Prevalence of JAK2V617F, CALR in Philadelphia Positive and Negative Myeloproliferative Neoplasm

Background: Myeloproliferative neoplasms (MPNs) are heterogeneous disorders with a variety of genetic abnormalities. We aim to assess the prevalence of Calreticulin (CALR) and JAK2 mutations in Iranian MPNs. Materials and Methods: In a cross-sectional study, CALR and JAK2 mutations among 130 MPNs patients, including 78 Philadelphia chromosome-negative (MPN-) and 52 Philadelphia chromosome-positive (MPN+) as well as 51 healthy control subjects, were investigated by GAP-PCR. Results: In MPN- group JAK2 and CALR gene mutations were found in 64.1% and 7.7%, respectively, that 5.1% were positive for both mutations, and 2.6% had only CALR mutation. In polycythemia vera (PV) patients 90% had JAK2 mutation, which was significantly higher than other MPN- or MPN+ patients. Most of the MPN+ patients had neither mutation in CALR nor JAK2 (70% CALR-/JAK2-). Among all patients’ groups, the prevalence of CALR+ mutation in either rs1450785140 (4 cases) or rs765476509 (5 cases) position was not statistically different. Conclusion: These results showed a low prevalence of CALR mutations in all types of MPNs in the Iranian population that its frequency may influence by ethnicity and genetic diversity. CALR mutation may be seen in JAK2 negative cases, also. The PV had the highest JAK2 mutation with a 90 percent positivity rate among MPNs cases. [GMJ.2021;10:e2127]

Retrospective cohort study of COVID-19 among children in Fulton County, Georgia, March 2020–June 2021

ObjectiveTo describe case rates, testing rates and percent positivity of COVID-19 among children aged 0–18 years by school-age grouping.DesignWe abstracted data from Georgia’s State Electronic Notifiable Disease Surveillance System on all 10 437 laboratory-confirmed COVID-19 cases among children aged 0–18 years during 30 March 2020 to 6 June 2021. We examined case rates, testing rates and percent positivity by school-aged groupings, namely: preschool (0–4 years), elementary school (5–10 years), middle school (11–13 years), and high school (14–18 years) and compared these data among school-aged children with those in the adult population (19 years and older).SettingFulton County, Georgia.Main outcome measuresCOVID-19 case rates, testing rates and percent positivity.ResultsOver time, the proportion of paediatric cases rose substantially from 1.1% (April 2020) to 21.6% (April 2021) of all cases in the county. Age-specific case rates and test rates were consistently highest among high-school aged children. Test positivity was similar across school-age groups, with periods of higher positivity among high-school aged children.ConclusionsLow COVID-19 testing rates among children, especially early in the pandemic, likely underestimated the true burden of disease in this age group. Despite children having lower measured incidence of COVID-19, we found when broader community incidence increased, incidence also increased among all paediatric age groups. As the COVID-19 pandemic continues to evolve, it remains critical to continue learning about the incidence and transmissibility of COVID-19 in children.

Longitudinal SARS-CoV-2 RNA Wastewater Monitoring Across a Range of Scales Correlates with Total and Regional COVID-19 Burden in a Well-Defined Urban Population

Wastewater-based epidemiology (WBE) is an emerging surveillance tool that has been used to monitor the ongoing COVID-19 pandemic by tracking SARS-CoV-2 RNA shed into wastewater. WBE was performed to monitor the occurrence and spread of SARS-CoV-2 from three wastewater treatment plants (WWTP) and six neighborhoods in the city of Calgary, Canada (population 1.3 million). A total of 222 WWTP and 192 neighborhood samples were collected from June 2020 to May 2021, encompassing the end of the first-wave (June 2020), the second-wave (November end to December, 2020) and the third-wave of the COVID-19 pandemic (mid-April to May, 2021). Flow-weighted 24-hour composite samples were processed to extract RNA that was then analyzed for two SARS-CoV-2-specific regions of the nucleocapsid gene, N1 and N2, using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Using this approach SARS-CoV-2 RNA was detected in 98.06 percent (406/414) of wastewater samples. SARS-CoV-2 RNA abundance was compared to clinically diagnosed COVID-19 cases organized by the three-digit postal code of affected individuals primary residences, enabling correlation analysis at neighborhood, WWTP and city-wide scales. Strong correlations were observed between N1 and N2 gene signals in wastewater and new daily cases for WWTPs and neighborhoods. Similarly, when flow rates at Calgarys three WWTPs were used to normalize observed concentrations of SARS-CoV-2 RNA and combine them into a city-wide signal, this was strongly correlated with regionally diagnosed COVID-19 cases and clinical test percent positivity rate. Linked census data demonstrated disproportionate SARS-CoV-2 in wastewater from areas of the city with lower socioeconomic status and more racialized communities. WBE across a range of urban scales was demonstrated to be an effective mechanism of COVID-19 surveillance.

SARS-CoV-2 Mortality Surveillance among Community Deaths brought to University Teaching Hospital Mortuary in Lusaka, Zambia, 2020

Introduction: During March-December 2020, Zambia recorded 20,725 confirmed COVID-19 cases, with the first wave peaking between July and August. Of the 388 COVID-19-related deaths occurring nationwide, most occurred in the community. We report findings from COVID-19 mortality surveillance among community deaths brought to the University Teaching Hospital (UTH) mortuary in Lusaka. Methods: In Zambia, when a person dies in the community, and is brought into a health facility mortuary, they are recorded as 'brought in dead' (BID). The UTH mortuary accepts persons BID for Lusaka District, the most populated district in Zambia. We analyzed data for persons BID at UTH during 2020. We analyzed two data sources: weekly SARS-CoV-2 test results for persons BID and monthly all-cause mortality numbers among persons BID. For all-cause mortality among persons BID, monthly deaths during 2020 that were above the upper bound of the 95% confidence interval for the historic mean (2017-2019) were considered significant. Spearman's rank test was used to correlate the overall percent positivity in Zambia with all-cause mortality and SARS-CoV-2 testing among persons BID at UTH mortuary. Results: During 2020, 7,756 persons were BID at UTH (monthly range 556-810). SARS-CoV-2 testing began in April 2020, and through December 3,131 (51.9%) of 6,022 persons BID were tested. Of these, 212 (6.8%) were SARS-CoV-2 positive with weekly percent test positivity ranging from 0-32%, with the highest positivity occurring during July 2020. There were 1,139 excess persons BID from all causes at UTH mortuary in 2020 compared to the 2017-2019 mean. The monthly number of persons BID from all causes was above the upper bound of the 95% confidence interval during June-September and December. Conclusion: Increases in all-cause mortality and SARS-CoV-2 test positivity among persons BID at UTH mortuary corresponded with the first peak of the COVID-19 epidemic in June and August 2020, indicating possible increased mortality related to the COVID-19 epidemic in Zambia. Combining all-cause mortality and SARS-CoV-2 testing for persons BID provides useful information about the severity of the epidemic in Lusaka and should be implemented throughout Zambia.

Expression of Programmed Cell Death-1 (PD-1) and Its Ligand (PD-L1) in Breast Cancers and Its Association with Clinicopathological Parameters: A Study from North India

Introduction Cancer immunotherapy targeting the programmed cell death ligand 1 (PD-L1) and programmed cell death-1 (PD-1) axis has revolutionized cancer therapy. PD-L1 also serves as a predictive marker for such therapy. To assess the potential of such therapy in any cancer, the positivity of PD-1 and PD-L1 in such cancers needs to be assessed. However, such studies for breast cancer are lacking in South Asia. We aimed to estimate the positivity of PD-L1 and PD-1 receptors in breast cancer and its various clinicopathological groups in our patient population. Materials and Methods We studied the immunoexpression of PD-1 and PD-L1 in 103 histologically proven invasive carcinoma breast cases from October 2018 to April 2019. The percent positivity of PD-1 and PD-L1 with 95% confidence intervals (CI) was estimated for all the cases as well as groups defined by stage, grade, molecular subtype, hormone receptor status, Ki-67, and age. Results PD-1 positivity was seen in 72 (69.9%) cases (95% CI: 60.1–78.6). PD-L1 immunoexpression was seen in 61 (59.2%) cases (95% CI: 49.1–68.8) in immune cells and in 39 (37.9%) cases (95% CI: 28.5–50.0) in tumor cells. No significant association was found between PD-1, PD-L1 and age, overall clinical stage, grade, size, estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and Ki-67. Moderate-to-high PD-1 and PD-L1 immunopositivity was seen in all subtypes of breast cancer. Conclusion PD-1 and PD-L1 is expressed in all subgroups of breast carcinoma. Patients in all such groups are amenable to immunotherapy, provided they are found suitable otherwise.

Multicenter comparison of nucleic acid amplification tests for the diagnosis of rectal and oropharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae infection.

Research using nucleic acid amplification tests (NAATs) have repeatedly found rectal and oropharyngeal infections with Chlamydia trachomatis and Neisseria gonorrhoeae to be common and potentially more difficult to treat than genital infections. Unfortunately, public health and patient care efforts have been hampered by the lack of FDA-cleared NAATs with claims for anorectal or oropharyngeal samples. At the time of the initiation of this study, no commercially available assays had these claims. We formed a novel partnership among academic institutions and diagnostic manufacturers to address this public health need. From May 2018 through August 2019 we recruited 1108 women, 1256 men and 26 transgender persons each of whom provided 3 anal and 3 oropharyngeal swab specimens. The 3 anal swabs were pooled into a single transport tube as were the 3 oropharyngeal swabs. The performance of each of three study assays was estimated by comparison to the composite result and relative to one another. Percent positivity for chlamydia was 5.9 and 1.2% from anal and oropharyngeal specimens, respectively compared to 4.2 and 4.1% for gonorrhea. Sensitivity for chlamydia detection ranged from 81.0-95.1% and 82.8-100% for anal and oropharyngeal specimens, respectively. Gonorrhea sensitivity ranged from 85.9-99.0% and 74.0-100% for anal and oropharyngeal samples, respectively. Specificity estimates were ≥ 98.9% for all assays, organisms and sample types. Although there was heterogeneity between sensitivity estimates, these assays offer better ability to detect extra genital infections than culture and potential solutions for providing appropriate sexual healthcare for populations in which these infections are of concern.

A Retrospective Cohort Study of COVID-19 among Children in Fulton County, Georgia, March 2020 - June 2021

Objective: To describe case rates, testing rates, and percent positivity of coronavirus disease 2019 (COVID-19) among children aged 0-18 years by school-age grouping. Design: We abstracted data from Georgia's State Electronic Notifiable Disease Surveillance System on all 10,437 laboratory-confirmed COVID-19 cases among children aged 0-18 years during March 30, 2020 to June 6, 2021. We examined case rates, testing rates, and percent positivity by school-aged groupings, namely: preschool (0-4 years), elementary school (5-10 years), middle school (11-13 years), and high school (14-18 years) and compared these data among school aged children to those in the adult population (19 years and older). Setting: Fulton County, Georgia. Main outcome measures: COVID-19 case rates, testing rates, and percent positivity. Results: Over time, the proportion of pediatric cases rose substantially from 1.1% (April 2020) to 21.6% (April 2021) of all cases in the county. Age-specific case rates and test rates were consistently highest among high-school aged children. Test positivity was similar across school-age groups, with periods of higher positivity among high-school aged children. Conclusions: Low COVID-19 testing rates among children, especially early in the pandemic, likely underestimate the true burden of disease in this age group. Despite children having lower measured incidence of COVID-19, we found when broader community incidence increased, incidence also increased among all pediatric age groups. As the COVID-19 pandemic continues to evolve, it remains critical to continue learning about the incidence and transmissibility of COVID-19 in children.

147. Defining the Optimal Serial Testing Interval and Features for Identifying Patients with Early SARS-CoV-2 Infection

Background Serial testing for SARS-CoV-2 is necessary to prevent spread from patients early in infection. Testing intervals are largely derived from viral kinetic studies performed early in the COVID-19 pandemic. Laboratory and epidemiologic data accrued over the past year present an opportunity to use empiric models to define optimal serial testing intervals and features predictive of early infection. Methods Retrospective analysis of 15,314 inpatients within the Mass General Brigham healthcare system who had two tests within a 36-hour period between May 1 2020 and May 29 2021. Early infection was defined as having a negative test followed by a positive test. Patients with prior positive tests were excluded. The primary outcome was the proportion of patients in early infection over the total number tested serially, stratified by 4-hour testing intervals from the timestamp of the first test. Multivariate modeling was used to identify features predictive of early infection. Covariates included demographics, body site, PCR assay, location, community incidence, percent positivity, and median / skew of Ct value distributions. Results Of 19,971 test pairs, 193 (0.97%) were characterized as a negative followed by a positive within 36 hours. Bivariate analysis showed a close association between negative to positive test pairs during the first surge in spring 2020 that was not present during the winter surge. Negative to positive test pairs were most common in the 12 to 16 hour time interval (51/193, 26%, Figure 1). After controlling for covariates, the Roche cobas assay was more likely to identify patients with a negative to positive test pair relative to the Cepheid Xpert, Hologic Panther Fusion and Roche Liat assays. A second specimen from the lower respiratory tract was more likely to lead to a positive relative to other body sites. Community incidence and Ct value distributions were not predictive and there were no differences between nasal and nasopharyngeal swabs. All 4-hour time intervals from 16 to 36 hours were significant for predicting a negative to positive test pair (Table 1). Figure 1. Distribution of negative to positive test pairs by 4 hour time intervals Table 1. Multivariate regression predicting a negative to positive test pair Conclusion The likelihood of detecting early infection is dependent on PCR platform and body site of sampling. A range of time intervals between 16 to 36 hours after the initial test were likely to identify positive cases. Disclosures Sanjat Kanjilal, MD, MPH, GlaskoSmithKline (Advisor or Review Panel member)

174. Increase in Candida auris cases in New Jersey healthcare facilities during the COVID-19 pandemic — 2017–2020

Background Candida auris is a fungal pathogen associated with multidrug resistance, high mortality, and healthcare transmission. Since its U.S. emergence in 2017, to March 19, 2021, 1708 clinical infections were reported nationwide, of which 235 (13.8%) were reported in New Jersey. The New Jersey Department of Health (NJDOH) maintains C. auris surveillance in healthcare facilities (HCF) such as acute care hospitals, long-term acute care hospitals (LTACHs), and skilled nursing facilities, to monitor clinical infections and patient colonization. We aimed to characterize the epidemiology of C. auris infection and colonization among HCF patients during 2017–2020. Methods HCFs report C. auris cases identified from clinical specimens and surveillance activities such as admission screenings and point prevalence surveys (PPS) to NJDOH. Cases are classified as either infection or colonization using National Notifiable Diseases Surveillance System case definitions. We analyzed cases reported during 2017–2020 to describe types of cases, facilities reporting cases, and demographics of affected patients. We analyzed PPS results to calculate percent positivity of tests from patients without previously identified infection and compared percent positivity between types of facilities. We examined quarterly trends for all variables before and after the COVID-19 pandemic peak in the second quarter of 2020. Results During 2017–2020, 614 C. auris cases identified from clinical specimens were reported to NJDOH [243 (39.6%) infection, 371 (60.4%) colonization]; of these, 139 (57.2%) and 301 (81.1%) , respectively, were identified at long-term acute care hospitals (LTACHs). PPS percent positivity was higher at LTACHs (mean 7.6%) compared with all other facility types (mean 3.6%) for 13 of 16 quarters during 2017–2020. Case reports increased 2.6-fold from the Q2 2020 peak of the COVID-19 pandemic to Q3 2020.From Q1 to Q4 2020, PPS percent positivity increased from 4.8% to 10.5%. Figure 1. Candida auris cases reported to New Jersey Department of Health, 2017–2020 Figure 2. Candida auris test percent positivity among healthcare facility patients sampled for point prevalence surveys* and total number of C. auris point prevalence tests performed, New Jersey, 2017–2020. *Excluding individuals already known to be cases Conclusion The COVID-19 pandemic may have exacerbated C. auris transmission in HCF and potential causes should be further explored. LTACHs carry a disproportionate burden of patients colonized with C. auris and should be prioritized for surveillance and containment efforts. Disclosures All Authors: No reported disclosures

154. Circulation of Rhinovirus/Enterovirus Respiratory Infections in Children During 2020-21 in the United States

Background Sharp declines in influenza and respiratory syncytial virus (RSV) circulation across the U.S. have been described during the pandemic in temporal association with community mitigation for control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to determine relative frequencies of rhinovirus/enterovirus (RV/EV) and other respiratory viruses in children presenting to emergency departments or hospitalized with acute respiratory illness (ARI) prior to and during the COVID-19 pandemic. Methods We conducted a multi-center active prospective ARI surveillance study in children as part of the New Vaccine Surveillance Network (NVSN) from December 2016 through January 2021. Molecular testing for RV/EV, RSV, influenza, and other respiratory viruses [i.e., human metapneumovirus, parainfluenza virus (Types 1-4), and adenovirus] were performed on specimens collected from children enrolled children. Cumulative percent positivity of each virus type during March 2020–January 2021 was compared from March-January in the prior seasons (2017-2018, 2018-2019, 2019-2020) using Pearson’s chi-squared. Data are provisional. Results Among 69,403 eligible children, 37,676 (54%) were enrolled and tested for respiratory viruses. The number of both eligible and enrolled children declined in early 2020 (Figure 1), but 4,691 children (52% of eligible) were enrolled and tested during March 2020-January 2021. From March 2020-January 2021, the overall percentage of enrolled children with respiratory testing who had detectable RV/EV was similar compared to the same time period in 2017-2018 and 2019-2020 (Figure 1, Table 1). In contrast, the percent positivity of RSV, influenza, and other respiratory viruses combined declined compared to prior years, (p< 0.001, Figure 1, Table 1). Figure 1. Percentage of Viral Detection Among Enrolled Children Who Received Respiratory Testing, New Vaccine Surveillance Network (NVSN), United States, December 2016 – January 2021 Table 1. Percent of Respiratory Viruses Circulating in March 2020– January 2021, compared to March-January in Prior Years, New Vaccine Surveillance Network (NVSN), United States, March 2017 – January 2021 Conclusion During 2020, RV/EV continued to circulate among children receiving care for ARI despite abrupt declines in other respiratory viruses within this population. These findings warrant further studies to understand virologic, behavioral, biological, and/or environmental factors associated with this continued RV/EV circulation. Disclosures Jennifer E. Schuster, MD, Merck, Sharpe, and Dohme (Individual(s) Involved: Self): Grant/Research Support Marian G. Michaels, MD, MPH, Viracor (Grant/Research Support, performs assay for research study no financial support) John V. Williams, MD, GlaxoSmithKline (Advisor or Review Panel member, Independent Data Monitoring Committee)Quidel (Advisor or Review Panel member, Scientific Advisory Board) Elizabeth P. Schlaudecker, MD, MPH, Pfizer (Grant/Research Support)Sanofi Pasteur (Advisor or Review Panel member) Christopher J. Harrison, MD, GSK (Grant/Research Support)Merck (Grant/Research Support)Pfizer (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support) Janet A. Englund, MD, AstraZeneca (Consultant, Grant/Research Support)GlaxoSmithKline (Research Grant or Support)Meissa Vaccines (Consultant)Pfizer (Research Grant or Support)Sanofi Pasteur (Consultant)Teva Pharmaceuticals (Consultant) Claire Midgley, PhD, Nothing to disclose Natasha B. Halasa, MD, MPH, Genentech (Other Financial or Material Support, I receive an honorarium for lectures - it’s a education grant, supported by genetech)Quidel (Grant/Research Support, Other Financial or Material Support, Donation of supplies/kits)Sanofi (Grant/Research Support, Other Financial or Material Support, HAI/NAI testing) Natasha B. Halasa, MD, MPH, Genentech (Individual(s) Involved: Self): I receive an honorarium for lectures - it’s a education grant, supported by genetech, Other Financial or Material Support, Other Financial or Material Support; Sanofi (Individual(s) Involved: Self): Grant/Research Support, Research Grant or Support