Vaccination is preventing development of placental pathologies in SARS-CoV-2 infected pregnant patients.

INTRODUCTION: The coronavirus disease (COVID-19) has created a serious health problem in pregnant people. We aimed to address whether vaccination can prevent development of placental disease in SARS-CoV-2 infected mothers. METHODS: We reported the pathology findings obtained from routine histopathological examination of placentas of overall 38 cases. RESULTS: We found low prevalence of placental pathology in vaccinated pregnant people with active SARS-CoV-2 infection in comparison to those unvaccinated cases. CONCLUSION: Based on our findings, SARS-CoV-2 vaccination can prevent development of placental pathological lesions and may lower the risk of serious illness in pregnant people.

Increased Prevalence of Group A Streptococcus (GAS) High Level Macrolide Resistance During the COVID-19 Pandemic

Background. COVID-19 affected the epidemiology ofmany respiratory pathogens including GAS. Assessing genetic heterogeneity (emmtype, antimicrobial resistance, virulence factors) can inform treatment recommendations and targets for potential GAS vaccines. We assessed GAS clinical antibiotic susceptibility and performed whole genome sequencing (WGS) among pediatric pharyngeal isolates from 2020-2022. Methods. From 1/2020-3/2022 we collected throat swabs in pediatric clinics and EDs from children aged 3-18 years in Chicago, IL;Atlanta, GA;Portland, OR;and Phoenix, AZ: 1) with acute GAS pharyngitis and 2) among a convenience sample of asymptomatic children to assess for GAS colonization. Swabs were plated on blood agar. E-tests were used to assess clinical susceptibility to erythromycin (ERY) and ciprofloxacin (CIP). emm type and antimicrobial resistance genes (ERY, Clindamycin (CLI), and fluoroquinolones) were assessed by WGS. Results. 1144 pharyngeal swabs were collected: 359/684 (52%) from children with GAS pharyngitis by rapid test and 20/460 (4.3%) from asymptomatic children yielded GAS on culture. Phenotypic resistance: 55/364 (15%) tested isolates were ERY resistant and 5/364 (1.4%) CIP resistant. The proportion of isolates with ERY resistance increased significantly from 2020 (6%) to 2021-2022 (25%) (chi2 = 23.70, p< .00001) (Figure 1). MICs were high among ERY resistant GAS (Table 1). Genotypic resistance: Of 304 sequenced GAS isolates 40/304 (13%) were ERY resistant, 35/304 (11.5%) were both ERY resistant and CLI (inducible or constitutive) resistant, and 4/304 (1.3%) fluoroquinolone resistant. ermB (62%) was the most common gene for ERY resistance and constitutive CLI resistance, followed by ermTR (23%) and ermT (11%) both conferring inducible CLI resistance. Among the 20 isolates from asymptomatic children no ERY, CLI, or CIP resistance occurred, and no resistance genes were identified. emm types 11, 9, 77, 58 and 94 were associated with ERY and CLI resistance. Conclusion. ERY resistance increased from 2020-2022. The high rate of CLI resistance among ERY resistant GAS was associated with erm genes. These results are important to inform treatment recommendations for GAS pharyngitis and targets for vaccine development that can reduce antimicrobial-resistant GAS disease.

A hypermutator strain of Pseudomonas aeruginosa in a COVID-19 patient with ventilator-associated pneumonia

Background. P. aeruginosa is a cause of hospital-acquired and ventilatorassociated pneumonia. Hypermutator P. aeruginosa strains have been described in patients with cystic fibrosis and chronic respiratory infections but are rare in patients with acute P. aeruginosa infection. This case describes a hypermutator strain of P. aeruginosa found in a patient with COVID-19-associated acute respiratory distress syndrome (ARDS). Methods. Serial respiratory and blood cultures were collected. Short-read sequencing libraries were prepared using the Illumina Nextera XT kit, and wholegenome sequencing was performed using the Illumina NextSeq platform. Long-read sequencing libraries were prepared from unsheared genomic DNA using ligation sequencing kit SQK-LSK109 and sequenced on the Oxford MinION platform. Single nucleotide variants were identified by aligning reads from each isolate to the complete genome of the first available clinical isolate. Hypermutator assays were performed by measuring the mutation frequency rate for rifampin resistance. Antibiotic minimal inhibitory concentrations (MICs) were performed. Growth curves were performed with a starting OD600 of 0.1 with measurements taken every 30 minutes for 24 hours. Results. Seventeen respiratory and five blood isolates were obtained throughout 62 days of hospitalization. Fourteen of the 22 isolates exhibited hypermutator phenotypes by rifampin resistance assays, which demonstrated rapid accumulation of mutations. All five bloodstream isolates were hypermutators. MIC testing noted increased resistance to aminoglycosides, fluoroquinolones, and aztreonam in the hypermutator isolates. All bloodstream isolates descended from a single progenitor noted on whole-genome sequencing. Each hypermutator strain contained a mutation in the mismatch repair gene mutL, previously associated with the hypermutator phenotype. Genetic Tree of Patient Isolates The genetic tree highlights hypermutator versus non-hypermutator single nucleotide variants Conclusion. This case was notable for multiple isolates of hypermutator P. aeruginosa that persisted over weeks. The patient's COVID-19 infection and acute respiratory distress syndrome may have facilitated persistence of the P. aeruginosa lineage, allowing a hypermutator lineage to emerge.

MUTATIONS in PERSISTENT SARS-CoV-2 CASES

Background: The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with decreased susceptibility to neutralizing antibodies are of clinical importance. While several demographic and clinical correlates of Coronavirus Disease 2019 (COVID-19) outcome have been identified, their relationship to virological and immunological parameters remain poorly defined. Here, we evaluate viral diversity and the accumulation of intra-host mutations over time in a population of hospitalized adults positive for SARS-CoV-2. Methods: We performed longitudinal collection of nasopharyngeal swabs and blood samples from a small cohort of hospitalized adults with COVID-19. Clinical information regarding study subject's immunocompromised status was collected. Samples were assessed for SARS-CoV-2 viral load, viral genotype, viral diversity, and antibody titer. Results: Intra-host viral genetic diversity remained constant through disease course in study subjects that were non-immunocompromised and resulted in changes in viral genotype in some participants. We report the de novo emergence of Spike mutations that have been previously associated with circulating variants of concern in two immunosuppressed patients with persistent SARS-CoV-2 infection. Conclusion: Constant rates of viral evolution suggest the emergence of variants as a function of time, emphasizing the need for effective antivirals to control viral load over long disease courses.

MOLECULAR EPIDEMIOLOGY of the COVID-19 PANDEMIC in CHICAGO

Background: The greater Chicagoland area has recorded over 10,000 COVID-related deaths and nearly 600,000 cases since the start of the COVID-19 pandemic in March of 2020. SARS-CoV-2, the causative agent of COVID-19, has continually changed over that time, with some variants evolving to become more transmissible or more resistant to neutralizing antibody responses. Methods: To better understand how viral genetic variation has contributed to differences in COVID-19 pathogenesis and patient outcome, we established a biobank of residual diagnostic samples from adult patients who tested positive for COVID-19 in a PCR-based test at Northwestern Memorial Hospital. Thus far, we have collected samples from 6448 out-patients and 632 in-patients. Of these, we have performed whole genome sequencing and viral load calculations on 1373 samples. Clinical and demographic information, including composite measures of disease severity, were extracted from available electronic health records. These data were assessed for longitudinal patterns and for specific association with viral lineage. Results: We found that the early epidemic in March of 2020 was defined by three distinct lineages reflecting the outbreaks in China (19B/A), Washington state (19B/A.1), and New York state (19A/B.1). By November of 2020, we saw a large increase in the number of confirmed cases, dominated by the 20G clade. This lineage remained predominant until March of 2021, when the Alpha and Gamma variants of concern became more established. These were recently supplanted by the Delta variant, which now accounts for over 90% of Chicago cases. At the height of the pandemic in November of 2020, case counts peaked at over 5000 cases per day, but hospitalizations, ICU admissions, and deaths over this period remained flat. Statistical testing revealed that the predominant clade at that time, 20G, was associated with better outcomes and less severe disease as measured by clinical measures of patient deterioration, even when controlling for patient demographics. These results suggest that a viral variant associated with less severe disease was predominant in late 2020 before the emergence of the more transmissible variants of concern. Conclusion: Current work is being done to determine if the less severe outcomes associated with this clade also contributed to more asymptomatic transmission, potentially contributing to the high case counts recorded over this period. These data emphasize the need for continued genomic surveillance of SARS-CoV-2 to character.

Drug eruption: A mimicker of Coronavirus disease-2019 rash

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infections can be associated with several cutaneous lesions, among which maculopapular rash is the most common. A maculopapular rash can also be induced by medications used for Coronavirus disease-2019 (COVID-19) treatment. The distinction between viral rash and drug eruption may be difficult especially in case of several medication use for COVID-19. Thus, this study aimed to describe cutaneous manifestations in six patients with COVID-19 and highlight clues for distinguishing SARS-CoV-2-related rash and drug eruption. Between March and June 2020, 1,492 patients were hospitalized for COVID-19 and treated with hydroxychloroquine in Marmara University Hospital. Among them, six cases were consulted for possible COVID-19-related rash or drug reaction. Hydroxychloroquine was given as monotherapy in one patient. All six patients developed an erythematous, symmetrical, and maculopapular eruption that mainly affected the trunk, axilla, and genitocrural region, 5-21 days after the onset of COVID-19 symptoms. Five patients developed rash in 4-11 days after treatment completion. Pruritus was severe. All were treated with topical corticosteroids and oral antihistamines, which provided partial relief. The resolution of the eruption was typically slow, which took a few weeks. A long period between the COVID-19 symptoms and the eruption, as well as slow recovery, is in favor of drug eruption. The effects of co-existent viral infection, a well-known promoting drug eruption factor, in facilitating adverse drug reaction in patients with COVID-19 needs further observations and research. © 2022 Istanbul Assoc. of Dermatology and Venerology. All rights reserved.

Drug eruption: A mimicker of Coronavirus disease-2019 rash

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infections can be associated with several cutaneous lesions, among which maculopapular rash is the most common. A maculopapular rash can also be induced by medications used for Coronavirus disease-2019 (COVID-19) treatment. The distinction between viral rash and drug eruption may be difficult especially in case of several medication use for COVID-19. Thus, this study aimed to describe cutaneous manifestations in six patients with COVID-19 and highlight dues for distinguishing SARS-CoV-2-related rash and drug eruption. Between March and June 2020, 1,492 patients were hospitalized for COVID-19 and treated with hydroxychloroquine in Marmara University Hospital. Among them, six cases were consulted for possible COVID-19-related rash or drug reaction. Hydroxychloroquine was given as monotherapy in one patient. All six patients developed an erythematous, symmetrical, and maculopapular eruption that mainly affected the trunk, axilla, and genitocrural region, 5-21 days after the onset of COVID-19 symptoms. Five patients developed rash in 4-11 days after treatment completion. Pruritus was severe. All were treated with topical corticosteroids and oral antihistamines, which provided partial relief. The resolution of the eruption was typically slow, which took a few weeks. A long period between the COVID-19 symptoms and the eruption, as well as slow recovery, is in favor of drug eruption. The effects of co-existent viral infection, a well-known promoting drug eruption factor, in facilitating adverse drug reaction in patients with COVID-19 needs further observations and research.

Important factors affecting the transmission rate of COVID-19 in G20 and EU

Coronavirus 2019 (COVID-19) is an infectious respiratory disease that might be fatal to humans due to severe acute respiratory syndrome coronovirus-2. COVID-19 first appeared in Wuhan, China in 2019 and soon have spread all over the world. Therefore, it was accepted as a global epidemic by the World Health Organization in March 2020. The aim of this study is to reveal the effects of the demographic structure of the countries, their socio-economic development, the precautions, and health practices implemented by the governments against COVID-19 on the rate of transmission until the first peak days (plateaus) are appeared. Due to the socio-economic developments and reaching out the clear and transparent COVID-19 dataset, the sample of the study was formed from G20 and EU countries. The in terpretable factors affecting the transmission rate of COVID-19 were extracted with factor analysis and multidimensional scaling. Multivariate analysis figures out the effects of th e pr ecautions an d health practices implemented by G20 and EU countries with similar/different socio-economic development characteristics on the transmission rate. For instance, a result obtained from the multivariate analyzes is that COVID-19 cases in developed and developing countries differ from each other at their first plateaus. Another noteworthy inference is that COVID-19 cases are trending similarly within some developed countries with the higher ratio of population (65+) and Human Development Index (HDI). Furthermore, the population ratio (15-64) is itself an explanatory factor that can be used to characterize similar transmission patterns between countries. Consequently, these findings may help state authorities to take urgent precautions and manage such a global epidemic by much more efficient health policies.

Longitudinal analysis of SARS-CoV-2 viruses in hospitalized adults

Background: The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of viral mutations, some of which may have distinct virological and clinical consequences. While whole genome sequencing efforts have worked to map this viral diversity at the population level, little is known about how SARS-CoV-2 may diversify within a host over time. This is particularly important for understanding the emergence of viral resistance to therapeutic interventions and immune pressure. The goal of this study was to assess the change in viral load and viral genome sequence within patients over time and determine if these changes correlate with clinical and/or demographic parameters. Methods: Hospitalized patients admitted to Northwestern Memorial Hospital with a positive SARS-CoV-2 test were enrolled in a longitudinal study for the serial collection of nasopharyngeal specimens. Swabs were administered to patients by hospital staff every 4 ± 1 days for up to 32 days or until the patients were discharged. RNA was extracted from each specimen and viral loads were calculated by quantitative reverse transcriptase PCR (qRT-PCR). Specimens with qRT-PCR cycle threshold values less than or equal to 30 were subject to whole viral genome sequencing by reverse transcription, multiplex PCR, and deep sequencing. Variant populations sizes were estimated and subject to phylogenetic analysis relative to publicly available SARS-CoV-2 sequences. Sequence and viral load data were subsequently correlated to available demographic and clinical data. Results: 60 patients were enrolled from March 26th to June 20th, 2020. We observed an overall decrease in nasopharyngeal viral load over time across all patients. However, the temporal dynamics of viral load differed on a patient-by-patient basis. Several mutations were also observed to have emerged within patients over time. Distribution of SARS-CoV-2 viral loads in serially collected nasopharyngeal swabs in hospitalized adults as determined by qRT-PCR. Samples were collected every 4 ± 1 days (T#1-8) and viral load is displayed by log(copy number). Conclusion: These data indicate that SARS-CoV-2 viral loads in the nasopharynx decrease over time and that the virus can accumulate mutations during replication within individual patients. Future studies will examine if some of these mutations may provide fitness advantages in the presence of therapeutic and/or immune selective pressures.

SARS-CoV-2 exhibits clade-specific differences in nasopharyngeal viral loads

Background: The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of distinct viral clades, although their clinical significance has yet to be fully elucidated. While whole genome sequencing efforts have identified viral diversity over time, less is known about the clinical significance of this diversity. This study assessed the nasopharyngeal viral loads within patients over time to determine if these changes affect clinical parameters. Methods: Samples were collected from patients presenting to Northwestern Memorial Hospital in Chicago, IL with a positive SARS-CoV-2 RT-PCR from nasopharyngeal swabs. Cycle threshold (Ct) values less than 35 were considered positive, and whole genome sequencing was performed by reverse transcription, multiplex PCR, and Nanopore sequencing. Phylogenetic analysis was conducted on sequenced isolates and compared with publicly available global sequences. Sequence characteristics and viral loads were correlated with each clade. Results: 177 samples were analyzed from March 14, 2020, through May 1, 2020. Most of the sequences (92.6%) clustered in three main clades [Figure 1]. Clade IDs were ordered by relative abundance as Clades 1 (n=122, 68.9%), 2 (n=34, 19.2%), and 3 (n=8, 4.5%). Over this time, Clade 1 viruses have been increasing in incidence across the USA and globally while Clade 2 viruses were uniquely predominant in Illinois with limited global distribution. Ct values were compared across clades [Figure 2]. Significantly lower average Ct values (higher viral loads) were observed in Clade 1 relative to both Clade 2 (p=0.0002) and Clade 3 (p=0.0011). These findings were independent of time from symptom onset to specimen collection. Phylogenetic Analysis of SARS-CoV-2 Isolates with Number of Clades and Clade Distribution Conclusion: These data suggest that SARS-CoV-2 genotype may impact viral load in the upper airways. It remains to be determined whether this difference in clades may impact transmission potential and overall viral spread. Further longitudinal studies with more specimens and associated clinical data are needed.