T. Meister, M. Dreismeier, E. V. Blanco, Y. Brüggemann, N. Heinen, G. Kampf, D. Todt, H. Nguyen, J. Steinmann, W. Schmidt, E. Steinmann, D. Quast, S. Pfaender
Abstract Background The contribution of droplet-contaminated surfaces for virus transmission has been discussed controversially in the context of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. More importantly, the risk of fomite-based transmission has not been systematically addressed. Therefore, the aim of this study was to evaluate whether confirmed hospitalized coronavirus disease 2019 (COVID-19) patients can contaminate stainless steel carriers by coughing or intensive moistening with saliva and to assess the risk of SARS-CoV-2 transmission upon detection of viral loads and infectious virus in cell culture. Methods We initiated a single-center observational study including 15 COVID-19 patients with a high baseline viral load (cycle threshold value ≤25). We documented clinical and laboratory parameters and used patient samples to perform virus culture, quantitative polymerase chain reaction, and virus sequencing. Results Nasopharyngeal and oropharyngeal swabs of all patients were positive for viral ribonucleic acid on the day of the study. Infectious SARS-CoV-2 could be isolated from 6 patient swabs (46.2%). After coughing, no infectious virus could be recovered, however, intensive moistening with saliva resulted in successful viral recovery from steel carriers of 5 patients (38.5%). Conclusions Transmission of infectious SARS-CoV-2 via fomites is possible upon extensive moistening, but it is unlikely to occur in real-life scenarios and from droplet-contaminated fomites.
{"title":"Low Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission by Fomites: A Clinical Observational Study in Highly Infectious Coronavirus Disease 2019 Patients","authors":"T. Meister, M. Dreismeier, E. V. Blanco, Y. Brüggemann, N. Heinen, G. Kampf, D. Todt, H. Nguyen, J. Steinmann, W. Schmidt, E. Steinmann, D. Quast, S. Pfaender","doi":"10.1093/infdis/jiac170","DOIUrl":"https://doi.org/10.1093/infdis/jiac170","url":null,"abstract":"Abstract Background The contribution of droplet-contaminated surfaces for virus transmission has been discussed controversially in the context of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. More importantly, the risk of fomite-based transmission has not been systematically addressed. Therefore, the aim of this study was to evaluate whether confirmed hospitalized coronavirus disease 2019 (COVID-19) patients can contaminate stainless steel carriers by coughing or intensive moistening with saliva and to assess the risk of SARS-CoV-2 transmission upon detection of viral loads and infectious virus in cell culture. Methods We initiated a single-center observational study including 15 COVID-19 patients with a high baseline viral load (cycle threshold value ≤25). We documented clinical and laboratory parameters and used patient samples to perform virus culture, quantitative polymerase chain reaction, and virus sequencing. Results Nasopharyngeal and oropharyngeal swabs of all patients were positive for viral ribonucleic acid on the day of the study. Infectious SARS-CoV-2 could be isolated from 6 patient swabs (46.2%). After coughing, no infectious virus could be recovered, however, intensive moistening with saliva resulted in successful viral recovery from steel carriers of 5 patients (38.5%). Conclusions Transmission of infectious SARS-CoV-2 via fomites is possible upon extensive moistening, but it is unlikely to occur in real-life scenarios and from droplet-contaminated fomites.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"16 1","pages":"1608 - 1615"},"PeriodicalIF":0.0,"publicationDate":"2022-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82363869","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}
Anna Gibbs, K. Healy, Vilde Kaldhusdal, C. Sundling, Mathias Franzén-Boger, Gabriella Edfeldt, M. Buggert, J. Lajoie, K. Fowke, J. Kimani, D. Kwon, S. Andersson, J. Sandberg, K. Broliden, Haleh Davanian, M. Chen, Annelie Tjernlund
Abstract Background Mucosa-associated invariant T (MAIT) cells are innate-like T cells with specialized antimicrobial functions. Circulating MAIT cells are depleted in chronic human immunodeficiency virus (HIV) infection, but studies examining this effect in peripheral tissues, such as the female genital tract, are lacking. Methods Flow cytometry was used to investigate circulating MAIT cells in a cohort of HIV-seropositive (HIV+) and HIV-seronegative (HIV−) female sex workers (FSWs), and HIV− lower-risk women (LRW). In situ staining and quantitative polymerase chain reaction were performed to explore the phenotype of MAIT cells residing in paired cervicovaginal tissue. The cervicovaginal microbiome was assessed by means of 16S ribosomal RNA gene sequencing. Results MAIT cells in the HIV+ FSW group were low in frequency in the circulation but preserved in the ectocervix. MAIT cell T-cell receptor gene segment usage differed between the HIV+ and HIV− FSW groups. The TRAV1-2–TRAJ20 transcript was the most highly expressed MAIT TRAJ gene detected in the ectocervix in the HIV+ FSW group. MAIT TRAVJ usage was not associated with specific genera in the vaginal microbiome. Conclusions MAIT cells residing in the ectocervix are numerically preserved irrespective of HIV infection status and displayed dominant expression of TRAV1-2–TRAJ20. These findings have implications for understanding the role of cervical MAIT cells in health and disease.
{"title":"Preserved Mucosal-Associated Invariant T Cells in the Cervical Mucosa of HIV-Infected Women with Dominant Expression of the TRAV1-2–TRAJ20 T Cell Receptor α-Chain","authors":"Anna Gibbs, K. Healy, Vilde Kaldhusdal, C. Sundling, Mathias Franzén-Boger, Gabriella Edfeldt, M. Buggert, J. Lajoie, K. Fowke, J. Kimani, D. Kwon, S. Andersson, J. Sandberg, K. Broliden, Haleh Davanian, M. Chen, Annelie Tjernlund","doi":"10.1093/infdis/jiac171","DOIUrl":"https://doi.org/10.1093/infdis/jiac171","url":null,"abstract":"Abstract Background Mucosa-associated invariant T (MAIT) cells are innate-like T cells with specialized antimicrobial functions. Circulating MAIT cells are depleted in chronic human immunodeficiency virus (HIV) infection, but studies examining this effect in peripheral tissues, such as the female genital tract, are lacking. Methods Flow cytometry was used to investigate circulating MAIT cells in a cohort of HIV-seropositive (HIV+) and HIV-seronegative (HIV−) female sex workers (FSWs), and HIV− lower-risk women (LRW). In situ staining and quantitative polymerase chain reaction were performed to explore the phenotype of MAIT cells residing in paired cervicovaginal tissue. The cervicovaginal microbiome was assessed by means of 16S ribosomal RNA gene sequencing. Results MAIT cells in the HIV+ FSW group were low in frequency in the circulation but preserved in the ectocervix. MAIT cell T-cell receptor gene segment usage differed between the HIV+ and HIV− FSW groups. The TRAV1-2–TRAJ20 transcript was the most highly expressed MAIT TRAJ gene detected in the ectocervix in the HIV+ FSW group. MAIT TRAVJ usage was not associated with specific genera in the vaginal microbiome. Conclusions MAIT cells residing in the ectocervix are numerically preserved irrespective of HIV infection status and displayed dominant expression of TRAV1-2–TRAJ20. These findings have implications for understanding the role of cervical MAIT cells in health and disease.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"777 1","pages":"1428 - 1440"},"PeriodicalIF":0.0,"publicationDate":"2022-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76120096","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}
Nicole D Derksen-Lazet, Corline E J Parmentier, J. Wildenbeest, L. Bont
Respiratory syncytial virus (RSV) causes a substantial disease burden among children, elderly and immunocompromised adults. Recognition of patient involvement in research is gradually increasing. Most research is being carried out without active patient involvement other than patients participating as study subjects, and most knowledge gained through research only partially reaches the general public. Since 2016, the RSV Patient Advisory Board has officially been involved as an advisory group in the Respiratory Syncytial Virus Consortium in Europe (RESCEU). What started as a small single-center initiative, is now growing towards an international organization providing patient perspectives as inputs to scientists, and improving awareness of RSV. This article summarizes the history, current role, and future aims of the RSV Patient Advisory Board as an advocate to improve patient involvement in research. RSV patients and their representatives are important stakeholders in setting the global research agenda, and educating patients, professionals, and the general public.
{"title":"Patient Involvement in RSV Research: Towards Patients Setting the Research Agenda.","authors":"Nicole D Derksen-Lazet, Corline E J Parmentier, J. Wildenbeest, L. Bont","doi":"10.1093/infdis/jiac110","DOIUrl":"https://doi.org/10.1093/infdis/jiac110","url":null,"abstract":"Respiratory syncytial virus (RSV) causes a substantial disease burden among children, elderly and immunocompromised adults. Recognition of patient involvement in research is gradually increasing. Most research is being carried out without active patient involvement other than patients participating as study subjects, and most knowledge gained through research only partially reaches the general public. Since 2016, the RSV Patient Advisory Board has officially been involved as an advisory group in the Respiratory Syncytial Virus Consortium in Europe (RESCEU). What started as a small single-center initiative, is now growing towards an international organization providing patient perspectives as inputs to scientists, and improving awareness of RSV. This article summarizes the history, current role, and future aims of the RSV Patient Advisory Board as an advocate to improve patient involvement in research. RSV patients and their representatives are important stakeholders in setting the global research agenda, and educating patients, professionals, and the general public.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72755798","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}
S. Assawakosri, S. Kanokudom, N. Suntronwong, Jiratchaya Puenpa, T. Duangchinda, W. Chantima, P. Pakchotanon, J. Mongkolsapaya, Nasamon Wanlapakorn, S. Honsawek, Y. Poovorawan
TO THE EDITOR—In reply to the correspondence from Tjan et al [1] regarding the heterologous booster in healthy adults previously immunized with 2 doses of CoronaVac [2], the additional knowledge on immunogenicity of the booster (third dose) with BNT162b2 in BNT162b2primed individuals against the BA.2 omicron variant will help promote the vaccine uptake and coverage in themidst of a surge in BA.2 omicron worldwide. As of February 2022, the omicron variant was further classified into 4 main sublineages, BA.1, BA.1.1, BA.2, and BA.3. Moreover, an epidemiological surveillance on coronavirus disease 2019 (COVID-19) showed that BA.2 sublineages have become the dominant variant globally [3]. In Thailand, the BA.2 sublineages have been detected since the end of January 2022. The proportion of BA.2 sublineages rapidly increased and accounted for more than 90% of positive cases reported in March 2022 [Puenpa J et al. unpublished]. Potent serum neutralizing antibody (nAbs) against BA.1 was observed after the heterologous booster in individuals previously immunized with 2 doses of CoronaVac [2]. Considering the waning immunity after primary series vaccination and the high transmissibility and potential immune escape of BA.2 sublineage, we further determined the immunogenicity of the mRNA-1273 booster against BA.1 and BA.2 in AZD1222-primed individuals using the 50% focus reduction neutralization test (FRNT50) as previously described [2].
致编辑:在Tjan等人[1]的信函中，我们回复了之前接种过2剂CoronaVac的健康成人[2]的异种增强剂，关于BNT162b2增强剂(第三剂)在BNT162b2引发的个体中对BA.2组克隆变体的免疫原性的额外知识，将有助于在全球BA.2组克隆激增期间促进疫苗的吸收和覆盖。截至2022年2月，该组粒变体进一步分为4个主要亚系，BA.1、BA.1.1、BA.2和BA.3。此外，对2019冠状病毒病(COVID-19)的流行病学监测显示，BA.2亚系已成为全球优势变异体[3]。在泰国，自2022年1月底以来一直检测到BA.2亚型。BA.2亚型的比例迅速增加，占2022年3月报告的阳性病例的90%以上[Puenpa J et al.未发表]。在先前接种过2剂CoronaVac的个体中，在异种增强剂后观察到针对BA.1的有效血清中和抗体(nab)[2]。考虑到一次系列疫苗接种后的免疫力下降，以及BA.2亚系的高传播性和潜在的免疫逃逸，我们采用先前描述的50%减焦中和试验(FRNT50)进一步确定了mRNA-1273增强剂对azd1222引物个体BA.1和BA.2的免疫原性[2]。
{"title":"Omicron BA.1, BA.2 and COVID-19 Booster Vaccination","authors":"S. Assawakosri, S. Kanokudom, N. Suntronwong, Jiratchaya Puenpa, T. Duangchinda, W. Chantima, P. Pakchotanon, J. Mongkolsapaya, Nasamon Wanlapakorn, S. Honsawek, Y. Poovorawan","doi":"10.1093/infdis/jiac158","DOIUrl":"https://doi.org/10.1093/infdis/jiac158","url":null,"abstract":"TO THE EDITOR—In reply to the correspondence from Tjan et al [1] regarding the heterologous booster in healthy adults previously immunized with 2 doses of CoronaVac [2], the additional knowledge on immunogenicity of the booster (third dose) with BNT162b2 in BNT162b2primed individuals against the BA.2 omicron variant will help promote the vaccine uptake and coverage in themidst of a surge in BA.2 omicron worldwide. As of February 2022, the omicron variant was further classified into 4 main sublineages, BA.1, BA.1.1, BA.2, and BA.3. Moreover, an epidemiological surveillance on coronavirus disease 2019 (COVID-19) showed that BA.2 sublineages have become the dominant variant globally [3]. In Thailand, the BA.2 sublineages have been detected since the end of January 2022. The proportion of BA.2 sublineages rapidly increased and accounted for more than 90% of positive cases reported in March 2022 [Puenpa J et al. unpublished]. Potent serum neutralizing antibody (nAbs) against BA.1 was observed after the heterologous booster in individuals previously immunized with 2 doses of CoronaVac [2]. Considering the waning immunity after primary series vaccination and the high transmissibility and potential immune escape of BA.2 sublineage, we further determined the immunogenicity of the mRNA-1273 booster against BA.1 and BA.2 in AZD1222-primed individuals using the 50% focus reduction neutralization test (FRNT50) as previously described [2].","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87555355","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}
Yufei Zhang, Jindong Gao, Kun Huang, Ya Zhao, Xianfeng Hui, Ting Wang, Changmin Hu, Xiaomei Sun, Ying Yang, Chao Wu, Xi Chen, Zhong Zou, Lianzhong Zhao, M. Jin
Abstract Isolated reports of new-onset diabetes in patients with COVID-19 have led researchers to hypothesise that SARS-CoV-2 infects the human exocrine and endocrine pancreatic cells ex vivo and in vivo. However, existing research lacks experimental evidence indicating that SARS-CoV-2 can infect pancreatic tissue. Here, we found that cats infected with a high dose of SARS-CoV-2 exhibited hyperglycaemia. We also detected SARS-CoV-2 RNA in the pancreatic tissues of these cats, and immunohistochemical staining revealed the presence of SARS-CoV-2 nucleocapsid protein (NP) in the islet cells. SARS-CoV-2 NP and Spike proteins were primarily detected in Glu+ cells, and most Glu+ cells expressed ACE2. Additionally, immune protection experiments conducted on cats showed that the blood glucose levels of immunised cats did not increase post-challenge. Our data indicate the cat pancreas as a SARS-CoV-2 target and suggest that the infection of Glu+ cells could contribute to the metabolic dysregulation observed in SARS-CoV-2-infected cats.
{"title":"SARS-CoV-2 infection causes hyperglycaemia in cats","authors":"Yufei Zhang, Jindong Gao, Kun Huang, Ya Zhao, Xianfeng Hui, Ting Wang, Changmin Hu, Xiaomei Sun, Ying Yang, Chao Wu, Xi Chen, Zhong Zou, Lianzhong Zhao, M. Jin","doi":"10.1093/infdis/jiac143","DOIUrl":"https://doi.org/10.1093/infdis/jiac143","url":null,"abstract":"Abstract Isolated reports of new-onset diabetes in patients with COVID-19 have led researchers to hypothesise that SARS-CoV-2 infects the human exocrine and endocrine pancreatic cells ex vivo and in vivo. However, existing research lacks experimental evidence indicating that SARS-CoV-2 can infect pancreatic tissue. Here, we found that cats infected with a high dose of SARS-CoV-2 exhibited hyperglycaemia. We also detected SARS-CoV-2 RNA in the pancreatic tissues of these cats, and immunohistochemical staining revealed the presence of SARS-CoV-2 nucleocapsid protein (NP) in the islet cells. SARS-CoV-2 NP and Spike proteins were primarily detected in Glu+ cells, and most Glu+ cells expressed ACE2. Additionally, immune protection experiments conducted on cats showed that the blood glucose levels of immunised cats did not increase post-challenge. Our data indicate the cat pancreas as a SARS-CoV-2 target and suggest that the infection of Glu+ cells could contribute to the metabolic dysregulation observed in SARS-CoV-2-infected cats.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76318595","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}
Nadine Peart Akindele, L. Pieterse, San Suwanmanee, D. Griffin
Abstract Multisystem inflammatory syndrome in children (MIS-C) can complicate infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but differences in the immune responses during MIS-C compared to coronavirus disease 2019 (COVID-19) are poorly understood. We longitudinally compared the amounts and avidity of plasma anti-nucleocapsid (N) and spike (S) antibodies, phenotypes of B cells, and numbers of virus-specific antibody-secreting cells in circulation of children hospitalized with COVID-19 (n = 10) and with MIS-C (n = 12). N-specific immunoglobulin G (IgG) was higher early after presentation for MIS-C than COVID-19 patients and avidity of N- and S-specific IgG at presentation did not mature further during follow-up as it did for COVID-19. Both groups had waning proportions of B cells in circulation and decreasing but sustained production of virus-specific antibody-secreting cells for months. Overall, B-cell responses were similar, but those with MIS-C demonstrated a more mature antibody response at presentation compared to COVID-19, suggesting a postinfectious entity.
{"title":"B-Cell Responses in Hospitalized Severe Acute Respiratory Syndrome Coronavirus 2–Infected Children With and Without Multisystem Inflammatory Syndrome","authors":"Nadine Peart Akindele, L. Pieterse, San Suwanmanee, D. Griffin","doi":"10.1093/infdis/jiac119","DOIUrl":"https://doi.org/10.1093/infdis/jiac119","url":null,"abstract":"Abstract Multisystem inflammatory syndrome in children (MIS-C) can complicate infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but differences in the immune responses during MIS-C compared to coronavirus disease 2019 (COVID-19) are poorly understood. We longitudinally compared the amounts and avidity of plasma anti-nucleocapsid (N) and spike (S) antibodies, phenotypes of B cells, and numbers of virus-specific antibody-secreting cells in circulation of children hospitalized with COVID-19 (n = 10) and with MIS-C (n = 12). N-specific immunoglobulin G (IgG) was higher early after presentation for MIS-C than COVID-19 patients and avidity of N- and S-specific IgG at presentation did not mature further during follow-up as it did for COVID-19. Both groups had waning proportions of B cells in circulation and decreasing but sustained production of virus-specific antibody-secreting cells for months. Overall, B-cell responses were similar, but those with MIS-C demonstrated a more mature antibody response at presentation compared to COVID-19, suggesting a postinfectious entity.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"23 1","pages":"822 - 832"},"PeriodicalIF":0.0,"publicationDate":"2022-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80559119","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}
Pub Date : 2022-04-16DOI: 10.1101/2022.04.15.22273412
E. Grebe, Elaine A. Yu, M. Bravo, A. Welte, R. Bruhn, M. Stone, Valerie Green, P. Williamson, Leora R. Feldstein, Jefferson M. Jones, M. Busch, B. Custer
To inform public health policy, it is critical to monitor COVID-19 vaccine effectiveness (VE), including against acquiring infection. We estimated VE using a retrospective cohort study among repeat blood donors who donated during the first half of 2021, demonstrating a viable approach for monitoring of VE via serological surveillance. Using Poisson regression, we estimated overall VE was 88.8% (95% CI: 86.2-91.1), adjusted for demographic covariates and variable baseline risk. Time since first reporting vaccination, age, race-ethnicity, region, and calendar time were statistically significant predictors of incident infection. Studies of VE during periods of Delta and Omicron spread are underway.
{"title":"COVID-19 vaccine effectiveness against SARS-CoV-2 infection in the United States prior to the Delta and Omicron-associated surges: a retrospective cohort study of repeat blood donors","authors":"E. Grebe, Elaine A. Yu, M. Bravo, A. Welte, R. Bruhn, M. Stone, Valerie Green, P. Williamson, Leora R. Feldstein, Jefferson M. Jones, M. Busch, B. Custer","doi":"10.1101/2022.04.15.22273412","DOIUrl":"https://doi.org/10.1101/2022.04.15.22273412","url":null,"abstract":"To inform public health policy, it is critical to monitor COVID-19 vaccine effectiveness (VE), including against acquiring infection. We estimated VE using a retrospective cohort study among repeat blood donors who donated during the first half of 2021, demonstrating a viable approach for monitoring of VE via serological surveillance. Using Poisson regression, we estimated overall VE was 88.8% (95% CI: 86.2-91.1), adjusted for demographic covariates and variable baseline risk. Time since first reporting vaccination, age, race-ethnicity, region, and calendar time were statistically significant predictors of incident infection. Studies of VE during periods of Delta and Omicron spread are underway.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78518710","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}
K. Wamae, K. Kimenyi, Victor Osoti, Z. D. de Laurent, L. Ndwiga, Oksana Kharabora, N. Hathaway, J. Bailey, J. Juliano, P. Bejon, L. Ochola-Oyier
Abstract Background Genotyping Plasmodium falciparum subpopulations in malaria infections is an important aspect of malaria molecular epidemiology to understand within-host diversity and the frequency of drug resistance markers. Methods We characterized P. falciparum genetic diversity in asymptomatic infections and subsequent first febrile infections using amplicon sequencing (AmpSeq) of ama1 in Coastal Kenya. We also examined temporal changes in haplotype frequencies of mdr1, a drug-resistant marker. Results We found >60% of the infections were polyclonal (complexity of infection [COI] >1) and there was a reduction in COI over time. Asymptomatic infections had a significantly higher mean COI than febrile infections based on ama1 sequences (2.7 [95% confidence interval {CI}, 2.65–2.77] vs 2.22 [95% CI, 2.17–2.29], respectively). Moreover, an analysis of 30 paired asymptomatic and first febrile infections revealed that many first febrile infections (91%) were due to the presence of new ama1 haplotypes. The mdr1-YY haplotype, associated with chloroquine and amodiaquine resistance, decreased over time, while the NY (wild type) and the NF (modulates response to lumefantrine) haplotypes increased. Conclusions This study emphasizes the utility of AmpSeq in characterizing parasite diversity as it can determine relative proportions of clones and detect minority clones. The usefulness of AmpSeq in antimalarial drug resistance surveillance is also highlighted.
{"title":"Amplicon Sequencing as a Potential Surveillance Tool for Complexity of Infection and Drug Resistance Markers in Plasmodium falciparum Asymptomatic Infections","authors":"K. Wamae, K. Kimenyi, Victor Osoti, Z. D. de Laurent, L. Ndwiga, Oksana Kharabora, N. Hathaway, J. Bailey, J. Juliano, P. Bejon, L. Ochola-Oyier","doi":"10.1093/infdis/jiac144","DOIUrl":"https://doi.org/10.1093/infdis/jiac144","url":null,"abstract":"Abstract Background Genotyping Plasmodium falciparum subpopulations in malaria infections is an important aspect of malaria molecular epidemiology to understand within-host diversity and the frequency of drug resistance markers. Methods We characterized P. falciparum genetic diversity in asymptomatic infections and subsequent first febrile infections using amplicon sequencing (AmpSeq) of ama1 in Coastal Kenya. We also examined temporal changes in haplotype frequencies of mdr1, a drug-resistant marker. Results We found >60% of the infections were polyclonal (complexity of infection [COI] >1) and there was a reduction in COI over time. Asymptomatic infections had a significantly higher mean COI than febrile infections based on ama1 sequences (2.7 [95% confidence interval {CI}, 2.65–2.77] vs 2.22 [95% CI, 2.17–2.29], respectively). Moreover, an analysis of 30 paired asymptomatic and first febrile infections revealed that many first febrile infections (91%) were due to the presence of new ama1 haplotypes. The mdr1-YY haplotype, associated with chloroquine and amodiaquine resistance, decreased over time, while the NY (wild type) and the NF (modulates response to lumefantrine) haplotypes increased. Conclusions This study emphasizes the utility of AmpSeq in characterizing parasite diversity as it can determine relative proportions of clones and detect minority clones. The usefulness of AmpSeq in antimalarial drug resistance surveillance is also highlighted.","PeriodicalId":22572,"journal":{"name":"The Indonesian Journal of Infectious Diseases","volume":"38 1","pages":"920 - 927"},"PeriodicalIF":0.0,"publicationDate":"2022-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86505482","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}
Pub Date : 2022-04-16DOI: 10.1101/2022.04.15.22273909
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
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.
{"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}
Ka-Li Zhu, Huixia Gao, Lin Yao, Jun Rong, Li Yang, Zhi Zhang, Ping Jiang, L. Duan, Guo-Lin Wang, E. Dai, M. Ma
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.
{"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}
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