المؤلفون: Yang, Shangxin, Hemarajata, Peera, Hilt, Evann E, Price, Travis K, Garner, Omai B, Green, Nicole M

المصدر: American Journal of Clinical Pathology. 157(5)

مصطلحات موضوعية: Infectious Diseases, Vaccine Related, Emerging Infectious Diseases, Lung, Biodefense, Prevention, Pneumonia, Good Health and Well Being, COVID-19, California, Genomics, Hospitalization, Humans, Intensive Care Units, SARS-CoV-2, Epsilon variant, B, 1, 429, 427, ICU, Genomic surveillance, B.1.427, B.1.429, Medical and Health Sciences, Pathology

الوصف: ObjectivesThis study aimed to assess whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Epsilon variant (B.1.429/427) is more virulent, leading to more hospitalization and more severe disease requiring intensive care unit (ICU) admission.MethodsSARS-CoV-2 genomic surveillance was performed on respiratory samples from 231 unique patients, collected at a single large health system in Southern California between November 2020 and March 2021 during the winter surge.ResultsThe frequencies of the Epsilon variant among outpatients, hospitalized patients, and ICU patients were indifferent.ConclusionsOur study suggests that the Epsilon variant is not associated with increased hospitalization and ICU admission.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/7zk2q5kwTest

المؤلفون: Chen, Nicholas F.G., Chaguza, Chrispin, Gagne, Luc, Doucette, Matthew, Smole, Sandra, Buzby, Erika, Hall, Joshua, Ash, Stephanie, Harrington, Rachel, Cofsky, Seana, Clancy, Selina, Kapsak, Curtis J., Sevinsky, Joel, Libuit, Kevin, Park, Daniel J., Hemarajata, Peera, Garrigues, Jacob M., Green, Nicole M., Sierra-Patev, Sean, Carpenter-Azevedo, Kristin, Huard, Richard C., Pearson, Claire, Incekara, Kutluhan, Nishimura, Christina, Huang, Jian Ping, Gagnon, Emily, Reever, Ethan, Razeq, Jafar, Muyombwe, Anthony, Borges, Vítor, Ferreira, Rita, Sobral, Daniel, Duarte, Silvia, Santos, Daniela, Vieira, Luís, Gomes, João Paulo, Aquino, Carly, Savino, Isabella M., Felton, Karinda, Bajwa, Moneeb, Hayward, Nyjil, Miller, Holly, Naumann, Allison, Allman, Ria, Greer, Neel, Fall, Amary, Mostafa, Heba H., McHugh, Martin P., Maloney, Daniel M., Dewar, Rebecca, Kenicer, Juliet, Parker, Abby, Mathers, Katharine, Wild, Jonathan, Cotton, Seb, Templeton, Kate E., Churchwell, George, Lee, Philip A., Pedrosa, Maria, McGruder, Brenna, Schmedes, Sarah, Plumb, Matthew R., Wang, Xiong, Barcellos, Regina Bones, Godinho, Fernanda M.S., Salvato, Richard Steiner, Ceniseros, Aimee, Breban, Mallery I., Grubaugh, Nathan D., Gallagher, Glen R., Vogels, Chantal B.F.

مصطلحات موضوعية: Mpox, Mpox Outbreak, Monkeypox Virus, Genomic Surveillance, Whole-genome Sequencing, Outbreak Response, Global Emergence, Pandemics, Infecções Emergentes

الوصف: The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented ...

العلاقة: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002151Test; PLoS Biol. 2023 Jun 13;21(6):e3002151. doi:10.1371/journal.pbio.3002151. eCollection 2023 Jun; http://hdl.handle.net/10400.18/8955Test

الإتاحة: https://doi.org/10.1371/journal.pbio.3002151Test
http://hdl.handle.net/10400.18/8955Test

المؤلفون: Deng, Xianding, Garcia-Knight, Miguel A, Khalid, Mir M, Servellita, Venice, Wang, Candace, Morris, Mary Kate, Sotomayor-González, Alicia, Glasner, Dustin R, Reyes, Kevin R, Gliwa, Amelia S, Reddy, Nikitha P, Sanchez San Martin, Claudia, Federman, Scot, Cheng, Jing, Balcerek, Joanna, Taylor, Jordan, Streithorst, Jessica A, Miller, Steve, Sreekumar, Bharath, Chen, Pei-Yi, Schulze-Gahmen, Ursula, Taha, Taha Y, Hayashi, Jennifer M, Simoneau, Camille R, Kumar, G Renuka, McMahon, Sarah, Lidsky, Peter V, Xiao, Yinghong, Hemarajata, Peera, Green, Nicole M, Espinosa, Alex, Kath, Chantha, Haw, Monica, Bell, John, Hacker, Jill K, Hanson, Carl, Wadford, Debra A, Anaya, Carlos, Ferguson, Donna, Frankino, Phillip A, Shivram, Haridha, Lareau, Liana F, Wyman, Stacia K, Ott, Melanie, Andino, Raul, Chiu, Charles Y

المصدر: Cell. 184(13)

مصطلحات موضوعية: 20C/L452R, B.1.427/B.1.429, COVID-19, L452R mutation, SARS-CoV-2, antibody neutralization, genomic epidemiology, molecular dating, pseudovirus infectivity studies, spike protein, variant of concern, viral whole-genome sequencing, Developmental Biology, Biological Sciences, Medical and Health Sciences

الوصف: We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6%-24% increased transmissibility relative to wild-type circulating strains. The variant carries three mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0- to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/9532h9t0Test

المؤلفون: Chen, Nicholas F. G., Chaguza, Chrispin, Gagne, Luc, Doucette, Matthew, Smole, Sandra, Buzby, Erika, Hall, Joshua, Ash, Stephanie, Harrington, Rachel, Cofsky, Seana, Clancy, Selina, Kapsak, Curtis J., Sevinsky, Joel, Libuit, Kevin, Park, Daniel J., Hemarajata, Peera, Garrigues, Jacob M., Green, Nicole M., Sierra-Patev, Sean, Carpenter-Azevedo, Kristin, Huard, Richard C., Pearson, Claire, Incekara, Kutluhan, Nishimura, Christina, Huang, Jian Ping, Gagnon, Emily, Reever, Ethan, Razeq, Jafar, Muyombwe, Anthony, Borges, Vítor, Ferreira, Rita, Sobral, Daniel, Duarte, Silvia, Santos, Daniela, Vieira, Luís, Gomes, João Paulo, Aquino, Carly, Savino, Isabella M., Felton, Karinda, Bajwa, Moneeb, Hayward, Nyjil, Miller, Holly, Naumann, Allison, Allman, Ria, Greer, Neel, Fall, Amary, Mostafa, Heba H., McHugh, Martin P., Maloney, Daniel M., Dewar, Rebecca

المساهمون: Sugden, Bill, National Center for Advancing Translational Sciences, European Center for Disease Control

المصدر: PLOS Biology ; volume 21, issue 6, page e3002151 ; ISSN 1545-7885

الوصف: The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented ...

الإتاحة: https://doi.org/10.1371/journal.pbio.3002151Test

المؤلفون: Karan, Abraar, Shah, Naman, Garrigues, Jacob M, Alarcόn, Jemma, Hemarajata, Peera, Finn, Lauren E, Poortinga, Kathleen, Danza, Phoebe, Kulkarni, Sonali, Kim, Moon, Terashita, Dawn, Green, Nicole M, Balter, Sharon

المصدر: Journal of Infectious Diseases; 2024 Supplement, Vol. 229, pS249-S254, 6p

مصطلحات موضوعية: MONKEYPOX, PUBLIC health surveillance, HIV, CD4 lymphocyte count

مصطلحات جغرافية: LOS Angeles (Calif.)

مستخلص: The Los Angeles County Department of Public Health established a surveillance system to identify complicated (advanced human immunodeficiency virus [HIV] or hospitalized) mpox cases. From 1 August to 30 November 2022, we identified 1581 mpox cases, of which 134 (8.5%) were complicated. A subset of 8 cases did not recover after either initiating or completing a course of oral tecovirimat. All 8 patients were HIV positive and had advanced HIV (CD4 count <200 cells/μL). We identified 8 distinct mutations previously associated with tecovirimat resistance in specimens collected from 6 patients. Ongoing surveillance of viral evolution requires close coordination between health departments and frontline providers. [ABSTRACT FROM AUTHOR]

: Copyright of Journal of Infectious Diseases is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

المؤلفون: Yang, Shangxin, Hemarajata, Peera, Hindler, Janet, Ward, Kevin, Adisetiyo, Helty, Li, Fan, Aldrovandi, Grace M, Green, Nicole M, Russell, Dana, Rubin, Zachary, Humphries, Romney M

المصدر: Diagnostic Microbiology and Infectious Disease. 84(4)

مصطلحات موضوعية: Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Lung, Clinical Research, Pneumonia & Influenza, Genetics, Biotechnology, Pneumonia, Bacterial Proteins, Cross Infection, Electrophoresis, Gel, Pulsed-Field, Genome, Bacterial, Genotype, Humans, Klebsiella Infections, Klebsiella pneumoniae, Molecular Epidemiology, Molecular Typing, Sequence Analysis, DNA, beta-Lactam Resistance, beta-Lactamases, Whole genome sequencing, WGS, Carbapenem resistance, CRE, CRKP, Nosocomial transmission, PFGE, Single nucleotide variant, SNV, Tn4401, Mutation, NGS, Microbiology, Clinical sciences, Medical microbiology

الوصف: Whole genome sequencing (WGS) was compared to pulse-field gel electrophoresis (PFGE) of XbaI-digested genomic DNA, as methods by which to evaluate a potential transmission of carbapenem-resistant Klebsiella pneumoniae between 2 hospital inpatients. PFGE result demonstrated only 1-band difference between the isolates, suggesting probable relatedness. In contrast, while WGS data demonstrated the same sequence type and very similar chromosomal sequences, over 20 single nucleotide variants were identified between the isolates, bringing into question whether there was a transmission event. WGS also identified an additional plasmid, with an XbaI restriction site in the isolates of the second patient that was not identified by PFGE. While WGS provided additional information that was not available by PFGE, in this study, neither method could definitively conclude the relatedness between the isolates.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/4pk4q9mxTest

المؤلفون: OYong, Kelsey, Killerby, Marie, Pan, Chao-Yang, Huynh, Thalia, Green, Nicole M., Wadford, Debra A., Terashita, Dawn

المصدر: Morbidity and Mortality Weekly Report, 2018 Dec 01. 67(48), 1347-1349.

الوصول الحر: https://www.jstor.org/stable/26574314Test

المؤلفون: Buono, Sean A., Basurto-Davila, Ricardo, Godwin, Hilary A., Green, Nicole M.

المصدر: Sexually Transmitted Diseases, 2018 Dec 01. 45(12), 834-841.

الوصول الحر: https://www.jstor.org/stable/48512517Test

المؤلفون: Leonard, Colleen M., Poortinga, Kathleen, Nguyen, Erin, Karan, Abraar, Kulkarni, Sonali, Cohen, Rebecca, Garrigues, Jacob M., Marutani, Amy N., Green, Nicole M., Kim, Andrea A., Sey, Kwa, Pérez, Mario J.

المصدر: MMWR: Morbidity & Mortality Weekly Report; 1/18/2024, Vol. 73 Issue 2, p44-48, 5p

مصطلحات موضوعية: PUBLIC health, MONKEYPOX virus, PREVENTIVE medicine, INFECTIOUS disease transmission

مصطلحات جغرافية: UNITED States

مستخلص: Since May 2022, approximately 2,500 mpox cases have been reported in Los Angeles County (LAC), California. Beginning in May 2023, the LAC Department of Public Health observed a consistent increase in mpox cases after a prolonged period of low incidence. A total of 56 cases were identified during May 4-August 17, 2023. A minority of mpox patients were fully vaccinated (29%). One patient was hospitalized; no deaths were reported. Two cases of reinfection occurred, both of which were associated with mild illness. The increasing number of cases during this period was significant, as few other health departments in the United States reported an increase in mpox cases during the same period. The outbreak spread similarly to the 2022 U.S. mpox outbreak, mainly through sexual contact among gay, bisexual, and other men who have sex with men. Vaccination against mpox became available in June 2022 and has been shown to be effective at preventing mpox disease. This outbreak was substantially smaller than the 2022 mpox outbreak in LAC (2,280 cases); possible explanations for the lower case count include increased immunity provided from vaccination against mpox and population immunity from previous infections. Nonetheless, mpox continues to spread within LAC, and preventive measures, such as receipt of JYNNEOS vaccination, are recommended for persons at risk of Monkeypox virus exposure. [ABSTRACT FROM AUTHOR]

: Copyright of MMWR: Morbidity & Mortality Weekly Report is the property of Centers for Disease Control & Prevention (CDC) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

المؤلفون: Yang, Shangxin, Hemarajata, Peera, Hilt, Evann E, Price, Travis K, Garner, Omai B, Green, Nicole M

المساهمون: CDC Epidemiology and Laboratory Capacity for Infectious Diseases, UCLA Department of Pathology and Laboratory Medicine

المصدر: American Journal of Clinical Pathology ; volume 157, issue 5, page 649-652 ; ISSN 0002-9173 1943-7722

مصطلحات موضوعية: General Medicine

الوصف: Objectives This study aimed to assess whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Epsilon variant (B.1.429/427) is more virulent, leading to more hospitalization and more severe disease requiring intensive care unit (ICU) admission. Methods SARS-CoV-2 genomic surveillance was performed on respiratory samples from 231 unique patients, collected at a single large health system in Southern California between November 2020 and March 2021 during the winter surge. Results The frequencies of the Epsilon variant among outpatients, hospitalized patients, and ICU patients were indifferent. Conclusions Our study suggests that the Epsilon variant is not associated with increased hospitalization and ICU admission.

الإتاحة: https://doi.org/10.1093/ajcp/aqab203Test
https://academic.oup.com/ajcp/article-pdf/157/5/649/49102755/aqab203.pdfTest