The Indonesian Journal of Infectious Diseases最新文献

{"title":"Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021","authors":"T. Vasylyeva, Courtney E. Fang, Michelle Su, J. L. Havens, Edyth Parker, Jade C. Wang, M. Zeller, A. Yakovleva, G. Hassler, Moinuddin A. Chowdhury, K. Andersen, S. Hughes, J. Wertheim","doi":"10.1101/2022.04.15.22273909","DOIUrl":"https://doi.org/10.1101/2022.04.15.22273909","url":null,"abstract":"Background. Monitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. Travel restrictions, aimed to prevent viral spread, have major economic consequences and unclear effectiveness despite considerable research. We investigated the introduction and establishment of the Gamma variant in New York City (NYC) in 2021. Methods. We performed phylogeographic analysis on 15,967 Gamma sequences available on GISAID and sampled between March 10th through May 1st, 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC. Findings. We identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes). Most of the NYC clusters were introduced from Florida and Illinois; only one was introduced from outside the United States (US). By the time the first Gamma case was reported by genomic surveillance in NYC on March 10th, the majority (57%) of circulating Gamma lineages had already been established in the city for at least two weeks. Interpretation. Despite the expansion of SARS-CoV-2 genomic surveillance in NYC, there was a substantial gap between Gamma variant introduction and establishment in January/February 2021, and its identification by genomic surveillance in March 2021. Although travel from Brazil to the US was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90866100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Delta infection following vaccination elicits potent neutralizing immunity against the SARS-CoV-2 Omicron","authors":"Ka-Li Zhu, Huixia Gao, Lin Yao, Jun Rong, Li Yang, Zhi Zhang, Ping Jiang, L. Duan, Guo-Lin Wang, E. Dai, M. Ma","doi":"10.1093/infdis/jiac149","DOIUrl":"https://doi.org/10.1093/infdis/jiac149","url":null,"abstract":"Abstract The SARS-CoV-2 Omicron (B.1.1.529) variant extensively escape neutralizing antibodies by vaccines or infection. We assessed serum neutralizing activity in sera from Delta infection following vaccination and Delta infection only against SARS-CoV-2 Wuhan-Hu-1 (WA1), Beta, Delta, and Omicron. Sera from Delta infection only could neutralize WA1 and Delta but nearly completely lost capacity to neutralize Beta and Omicron. However, Delta infection following vaccination resulted in a significant increase of serum neutralizing activity against WA1, Beta, and Omicron. This study demonstrates that breakthrough infection of Delta substantially induced high potency humoral immune response against the Omicron variant and other emerged variants.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90741010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global Prevalence of Post COVID-19 Condition or Long COVID: A Meta-Analysis and Systematic Review","authors":"Chen Chen, Spencer R. Haupert, Lauren Zimmermann, Xu Shi, L. Fritsche, B. Mukherjee","doi":"10.1093/infdis/jiac136","DOIUrl":"https://doi.org/10.1093/infdis/jiac136","url":null,"abstract":"Abstract Introduction This study aims to examine the worldwide prevalence of post COVID-19 condition, through a systematic review and meta-analysis. Methods PubMed, Embase, and iSearch were searched on July 5, 2021 with verification extending to March 13, 2022. Using a random effects framework with DerSimonian-Laird estimator, we meta-analyzed post COVID-19 condition prevalence at 28+ days from infection. Results 50 studies were included, and 41 were meta-analyzed. Global estimated pooled prevalence of post COVID-19 condition was 0.43 (95% CI: 0.39,0.46). Hospitalized and non-hospitalized patients have estimates of 0.54 (95% CI: 0.44,0.63) and 0.34 (95% CI: 0.25,0.46), respectively. Regional prevalence estimates were Asia— 0.51 (95% CI: 0.37,0.65), Europe— 0.44 (95% CI: 0.32,0.56), and North America— 0.31 (95% CI: 0.21,0.43). Global prevalence for 30, 60, 90, and 120 days after infection were estimated to be 0.37 (95% CI: 0.26,0.49), 0.25 (95% CI: 0.15,0.38), 0.32 (95% CI: 0.14,0.57) and 0.49 (95% CI: 0.40,0.59), respectively. Fatigue was the most common symptom reported with a prevalence of 0.23 (95% CI: 0.17,0.30), followed by memory problems (0.14 [95% CI: 0.10,0.19]). Discussion This study finds post COVID-19 condition prevalence is substantial; the health effects of COVID-19 appear to be prolonged and can exert stress on the healthcare system.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"186 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74175250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Breakthrough Gastrointestinal COVID-19 and Intrahost Evolution Consequent to Combination Monoclonal Antibody Prophylaxis","authors":"B. Beddingfield, Lori A Rowe, K. Russell-Lodrigue, Lara A. Doyle-Meyers, Nadia Golden, S. Spencer, N. Chirichella, R. Blair, N. Maness, C. Roy","doi":"10.1093/infdis/jiac134","DOIUrl":"https://doi.org/10.1093/infdis/jiac134","url":null,"abstract":"Abstract Breakthrough gastrointestinal COVID-19 was observed after experimental SARS-CoV-2 upper mucosal infection in a rhesus macaque undergoing low-dose monoclonal antibody prophylaxis. High levels of viral RNA were detected in intestinal sites contrasting with minimal viral replication in upper respiratory mucosa. Sequencing of virus recovered from tissue in 3 gastrointestinal sites and rectal swab revealed loss of furin cleavage site deletions present in the inoculating virus stock and 2 amino acid changes in spike that were detected in 2 colon sites but not elsewhere, suggesting compartmentalized replication and intestinal viral evolution. This suggests suboptimal antiviral therapies promote viral sequestration in these anatomies.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"305 1","pages":"1588 - 1592"},"PeriodicalIF":0.0,"publicationDate":"2022-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76859962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A retrospective cohort study on infant respiratory tract infection hospitalizations and recurrent wheeze and asthma risk: impact of respiratory syncytial virus.","authors":"M. van Wijhe, Caroline K Johannesen, L. Simonsen, I. M. Jørgensen, T. Fischer","doi":"10.1093/infdis/jiac141","DOIUrl":"https://doi.org/10.1093/infdis/jiac141","url":null,"abstract":"AIM\u0000Infant respiratory syncytial virus infection (RSV) has been associated with asthma later in life. We explored the risk of recurrent wheeze or asthma in children with infant RSV-associated hospitalization compared to other respiratory infections.\u0000\u0000\u0000METHODS\u0000We performed a retrospective cohort study using Danish national hospital discharge registers. Infants under 6 months, born between January 1995 and October 2018, and with a RSV hospital admission were compared to infants hospitalized for injuries, non-RSV acute upper respiratory tract infection (AURTI), pneumonia and other respiratory pathogens, non-pathogen coded lower respiratory tract infections (LRTI), pertussis, or non-specific respiratory infections. Infants were followed until recurrent wheeze or asthma diagnosis, death, migration, age 10 years, or study end. We estimated cumulative incidence rate ratios (CIRR) and hazard ratios (HR) adjusted for sex, age at inclusion, hospital length of stay (LOS), maternal smoking, 5 minute APGAR score (APGAR5), prematurity, and congenital risk factors (CRF).\u0000\u0000\u0000RESULTS\u0000We included 68130 infants, of whom 20920 (30.7%) had RSV hospitalization. The cumulative incidence rate of recurrent wheeze or asthma was 16.6 per 1000 person-years after RSV hospitalization, higher than after injury (CIRR: 2.69; 95% CI: 2.48-2.92), AURTI (1.48; 1.34-1.58), or pertussis (2.32; 1.85-2.91), similar to pneumonia and other respiratory pathogens (1.15; 0.99-1.34) and LRTI (0.79; 0.60-1.04), but lower than non-specific respiratory infections (0.79; 0.73-0.87).Adjusted HRs for recurrent wheeze or asthma after RSV hospitalization compared to injuries decreased from 2.37 (95% CI: 2.08-2.70) for 0 to <1 year to 1.23 (0.88-1.73) for 6 to <10 years for term-born children, and from 1.48 (1.09-2.00) to 0.60 (0.25-1.43) for preterm-born children. Sex, maternal smoking, LOS, CRF, and APGAR5 were independent risk factors.\u0000\u0000\u0000CONCLUSIONS\u0000Infant RSV hospitalization is associated with recurrent wheeze and asthma hospitalization, predominantly in preschool age. If causal, RSV-prophylaxis, including vaccines, may significantly reduce disease burden of wheeze and asthma.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77416432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional Compartmentalization of Antibodies in the Central Nervous System During Chronic HIV Infection","authors":"M. Spatola, C. Loos, D. Cizmeci, Nicholas Webb, M. Gorman, Evan Rossignol, S. Shin, D. Yuan, Laura Fontana, S. Mukerji, D. Lauffenburger, D. Gabuzda, G. Alter","doi":"10.1093/infdis/jiac138","DOIUrl":"https://doi.org/10.1093/infdis/jiac138","url":null,"abstract":"Abstract The central nervous system (CNS) has emerged as a critical HIV reservoir. Thus, interventions aimed at controlling and eliminating HIV must include CNS-targeted strategies. Given the inaccessibility of the brain, efforts have focused on cerebrospinal fluid (CSF), aimed at defining biomarkers of HIV-disease in the CNS, including HIV-specific antibodies. However, how antibodies traffic between the blood and CNS, and whether specific antibody profiles track with HIV-associated neurocognitive disorders (HAND) remains unclear. Here, we comprehensively profiled HIV-specific antibodies across plasma and CSF from 20 antiretroviral therapy (ART) naive or treated persons with HIV. CSF was populated by IgG1 and IgG3 antibodies, with reduced Fc-effector profiles. While ART improved plasma antibody functional coordination, CSF profiles were unaffected by ART and were unrelated to HAND severity. These data point to a functional sieving of antibodies across the blood-brain barrier, providing previously unappreciated insights for the development of next-generation therapeutics targeting the CNS reservoir.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"24 1","pages":"738 - 750"},"PeriodicalIF":0.0,"publicationDate":"2022-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74793535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Elimination Settings, Measles Antibodies Wane Following Vaccination but Not Following Infection - A Systematic Review and Meta-Analysis.","authors":"S. Bolotin, S. Osman, S. Hughes, A. Ariyarajah, A. Tricco, Sumaiya Khan, Lennon Li, Caitlin Johnson, L. Friedman, Nazish Gul, Rachel Jardine, Maryrose Faulkner, S. Hahné, J. Heffernan, A. Dabbagh, P. Rota, A. Severini, M. Jit, D. Durrheim, W. Orenstein, W. Moss, S. Funk, N. Turner, W. Schluter, J. Jawad, N. Crowcroft","doi":"10.1093/infdis/jiac039","DOIUrl":"https://doi.org/10.1093/infdis/jiac039","url":null,"abstract":"BACKGROUND\u0000We conducted a systematic review to assess whether measles humoral immunity wanes in previously infected or vaccinated populations in measles elimination settings.\u0000\u0000\u0000METHODS\u0000After screening 16,822 citations, we identified nine articles from populations exposed to wild-type measles and 16 articles from vaccinated populations that met our inclusion criteria.\u0000\u0000\u0000RESULTS\u0000Using linear regression, we found that geometric mean titers (GMTs) decreased significantly in individuals who received two doses of measles-containing vaccine (MCV) by 121.8 mIU/mL (95% CI -212.4, -31.1) per year since vaccination over one to five years, 53.7 mIU/mL (95% CI -95.3, -12.2) five to ten years, 33.2 mIU/mL (95% CI -62.6, -3.9) ten to 15 years, and 24.1 mIU/mL (95% CI -51.5,3.3) 15 to 20 years since vaccination. Decreases in GMT over time were not significant after one dose of MCV or after infection. Decreases in the proportion of seropositive individuals over time were not significant after one or two doses of MCV, or after infection.\u0000\u0000\u0000CONCLUSIONS\u0000Measles antibody waning in vaccinated populations should be considered in planning for measles elimination.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"62 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81262896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polio by the Numbers—A Global Perspective","authors":"K. Badizadegan, D. A. Kalkowska, K. Thompson","doi":"10.1093/infdis/jiac130","DOIUrl":"https://doi.org/10.1093/infdis/jiac130","url":null,"abstract":"Abstract Background Investments in national immunization programs and the Global Polio Eradication Initiative (GPEI) have resulted in substantial reductions in paralytic polio worldwide. However, cases prevented because of investments in immunization programs and GPEI remain incompletely characterized. Methods Using a global model that integrates polio transmission, immunity, and vaccine dynamics, we provide estimates of polio incidence and numbers of paralytic cases prevented. We compare the results with reported cases and estimates historically published by the World Health Organization. Results We estimate that the existence and use of polio vaccines prevented 5 million cases of paralytic polio for 1960–1987 and 24 million cases worldwide for 1988–2021 compared to a counterfactual world with no polio vaccines. Since the 1988 resolution to eradicate polio, our estimates suggest GPEI prevented 2.5–6 million cases of paralytic polio compared to counterfactual worlds without GPEI that assume different levels of intensity of polio vaccine use in routine immunization programs. Conclusions Analysis of historical cases provides important context for understanding and communicating the benefits of investments made in polio eradication. Prospective studies will need to explore the expected benefits of future investments, the outcomes of which will depend on whether and when polio is globally eradicated.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"44 1","pages":"1309 - 1318"},"PeriodicalIF":0.0,"publicationDate":"2022-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81286799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical Burden of Respiratory Syncytial Virus in Hospitalized Children Aged ≤5 Years (INSPIRE Study)","authors":"K. Hartmann, J. Liese, D. Kemmling, C. Prifert, B. Weissbrich, P. Thilakarathne, J. Diels, K. Weber, A. Streng","doi":"10.1093/infdis/jiac137","DOIUrl":"https://doi.org/10.1093/infdis/jiac137","url":null,"abstract":"Abstract Background Respiratory syncytial virus (RSV) is a leading cause of hospitalizations in children (≤5 years of age); limited data compare burden by age. Methods This single-center retrospective study included children (≤5 years of age) hospitalized for >24 hours with reverse-transcription polymerase chain reaction (RT-PCR)–confirmed RSV infection (2015–2018). Hospital length of stay (LOS), intensive care unit (ICU) admissions, ICU LOS, supplemental oxygen, and medication use were assessed. Multivariate logistic regression analyses identified predictors of hospital LOS >5 days. Results Three hundred twelve patients had RSV infection (ages 0 to <6 months [35%], 6 to <12 months [15%], 1 to <2 years [25%], and 2–5 years [25%]); 16.3% had predefined comorbidities (excludes preterm infants). Median hospital LOS was 5.0 days and similar across age; 5.1% (16/312) were admitted to ICU (ICU LOS, 5.0 days), with those aged 0 to <6 months admitted most frequently (10/108 [9.3%]). Supplemental oxygen was administered in 57.7% of patients, with similar need across ages. Antibiotics were administered frequently during hospitalization (43.6%). Predictors of prolonged LOS included pneumonia (odds ratio [OR], 2.33), supplemental oxygen need (OR, 5.09), and preterm births (OR, 3.37). High viral load (RT-PCR RSV cycle threshold value <25) was associated with greater need for supplemental oxygen. Conclusions RSV causes substantial burden in hospitalized children (≤5 years), particularly preterm infants and those aged <6 months.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"7 1","pages":"386 - 395"},"PeriodicalIF":0.0,"publicationDate":"2022-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90320298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Economics of Eradication: Counting on the Polio Experience.","authors":"Ananda S. Bandyopadhyay, W. Orenstein","doi":"10.1093/infdis/jiac132","DOIUrl":"https://doi.org/10.1093/infdis/jiac132","url":null,"abstract":"","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80794040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}