bluuebunny/crossref_metadata_2025_split huggingface dataset:
1871. Clinical epidemiological characterization of patients affected by COVID-19 in a General Hospital of Veracruz, Mexico
Authors: Carpio-Orantes Luis Del , García-Mendez Sergio , Márquez-Uscanga Daniel , Sánchez-Díaz Jesús Salvador , García-Hernández Omar , Aguilar-Silva Andrés , Salazar-Lizárraga Raúl Enrique , González-Arce América Alejandrina , Martínez-Rojas Manuel , Jiménez-Flores Oscar Rodrigo , Villalobos-López Luis Roberto , Hernández-Gómez Héctor Nahín , Domínguez-Cámara Rubén 
Published: December 2022

Abstract

Background
Since the beginning of the pandemic and its passage through the different affected continents, there have been differences in the presentation depending in part on the characteristics of each population, so it is important to know how it behaves in the local population.

Methods
Clinical-epidemiological study in adults hospitalized for suspected COVID-19 at the General Hospital 71 of the City of Veracruz, Mexico, from April to December 2020. Demographic and clinical characteristics are studied, as well as a comparative and stratified analysis was performed by intubation and death.

Results
1212 patients are included, 53% are men, average age 49 years. 20.5% reported sudden onset of symptoms; the most frequent: fever (79.8%), headache (75.2%), cough (71%), myalgia (62%), arthralgia (58%) and dyspnea (46.3%). Comorbidities were reported in 54.7%, the most frequent: Hypertension (29.2%), Diabetes (29.1%) and obesity (13.9%). Regarding the outcomes, 120 (9.9%) required intubation and 300 (25%) died. Men requiring intubation were significantly older than women [62.5 vs 37.5%; p = 0.027]. The mean age of the intubated patients was higher compared to that of the non-intubated [60.5 vs 44.8 years; p = 0.001]. The male gender had a risk association for intubation. The group aged 60 years or older compared to those aged 59 years or younger had a higher risk of intubation. Clinical variables that had a risk association with intubation were: dyspnea, chest pain and prostration. Among comorbidities, hypertension and diabetes had a risk association with intubation. Female gender and headache had a protective association for intubation. In addition, odynophagia, rhinorrhea, and abdominal pain showed a protective association for intubation. There was no difference in terms of gender by death. The mean age of the patients who died was significantly older [64.5 vs 43.8 years; p = 0.001]. The clinical variables that had a risk association with death were: dyspnea, chest pain, polypnea, cyanosis and prostration. The protective variables were: rhinorrhea, odynophagia, headache and conjunctivitis.

Conclusion
By studying a population affected by COVID, its own characteristics and inherent risks can be known to help take local diagnosis and treatment strategies that ensure a better outcome for those affected.

Disclosures
All Authors: No reported disclosures.
1883. Epidemiological investigation of the COVID-19 outbreak in Vellore district in South India using Geographic Information Surveillance (GIS)
Authors: Rupali Priscilla , Murugesan Malathi , Mohan Venkata Raghava , Venkatesan Padmanaban , Kumar Senthil , Thangavelu Premkumar , Rose Winsley , John Jacob 
Published: December 2022

Abstract

Background
Geographical Information Surveillance (GIS) is an advanced digital technology tool that maps location-based data and helps in epidemiological modeling. During pandemics a rapid analysis of patterns of spread can help put in place strategies for containment and infection control. We applied GIS to analyze patterns of spread and hotspots of COVID-19 infected cases in Vellore district in Tamil Nadu, South India.

Methods
Laboratory-confirmed COVID-19 patients from Vellore district and neighboring taluks from March 2020 to June 2021 were geo coded (based on addresses) and spatial maps generated. These were then layered as points on the base map to illustrate the distribution of all COVID-19 cases. Time trends exploring urban-rural burden with age-sex distribution of COVID-19 cases and other variables were correlated with outcomes of death, symptoms and complications.
Map of undivided Vellore district showing rural and urban settlements.

Results
A total of 45,401 cases of COVID-19 were detected between 28 March 2020 to 31 June 2021 with 20730 cases during the first wave (28 March 2020 to 31 March 2021) and 24671 cases during the second wave (1 April 2021 to 30 June 2021). The overall incidence rates of COVID-19 across the study region was 462.8 per 100,000 and 588.6 per 100,000 population during the first and second waves respectively. Pattern of spread revealed epicentres in densely populated urban areas with radial spread, sparing rural areas, Heat maps also confirmed higher densities at these epicentres, however, the second wave had more peri-urban and rural area involvement. Case fatality rate was 1.89% and 1.6% during the first and second waves and increased with advancing age, i.e., 7.38% were aged more than 60 years in the first wave and 5.02% in the second wave. Incidence was higher in men, 2.40%, and 1.76% as compared to women who had 1.16% and 1.38% in the first and second waves respectively. Overall, case fatality rates were the highest among those who had &gt;2 comorbidities (9.52%).

Subdistrict level incidence of COVID-19 during the first and second waves.
Epidemic curve of the COVID-19 pandemic during the first and the second waves.

Conclusion
Modern surveillance systems like GIS can accurately predict the trends of the outbreak and pattern of spread during future respiratory pandemics. Employing this in real time can help design risk mitigation strategies improving health care access and monitoring with prevention of spread to rural areas.

Disclosures
Priscilla Rupali, MD, DTM&H, PFIZER: Grant/Research Support|PFIZER: Grant/Research Support.
1885. Experience using combined antigen and RT-PCR tests for COVID-19 diagnosis at a Veterans Affairs (VA) Health Care System during the Omicron surge
Authors: Chirumamilla Siri , Powell Krista , Gutman David , Webster Andrew S , Moanna Abeer , Epstein Lauren H 
Published: December 2022

Abstract

Background
Combining rapid antigen and RT-PCR tests optimizes detection of COVID-19 compared with either test alone. Therefore, coincident with the Omicron surge, in November 2021, the Atlanta VA Health Care System (AVAHCS) initiated combination testing for all patients admitted from the emergency department (ED) to the inpatient wards. We retrospectively compared test performance for all patients with combination testing performed at AVAHCS, assessed impact of combination testing on ED disposition, and reviewed clinical characteristics of those admitted from the ED with discordant results.

Methods
We assessed concordance of antigen (Abbott BinaxNOW®) and RT-PCR (either Cepheid GeneXpert® or Roche cobas® 6800) tests performed within 24 hours of each other (i.e., combination test-pairs) for any patient during November 25, 2021–January 27, 2022, and calculated test characteristics of the antigen test using RT-PCR as the gold standard. For those patients evaluated in the ED who had discordant results, we determined ED disposition then performed standardized medical record reviews for those admitted to ascertain clinical history and hospital course and disposition.
Combination Antigen and RT-PCR Testing Algorithm for Patients in the Emergency Department, Atlanta VA Healthcare System

Results
Of 836 combination test-pairs, 112 (13%) were discordant, of which 111 were antigen-negative/RT-PCR positive. Sensitivity of the antigen test was 50%, specificity was 100%, positive predictive value 99%, and negative predictive value was 85%. Of 68 patients evaluated in the ED who had antigen-negative/RT-PCR positive results, 21 (31%) were admitted, of whom 17 (81%) had COVID-19-related symptoms at time of ED evaluation. Of the 21 admitted patients, all were admitted to a COVID isolation unit, 20 (95%) had ≥1 chronic comorbidity, 12 (57%) had not completed vaccination, 14 (67%) received COVID-19-specific treatment while inpatient, 6 (29%) received care in an intensive care unit, 17 (81%) discharged home, and 1 (5%) died during hospitalization.
Flow Diagram of Initial Analysis
Flow Diagram of ED Discordant Results
Characteristics of Discordant Hospitalized Patients

Conclusion
The sensitivity of antigen testing was 50% compared to RT-PCR among patients tested across AVAHCS, consistent with published literature. Combination testing facilitated earlier diagnosis, isolation, and treatment of some patients hospitalized from the ED, likely preventing nosocomial transmission.

Disclosures
All Authors: No reported disclosures.
1887. Hyperglycemia and COVID-19: An independent risk factor for disease severity and death in the Dominican Republic
Authors: Roque Yori A , Luna David De , Mena Lora Alfredo J , Mercado Lisa Maria Castillo , Perdomo Carlos , Acosta Mariela 
Published: December 2022

Abstract

Background
The COVID-19 pandemic has caused an unprecedented global public health emergency. Vaccine uptake in low and middle income countries (LMICs) lags developing nations and immunity from vector-based vaccines commonly used in LMICs may be inferior to mRNA vaccines. Thus, defining clinical characteristics that can help identify and triage cases and allocate resources in LMICs of priority. Hyperglycemia has been associated with higher morbidity and mortality in numerous diseases and in critical illness. We seek to understand the relationship between COVID-19 and hyperglycemia.

Methods
This is a single center retrospective review of cases with COVID-19 between January 2021 and June 2021. Adult patients &gt;18 years of age were reviewed and those with a molecular-based laboratory confirmed SARS-CoV-2 infection were included in our study. Patients with known diabetes, elevated A1C or prior steroid use within 2 weeks of admission were excluded. Clinical characteristics, demographics, glucose levels, C-reactive protein (CRP) and ferritin were reviewed.

Results
A total of 120 patients were reviewed, of which 60.8% were male. Hyperglycemia ( &gt;140mg/dL) was present in 57.5%. Hyperglycemia was associated with elevation of inflammatory markers including CRP and Ferritin (p=0.12) (Table 1). Hyperglycemia was more common in patients requiring supplemental low flow oxygen (table 2) and was more common in patients who did not survive (Figure 1). The mortality rate was higher in the hyperglycemia group with 61.5%, a statistically significant finding.
Association between hyperglycemia and inflammatory markers.
Supplemental oxygen needs and hyperglycemia.
Survival and hyperglycemia.

Conclusion
Hyperglycemia on admission was an independent risk factor for disease progression and death. Inflammatory markers were also higher in patients with hyperglycemia. These patients had no prior steroid use or diabetes. Thus, it is possible that it reflects inflammation, stress, or endocrine end-organ damage due to SARS-CoV-2. If validated in larger studies, this simple test can help clinicians identify patients at risk of decompensation and allocate resources and therapeutics accordingly.

Disclosures
All Authors: No reported disclosures.
1896. Statewide Genomic Surveillance of SARS-CoV-2 Variants in Rhode Island
Authors: Singh Manjot , Novitsky Vladimir , Howison Mark , Carpenter-Azevedo Kristin , Huard Richard , King Ewa , Kantor Rami 
Published: December 2022

Abstract

Background
Global genomic surveillance has allowed identification of SARS-CoV-2 circulating variants responsible for the COVID-19 pandemic. Statewide variant characterization can guide local public health mitigations and provide educational opportunities. We characterized statewide evolution of SARS-CoV-2 variants in Rhode Island (RI).

Methods
Deidentified RI SARS-CoV-2 sequences since 2/2020, generated at authors, CDC and commercial laboratories, were extracted from https://www.gisaid.org. Genomic and phylogenetic analyses were conducted with available tools and custom python scripts and, after quality control, sequences were classified as variants of Concern (VOC), variants being monitored (VBM), or non-VOC/non-VBM, per CDC definitions. Specific mutations that are characteristic of the most recent VOCs (Delta or Omicron) were explored outside of their designated lineages.

Results
Of the 1.1 million RI population, 14,933 SARS-CoV-2 sequences were available between 2/2020 and 3/2022. These included 1,542 (11%) sequences from 37 non-VOC/non-VBM lineages until 2/2021, most commonly B.1.2 (21%), B.1.375 (13%), and B.1.517 (6%); 2,910 (19%) sequences from 7 VBM lineages between 3-6/2021, most commonly Alpha (48%), Iota (34%), and Gamma (10%); and 10,481 (70%) sequences from 2 VOC lineages, including 7,574 (72%) Delta mostly between 6/2021 and 12/2021, and 2,907 (28%) Omicron mostly between 1/2022 and 3/2022. Phylogeny showed expected clustering of local variants within regional and global sequences, and continued viral evolution over time. Further VOC evolution was observed, including 87 Delta sub-lineages, most commonly AY.103 (17%), AY.3 (15%), and AY.44 (12%); and 4 Omicron sub-lineages BA.1 (61%), BA.1.1 (32%), BA.2 (7%), and BA.3 (&lt; 1%). Omicron-associated mutations S:del69/70, S:H655Y, or N:P13L were observed in 219 Delta sequences, and Delta-associated mutations ORF1b:G662S, N:D377Y, or M:I82T were observed in 16 Omicron sequences.

Conclusion
Statewide SARS-CoV-2 genomic surveillance allows for continued characterization of locally circulating variants and monitoring of viral evolution. Such data guide public health policies, inform the local health force, and mitigate the impact of SARS-CoV-2 on public health.

Disclosures
Rami Kantor, MD, Gilead Sciences: Grant/Research Support.
1897. The Decline of Respiratory Viruses During the SARS-CoV-2 Pandemic: Public Health Interventions vs. Viral Competition?
Authors: Malik Waleed , Hao Ritche , Shepherd James 
Published: December 2022

Abstract

Background
With the spread of the SARS-CoV-2 pandemic in 2020 and the attendant global precautions such as masking, travel restrictions and social distancing, the WHO FluNet data indicated a decline in flu rates. The CDC data for the 2020-2021 season showed the same decline in US flu as well as other respiratory viruses. Two hypotheses to explain the observed phenomenon are the impact of non-pharmaceutical interventions (NPI) to prevent SARS-CoV-2 infection and suppression of other respiratory viruses by SARS-CoV-2 through a form of resource competition.

Methods
We conducted a study using the EPIC Slicer Dicer analytics tool and the Yale Internal Medicine COVID-19 Database to retrieve data from the Yale New Haven Health System (YNHHS). We tabulated the total number of positive and negative tests for SARS-CoV-2 and a panel of respiratory viruses from September 2, 2018 to April 30, 2022 to cover pre- and peri-pandemic periods. These results were divided into three age groups: ≤12, 13-59, and ≥60. Epidemic curves of each virus with respect to each other, the season, and the introduction of NPIs were constructed to help differentiate between the two hypotheses.

Results
Pre-pandemic data from 09/2018 to 02/2020 revealed seasonal spikes in influenza A and B with 254 positive weekly influenza A/B tests from 11/2018 to 02/2019 for a positivity rate of 7.97% and 481 positive weekly tests (10.53% positivity rate [PR]) from November 2019 to February 2020. There were only 0.35 positive weekly influenza A/B tests (0.05% PR) from 11/2020 to 02/2021 with 2018 positive weekly tests (6.45% PR) for SARS-CoV-2 over the same period. From 11/2020 to 02/2021, there were 56 positive weekly influenza A/B tests (1.44% PR) and 4347 positive weekly SARS-CoV-2 tests (10.35% PR). From 07/2021 to 11/2021, there was an increased rate of positive RSV tests (82 per week, 15.76% PR) and rhinovirus tests (58 per week, 18.73% PR). There were 803 positive weekly tests (2.53% positivity rate) for SARS-CoV-2 over this same period.

Conclusion
Since the start of the SARS-CoV-2 pandemic, the number of positive tests for influenza A/B and seasonal respiratory viruses have not reached pre-pandemic levels across the YNHHS. However, rates of influenza and other respiratory viruses have increased since the relaxation of NPIs.

Disclosures
All Authors: No reported disclosures.
1902. Whole Genome Sequence analysis of early community transmission SARS-CoV-2 samples in the Philippines
Authors: Arevalo Geraldine , Dungca Nina Theresa , Salvana Edsel Maurice , Schwem Brian 
Published: December 2022

Abstract

Background
The Philippines has recorded nearly 3.7 million COVID-19 cases and more than 60,000 deaths. The first three cases of COVID-19 in the country were reported in January 2020 (1 lineage A, 2 lineage B, all Chinese tourists), with the first death outside China occurring among these cases. No cases were reported in February 2020. The first Filipino cases were reported March 2020. With over one million overseas Filipinos repatriated, tracking the introduction of waves of variants and subsequent community spread is important in order to improve future control efforts.

Methods
We analyzed 35 archived samples collected from March to September 2020 at the Philippines National Institutes of Health. SARS-CoV2 RT-PCR positive samples with Ct values from 15 to 25 were sequenced using Illumina HiSeq and analyzed using an in-house bioinformatics pipeline. Lineages were assigned using PANGOLIN. 14 whole genome sequences were generated with sufficient coverage. These were analyzed with 439 whole genome sequences from February to September 2020 that were publicly available on ViruSurf and GISAID to generate transmission maps.

Results
Transmission maps are shown in Figure 1. The earliest community transmission of COVID-19 in the Philippines was from lineage B.6 in March 2020 most closely related to B.6 from India. There is no evidence of onward transmission from the initial reported cases in January 2020 (lineage A and B). In June 2020, the predominant lineage switched to B.1 and its sublineages from Europe, coincident with a surge in cases. Figure 1.Alignment of the whole genome sequences from early Philippine samples and related SARS-COV2 sequences from ViruSurf and GISAID.

Conclusion
Transmission maps are shown in Figure 1. The earliest community transmission of COVID-19 in the Philippines was from lineage B.6 in March 2020 most closely related to B.6 from India. There is no evidence of onward transmission from the initial reported cases in January 2020 (lineage A and B). In June 2020, the predominant lineage switched to B.1 and its sublineages from Europe, coincident with a surge in cases.

Disclosures
Edsel Maurice Salvana, MD, MSD: Advisor/Consultant|MSD: Honoraria|Pfizer: Advisor/Consultant|Pfizer: Honoraria.
1920. Lack of SARS-CoV-2 transmission from a Healthcare Worker to a Cohort of Immunosuppressed Patients during the Omicron Surge, California, 2022
Authors: Karan Abraar , Ferguson Jessica , Salinas Jorge 
Published: December 2022

Abstract

Background
The Omicron surge caused a significant strain on the healthcare system, particularly as it relates to healthcare worker (HCW) infections. Occult infection transmission from HCWs to patients is an important area upon which infection control programs can continue to improve.

Methods
We conducted a retrospective chart review of 9 patients on the immunocompromised solid organ transplant service who were exposed to a highly infectious vaccinated and boosted healthcare worker across 2 days during the Omicron surge in January 2022.

Results
The index healthcare worker began to show symptoms shortly after rounds on the second day of clinical service. Nasopharyngeal rtPCR testing for SARS CoV 2 was positive, Ct value 15.9; a routine screening Covid19 test the day prior using an anterior nares swab had been negative. All 9 patients who were exposed and received follow-up testing on days 3-5 since exposure were negative for SARS CoV 2. One additional healthcare worker who was also exposed tested negative on follow-up testing despite several hours of close contact across 2 days. Both HCWs wore N95 respirators during all patient care and in breakrooms. Patient exposures were less than 15 minutes in duration, but also less than 6 feet in distance.

Conclusion
The index healthcare worker did not transmit SARS CoV 2 to a cohort of immunocompromised patients or to a fellow HCW despite being very infectious. The index HCW wore an N95 respirator during all patient encounters which could have reduced the chance for transmission.

Disclosures
All Authors: No reported disclosures.
1926. Risky businesses: Carbon dioxide monitoring to assess ventilation in grocery stores as an indicator of risk for respiratory virus transmission
Authors: Teran Maria Torres , Cadnum Jennifer , Donskey Curtis 
Published: December 2022

Abstract

Background
Poorly ventilated indoor settings pose a risk for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses. Transmission often occurs in community, but limited information is available on the quality of ventilation in community settings.

Methods
We used carbon dioxide measurements to assess adequacy of ventilation in 6 grocery stores, including large warehouse stores, medium-sized stores, and small neighborhood groceries. Carbon dioxide levels were monitored continuously with values recorded once per minute using a handheld device during multiple shopping trips to each store during both busy (defined as long lines at checkout) and non-busy (defined as no lines at checkout) shopping times. Carbon dioxide readings above 800 parts per million (ppm) were considered an indicator of suboptimal ventilation for the number of people present.

Results
Carbon dioxide levels remained below 800 ppm in all 6 grocery stores during trips at non-busy shopping times, except for transient rises above 800 ppm (peak = 860 ppm) during check out in 2 stores. In 3 of the 6 stores (50%), carbon dioxide levels rose above 800 ppm for prolonged periods during busy shopping times, with considerable variability in levels in different store locations (ie, increased levels in crowded store locations). The figure shows carbon dioxide levels for 1 medium-sized grocery store during typical shopping trips during busy and non-busy shopping periods.
Increase in carbon dioxide levels in parts per million (ppm) in a grocery store during busy and non-busy shopping trips. Peak levels of carbon dioxide above 800 ppm (dotted lines) were considered an indicator of suboptimal ventilation for the number of occupants present.

Conclusion
Ventilation in grocery stores may be sufficient to minimize the risk for airborne transmission of respiratory pathogens during non-busy shopping periods, but in some stores may be sub-optimal in crowded locations during busy shopping times. There is a need for additional studies to assess the quality of ventilation in a wide range of community settings.

Disclosures
All Authors: No reported disclosures.