS

This is a retrospective cohort study of a 20% random sample of 15,229,713 fee-for-service Medicare beneficiaries, from January 2019 through December 2021. Unadjusted monthly mortality risks, COVID-19 infection rates, and case-fatality rates after COVID-19 diagnosis were calculated. Excess deaths in 2020, compared to 2019 were estimated from multivariable logistic regressions.

RESULTS

Of all included Medicare beneficiaries in 2020 (N = 5,140,619), 28.9% had a psychiatric diagnosis; 1.7% lived in nursing homes. In 2020, there were 246,422 observed deaths, compared to 215,264 expected, representing a 14.5% increase over expected. Patients with psychiatric diagnoses had more excess deaths than those without psychiatric diagnoses (1,107 vs. 403 excess deaths per 100,000 beneficiaries, p < 0.01). The largest increases in mortality risks were observed among patients with schizophrenia (32.4% increase) and bipolar disorder (25.4% increase). The pandemic-associated increase in deaths with psychiatric diagnoses was only found in the community, not in nursing homes. The increased mortality for patients with psychiatric diagnoses was limited to those with medical comorbidities. The increase in mortality for psychiatric diagnoses was associated with higher COVID-19 infection rates (1-year infection rate = 7.9% vs. 4.2% in 2020), rather than excess case fatality.

CONCLUSIONS

Excess deaths during the COVID-19 pandemic were disproportionally greater in beneficiaries with psychiatric diagnoses, at least in part due to higher infection rates. Policy interventions should focus on preventing COVID-19 infections and deaths among community-dwelling patients with major psychiatric disorders in addition to those living the nursing homes.

Neutralizing monoclonal antibody in patients with coronavirus disease 2019: an observational study

BACKGROUND

Clinical data on patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant are limited, especially on clinical status after the application of antibody therapy.

METHODS

We evaluated clinical status in patients with the SARS-CoV-2 delta variant after BRII-196 and BRII-198 treatment in an infectious disease hospital in China. We collected data on clinical symptoms, laboratory tests, radiological characteristics, viral load, anti-SARS-CoV-2 antibodies, treatment, and outcome.

RESULTS

In mid-June 2021, 36 patients with delta variant infection were identified in Shenzhen. The most common symptoms at illness onset were cough (30.6%), fever (22.2%), myalgia (16.7%), and fatigue (16.7%). A small number of patients in this study had underlying diseases, including diabetes (5.6%) and hypertension (8.3%). The application of BRII-196 and BRII-198 can rapidly increase anti-SARS-CoV-2 IgG. The median peak IgG levels in the antibody treatment group were 32 times higher than those in the control group (P < 0.001). The time from admission to peak IgG levels in the antibody treatment group (mean: 10.2 days) was significantly shorter than that in the control group (mean: 17.7 days). Chest CT score dropped rapidly after antibody therapy, with a mean duration of 5.74 days from admission to peak levels.

CONCLUSION

The results of this study suggest that the application of BRII-196 and BRII-198 antibody therapy improved clinical status in patients with SARS-CoV-2 delta variant infection.

The effectiveness of coronavirus disease 2019 (COVID-19) vaccine in the prevention of post-COVID-19 conditions: A systematic literature review and meta-analysis

Background

Although multiple studies have revealed that coronavirus disease 2019 (COVID-19) vaccines can reduce COVID-19-related outcomes, little is known about their impact on post-COVID-19 conditions. We performed a systematic literature review and meta-analysis on the effectiveness of COVID-19 vaccination against post-COVID-19 conditions (ie, long COVID).

Methods

We searched PubMed, CINAHL, EMBASE, Cochrane Central Register of Controlled Trials, Scopus, and Web of Science from December 1, 2019, to April 27, 2022, for studies evaluating COVID-19 vaccine effectiveness against post-COVID-19 conditions among individuals who received at least 1 dose of Pfizer/BioNTech, Moderna, AstraZeneca, or Janssen vaccine. A post-COVID-19 condition was defined as any symptom that was present 3 or more weeks after having COVID-19. Editorials, commentaries, reviews, study protocols, and studies in the pediatric population were excluded. We calculated the pooled diagnostic odds ratios (DORs) for post-COVID-19 conditions between vaccinated and unvaccinated individuals. Vaccine effectiveness was estimated as 100% × (1 - DOR).

Results

In total, 10 studies with 1,600,830 individuals evaluated the effect of vaccination on post-COVID-19 conditions, of which 6 studies were included in the meta-analysis. The pooled DOR for post-COVID-19 conditions among individuals vaccinated with at least 1 dose was 0.708 (95% confidence interval (CI), 0.692-0.725) with an estimated vaccine effectiveness of 29.2% (95% CI, 27.5%-30.8%). The vaccine effectiveness was 35.3% (95% CI, 32.3%-38.1%) among those who received the COVID-19 vaccine before having COVID-19, and 27.4% (95% CI, 25.4%-29.3%) among those who received it after having COVID-19.

Conclusions

COVID-19 vaccination both before and after having COVID-19 significantly decreased post-COVID-19 conditions for the circulating variants during the study period although vaccine effectiveness was low.

Drugs for COVID-19: An Update

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the seventh known human coronavirus, and it was identified in Wuhan, Hubei province, China, in 2020. It caused the highly contagious disease called coronavirus disease 2019 (COVID-19), declared a global pandemic by the World Health Organization (WHO) on 11 March 2020. A great number of studies in the search of new therapies and vaccines have been carried out in these three long years, producing a series of successes; however, the need for more effective vaccines, therapies and other solutions is still being pursued. This review represents a tracking shot of the current pharmacological therapies used for the treatment of COVID-19.

Year 3 of COVID-19: Harsh Truths, Brutal Realities, and Glimmers of Hope

Severe acute respiratory syndrome coronavirus 2, the virus causing coronavirus disease 2019 (COVID-19), has now killed 1 of every 303 Americans. Whereas 4 vaccines are approved in the United States and masks are widely available, too few are fully immunized and most of the population has stopped wearing protective masks. The ongoing consequences of this include continued excess morbidity and mortality and the generation of immune-evading variants and subvariants, which in toto are injurious and ultimately self-defeating. Herein we briefly update and review COVID-19 vaccines, waning immunity, and new variants.

Four Waves of the COVID-19 Pandemic: Comparison of Clinical and Pregnancy Outcomes

During the last two and a half years, clinical manifestations, disease severity, and pregnancy outcomes have differed among pregnant patients with SARS-CoV-2 infection. These changes were preceded by the presence of new variants of SARS-CoV-2, known in the literature as variants of concern. The aim of this study is to describe the differences between maternal clinical characteristics and perinatal outcomes among pregnant women with COVID-19 during four waves of the COVID-19 epidemic in Serbia. This retrospective study included a series of 192 pregnant patients who were hospitalized due to the severity of their clinical status of SARS-CoV-2 infection. During four outbreaks of COVID-19 infection in Serbia, we compared and analyzed three sets of variables, including signs, symptoms, and characteristics of COVID-19 infection, clinical endpoints, and maternal and newborn parameters. During the dominance of the Delta variant, the duration of hospitalization was the longest (10.67 ± 1.42 days), the frequency of stillbirths was the highest (17.4%), as well as the frequency of progression of COVID infection (28.9%) and the requirement for non-invasive oxygen support (37%). The dominance of the Delta variant was associated with the highest number of prescribed antibiotics (2.35 ± 0.28), the most common presence of nosocomial infections (21.7%), and the highest frequency of corticosteroid therapy use (34.8%). The observed differences during the dominance of four variants of concern are potential pathways for risk stratification and the establishment of timely and proper treatments for pregnant patients. Early identification of the Delta variant, and possibly some new variants with similar features in the future, should be a priority and, perhaps, even an opportunity to introduce more accurate and predictive clinical algorithms for pregnant patients.

Determining laboratory parameters in pregnant women with severe COVID-19

Objective

Coronavirus disease causes a wide spectrum of clinical picture in pregnant women. There are still a few studies concerning laboratory parameters to differentiate the severity of coronavirus disease-19 in pregnant patients. This article aims to identify the cut-off on laboratory parameters between pregnant women with asymptomatic/mild/moderate and severe/critical coronavirus disease-19 illness.

Methods

All coronavirus disease-19 pregnant women coming to Dr. Cipto Mangunkusumo hospital between January and August 2021 were recruited into this cross-sectional study. All data extracted from medical records were classified into demographic characteristics and laboratory parameters. We defined demographic characteristics as age, parity, systolic, and diastolic blood pressure, heart rate, temperature, respiratory rate, and oxygen saturation. Laboratory parameters measured in this study consisted of complete blood count, renal function test including urea, creatinine, liver function test including aspartate transferase, alanine transferase, infection marker test including procalcitonin, C-reactive protein, interleukin-6, cycle threshold values, ferritin, coagulation test including d-dimer, fibrinogen, random blood glucose, albumin, electrolytes. Data analysis was performed using SPSS statistics.

Results

There were 159 cases assessed in this study consisting of 130 (81.8%) patients with asymptomatic/mild/moderate illness and 29 (18.2%) patients with severe/critical illness of coronavirus disease-19. Of 28 laboratory parameters, 12 of them were significant statistically; thus, it resulted to make a cut-off using receiver operating characteristic curve and show relative risk, and 95% confidence interval. In multivariate analysis that aspartate transferase, D-dimer, and albumin were laboratory parameters impacted to the severity of coronavirus disease-19 in pregnant women. The area under receiver operating characteristic curve was 0.834 (95% CI 0.736-0.932).

Conclusion

Of all laboratory parameters, urea, aspartate transferase, alanine transferase, procalcitonin, C-reactive protein, lactate dehydrogenase (LDH), ferritin, D-dimer, random blood glucose, cycle threshold values, albumin, and chloride differs between asymptomatic/mild/moderate, and severe/critical illness coronavirus disease-19 in pregnant women; aspartate transferase, D-dimer, and albumin were laboratory parameters impacted the most to the severity of coronavirus disease-19 in pregnant women.

Local monitoring of SARS-CoV-2 variants in two large California counties in 2021

Coronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to persist due to mutations resulting in newer, more infectious variants of concern. We aimed to leverage an ongoing private SARS-CoV-2 testing laboratory's infrastructure to monitor SARS-CoV-2 variants in two large California counties. Study enrollment was offered to adults aged 18 years or older in Los Angeles County and Riverside County who recently tested positive for SARS-CoV-2 with a polymerase chain reaction (PCR) assay. A cycle threshold value less than or equal to 30 cycles was considered a positive test for sequencing purposes. Within 5 days of study enrollment, clinician-monitored, self-collected oral fluid and anterior nares swab specimens were obtained from participants. Specimens were transported and stored at 8 °C or cooler. Samples underwent ribonucleic acid extraction, library preparation, and sequencing. SARS-CoV-2 lineages were identified using sequencing data. Participant and genomic data were analyzed using statistical tools and visualized with toolkits. The study was approved by Advarra Institutional Review Board (Pro00053729). From May 27, 2021 to September 9, 2021, 503 individuals were enrolled and underwent specimen collection. Of the 503 participants, 238 (47.3%) participants were women, 329 (63.6%) participants were vaccinated, and 221 (43.9%) participants were of Hispanic or Spanish origin. Of the cohort, 496 (98.6%) participants had symptoms at the time of collection. Among the 503 samples, 443 (88.1%) nasal specimens and 353 (70.2%) oral specimens yielded positive sequencing results. Over our study period, the prevalence of the Alpha variant of SARS-CoV-2 decreased (initially 23.1% [95% confidence interval (95% CI): 0-0.49%] to 0% [95% CI 0.0-0.0%]) as the prevalence of the Delta variant of SARS-CoV-2 increased (initially 33.3% [95% CI 0.0-100.0%] to 100.0% [95% CI 100.0-100.0%]). A strain that carried mutations of both Delta and Mu was identified. We found that outpatient SARS-CoV-2 variant surveillance could be conducted in a timely and accurate manner. The prevalence of different variants changed over time. A higher proportion of nasal specimens yielded results versus oral specimens. Timely and regional outpatient SARS-CoV-2 variant surveillance could be used for public health efforts to identify changes in SARS-CoV-2 strain epidemiology.