scholarly journals Detection of Emerging Vaccine-Related Polioviruses by Deep Sequencing

2017 ◽  
Vol 55 (7) ◽  
pp. 2162-2171 ◽  
Author(s):  
Malaya K. Sahoo ◽  
Marisa Holubar ◽  
ChunHong Huang ◽  
Alisha Mohamed-Hadley ◽  
Yuanyuan Liu ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Read Depth ◽  
Polio Eradication ◽  
Oral Poliovirus Vaccine ◽  
Genomic Region ◽  
Sample Collection ◽  
Asymptomatic Children ◽  
National Immunization ◽  
Sequencing Method ◽  
Culture Independent

ABSTRACTOral poliovirus vaccine can mutate to regain neurovirulence. To date, evaluation of these mutations has been performed primarily on culture-enriched isolates by using conventional Sanger sequencing. We therefore developed a culture-independent, deep-sequencing method targeting the 5′ untranslated region (UTR) and P1 genomic region to characterize vaccine-related poliovirus variants. Error analysis of the deep-sequencing method demonstrated reliable detection of poliovirus mutations at levels of <1%, depending on read depth. Sequencing of viral nucleic acids from the stool of vaccinated, asymptomatic children and their close contacts collected during a prospective cohort study in Veracruz, Mexico, revealed no vaccine-derived polioviruses. This was expected given that the longest duration between sequenced sample collection and the end of the most recent national immunization week was 66 days. However, we identified many low-level variants (<5%) distributed across the 5′ UTR and P1 genomic region in all three Sabin serotypes, as well as vaccine-related viruses with multiple canonical mutations associated with phenotypic reversion present at high levels (>90%). These results suggest that monitoring emerging vaccine-related poliovirus variants by deep sequencing may aid in the poliovirus endgame and efforts to ensure global polio eradication.

Reasons for Non-Immunization of Children in an Urban, Low Income Group in North India

2002 ◽  
Vol 32 (3) ◽  
pp. 135-138 ◽  
Author(s):  
Joseph L Mathew ◽  
Harsh Babbar ◽  
Sangita Yadav
Keyword(s):  
Low Income ◽  
Rural Areas ◽  
Income Group ◽  
Polio Eradication ◽  
Oral Poliovirus Vaccine ◽  
North India ◽  
New Delhi ◽  
Significant Finding ◽  
National Immunization ◽  
Large Teaching Hospital

A study was undertaken on 500 children under the age of 5 years belonging to a low income group. All were attending the paediatrics outpatient department of a large teaching hospital in New Delhi, India. Only 25% were found to have received complete primary immunization as per the National Immunization Schedule (bacille Calmette-Guérin at birth, three doses of diphtheria, pertussis and tetanus and oral poliovirus vaccine at 6, 10 and 14 weeks and measles vaccine at 9 months). The major reasons for non-immunization of the children were: migration to a native village (26.4%); domestic problems (9.6%); the immunization centre was located too far from their home (9.6%); and the child was unwell when the vaccination was due (9%). Twelve per cent of mothers could not give any reason for non-immunization. In addition to the migration of children to rural areas, the other significant finding was an indirect effect of intensive OPV administration as part of polio eradication initiative. The lack of awareness and fear of side effects constituted a small minority of reasons for non-immunization.

scholarly journals Characterization of a recombinant type 3/type 2 poliovirus isolated from a healthy vaccinee and containing a chimeric capsid protein VP1

2003 ◽  
Vol 84 (3) ◽  
pp. 573-580 ◽  
Author(s):  
Soile Blomqvist ◽  
Anne-Lise Bruu ◽  
Mirja Stenvik ◽  
Tapani Hovi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Capsid Protein ◽  
Recombinant Virus ◽  
Antigenic Site ◽  
Neutralizing Antibody ◽  
Oral Poliovirus Vaccine ◽  
Genomic Region ◽  
Recombinant Type

A Sabin 3/Sabin 2/Sabin 3 (S3/2/3) intertypic recombinant poliovirus was isolated from a faecal specimen from a 2-year-old healthy boy approximately 12 weeks after administration of oral poliovirus vaccine. The first recombination junction was in the genomic region encoding the VP1 capsid protein between nucleotide positions 3274 and 3285 (numbering according to Sabin 3) and the second was in the RNA polymerase region (nucleotide positions 6824 and 6825). The recombination had introduced six Sabin 2-derived amino acids into the Sabin 3 capsid environment in the carboxyl terminus of VP1. The complete genome of the recombinant virus differed from corresponding parental Sabin strains at 33 nucleotide positions, nine of them resulting in an amino acid substitution. Four substitutions were in the capsid proteins and five were in the region encoding the non-structural proteins. One amino acid was changed in the antigenic site 2B and two in site 3B. In addition, the whole antigenic site 3A was replaced by Sabin 2-specific amino acids, but the antigenic characteristics of the S3/2/3 did not show type 2-specific features. Neutralizing antibody titres in sera from Finnish children immunized with the inactivated poliovirus vaccine were not lower against the recombinant virus than against Sabin 3. Our results suggest that the chimeric virus was most likely generated by recombination events in the vaccinee, rather than representing progeny of circulating vaccine-derived virus.

scholarly journals Strengthening National Immunization Technical Advisory Groups in resource-limited settings: current and potential linkages with polio national certification committees

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Sharon A. Greene ◽  
Blanche-Philomene Melanga Anya ◽  
Humayun Asghar ◽  
Irtaza A. Chaudhri ◽  
S. Deblina Datta ◽  
...  
Keyword(s):  
Response Rate ◽  
Eastern Mediterranean ◽  
Polio Eradication ◽  
Frequency Distributions ◽  
Immunization Policy ◽  
Advisory Groups ◽  
Resource Limited ◽  
National Immunization ◽  
National Certification ◽  
Question Survey

Abstract Background Countries are transitioning assets and functions from polio eradication to integrated immunization and surveillance activities. We assessed the extent of linkages between and perceptions of National Immunization Technical Advisory Groups (NITAGs) and National Certification Committees (NCCs) for polio eradication to understand how linkages can be leveraged to improve efficiencies of these expert bodies. Methods During May 2017 to May 2018, we administered a 15-question survey to a NITAG chair or member and an NCC counterpart in all countries of the WHO Regions for Africa (AFR) and for the Eastern Mediterranean (EMR) that had both a NITAG and an NCC. Data were analysed using frequency distributions. Results Of countries with both a NITAG and an NCC (n = 44), the response rate was 92% (22/24) in AFR and 75% (15/20) in EMR. Some respondents reported being very familiar with the functions of the other technical bodies, 36% (8/22) for NITAG members and 38% (14/37) for NCC members. Over 85% (51/59) of respondents felt it was somewhat useful or very useful to strengthen ties between bodies. Nearly all respondents (98%, 58/59) felt that NCC expertise could inform measles and rubella elimination programmes. Conclusions We observed a broad consensus that human resource assets of NCCs may serve an important technical role to support national immunization policy-making. At this stage of the polio eradication initiative, countries should consider how to integrate the technical expertise of NCC members to reinforce NITAGs and maintain the polio essential functions, beginning in countries that have been polio-free for several years.

scholarly journals A Deep-Sequencing Method Detects Drug-Resistant Mutations in the Hepatitis B Virus in Indonesians

Intervirology ◽  
2014 ◽  
Vol 57 (6) ◽  
pp. 384-392 ◽  
Author(s):  
Dewiyani Indah Widasari ◽  
Yoshihiko Yano ◽  
Didik Setyo Heriyanto ◽  
Takako Utsumi ◽  
Laura Navika Yamani ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Deep Sequencing ◽  
Drug Resistant ◽  
Sequencing Method ◽  
B Virus

scholarly journals Establishment of a Pediatric COVID-19 Biorepository: Unique Considerations and Opportunities for Studying the Impact of the COVID-19 Pandemic on Children

2020 ◽  
Author(s):  
Rosiane Lima ◽  
Elizabeth Gootkind ◽  
Denis De La Flor ◽  
Laura Yockey ◽  
Evan Bordt ◽  
...  
Keyword(s):  
Pediatric Population ◽  
Urgent Care ◽  
Sample Collection ◽  
Viral Susceptibility ◽  
Global Pandemic ◽  
Asymptomatic Children ◽  
Successful Establishment ◽  
Processing And Storage ◽  
Inflammatory Syndrome ◽  
The Impact

Abstract Background: COVID-19, the disease caused by the highly infectious and transmissible coronavirus SARS-CoV-2, has quickly become a morbid global pandemic. Although the impact of SARS-CoV-2 infection in children is less clinically apparent, collecting high-quality biospecimens from infants, children and adolescents in a standardized manner during the COVID-19 pandemic is essential to establish a biologic understanding of the disease in the pediatric population. This biorepository enables pediatric centers world-wide to collect samples in a standardized manner to drive forward our understanding of COVID-19 by addressing specific pediatric and neonatal COVID-19-related questions. Methods: A broad study was implemented with strategic enrollment guidelines to include patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2 infected mothers, and asymptomatic children. The methodology described here, details the importance of establishing collaborations between the clinical and research teams to harmonize protocols for patient recruitment and sample collection, processing and storage. Results: Considerations and challenges facing enrollment of neonatal and pediatric cohorts are described. A roadmap is laid out for successful collection, processing, storage and database management of multiple pediatric samples such as blood, nasopharyngeal and oropharyngeal swabs, sputum, saliva, tracheal aspirates, stool, and urine. Using this methodology, we enrolled 327 participants, who provided a total of 972 biospecimens.Conclusions: Pediatric biospecimens will be key in answering questions relating to viral transmission by children, differences between pediatric and adult viral susceptibility, and, immune responses, the impact of maternal SARS-CoV-2 infection on fetal development, and factors driving the Multisystem Inflammatory Syndrome in Children. The specimens in this biorepository will allow necessary comparative studies between children and adults, help determine the accuracy of current pediatric viral testing techniques, in addition to, understanding neonatal exposure to SARS-CoV-2 infection and disease abnormalities. The successful establishment of a pediatric biorepository is critical to provide insight into disease pathogenesis, and subsequently, develop future treatment and vaccination strategies.

scholarly journals Modeling poliovirus surveillance and immunization campaign quality monitoring costs for Pakistan and Afghanistan for 2019-2023

2021 ◽  
Author(s):  
Dominika A Kalkowska ◽  
Mark A Pallansch ◽  
Stephen L Cochi ◽  
Kimberly M Thompson
Keyword(s):  
Polio Eradication ◽  
Quality Monitoring ◽  
Supplementary Information ◽  
Sample Collection ◽  
Catchment Areas ◽  
Lot Quality Assurance Sampling ◽  
Global Polio Eradication Initiative ◽  
Monitoring And Surveillance ◽  
And Performance ◽  
Immunization Campaign

Abstract Background The Global Polio Eradication Initiative (GPEI) Strategic Plan for 2019-2023 includes commitments to monitor the quality of immunization campaigns using lot quality assurance sampling surveys (LQAS) and to support poliovirus surveillance in Pakistan and Afghanistan. Methods We analyzed LQAS and poliovirus surveillance data between 2016 and 2020, which included both acute flaccid paralysis (AFP) case-based detection and the continued expansion of environmental surveillance (ES). Using updated estimates for unit costs, we explore the costs of different options for future poliovirus monitoring and surveillance for Pakistan and Afghanistan. Results The relative value of the information provided by campaign quality monitoring and surveillance remains uncertain and depends on the design, implementation, and performance of the systems. Prospective immunization campaign quality monitoring (through LQAS) and poliovirus surveillance will require tens of millions of dollars each year for the foreseeable future for Pakistan and Afghanistan. Conclusions LQAS campaign monitoring as currently implemented in Pakistan and Afghanistan provides limited and potentially misleading information about immunization quality. AFP surveillance in Pakistan and Afghanistan provides the most reliable evidence of transmission, whereas ES provides valuable supplementary information about the extent of transmission in the catchment areas represented at the time of sample collection.

scholarly journals Frequency of the STRC-CATSPER2 deletion in STRC-associated hearing loss patients

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Shin-ya Nishio ◽  
Shin-ichi Usami
Keyword(s):  
Hearing Loss ◽  
Male Infertility ◽  
Genetic Counselling ◽  
Copy Number ◽  
Read Depth ◽  
Copy Number Variations ◽  
Genomic Region ◽  
High Prevalence ◽  
Homozygous Deletions ◽  
Next Generation Sequencing Ngs

AbstractThe STRC gene, located on chromosome 15q15.3, is one of the genetic causes of autosomal recessive mild-to-moderate sensorineural hearing loss. One of the unique characteristics of STRC-associated hearing loss is the high prevalence of long deletions or copy number variations observed on chromosome 15q15.3. Further, the deletion of chromosome 15q15.3 from STRC to CATSPER2 is also known to be a genetic cause of deafness infertility syndrome (DIS), which is associated with not only hearing loss but also male infertility, as CATSPER2 plays crucial roles in sperm motility. Thus, information regarding the deletion range for each patient is important to the provision of appropriate genetic counselling for hearing loss and male infertility. In the present study, we performed next-generation sequencing (NGS) analysis for 9956 Japanese hearing loss patients and analyzed copy number variations in the STRC gene based on NGS read depth data. In addition, we performed Multiplex Ligation-dependent Probe Amplification analysis to determine the deletion range including the PPIP5K1, CKMT1B, STRC and CATSPER2 genomic region to estimate the prevalence of the STRC-CATSPER deletion, which is causative for DIS among the STRC-associated hearing loss patients. As a result, we identified 276 cases with STRC-associated hearing loss. The prevalence of STRC-associated hearing loss in Japanese hearing loss patients was 2.77% (276/9956). In addition, 77.1% of cases with STRC homozygous deletions carried a two copy loss of the entire CKMT1B-STRC-CATSPER2 gene region. This information will be useful for the provision of more appropriate genetic counselling regarding hearing loss and male infertility for the patients with a STRC deletion.

188 DETECTION BY POLYMERASE CHAIN REACTION OF NEOSPORA CANINUM FROM OVUM PICKUP AND UTERINE FLUSHING FLUIDS FROM DAIRY CATTLE IN MEXICO

2010 ◽  
Vol 22 (1) ◽  
pp. 252
Author(s):  
A. F. Marques ◽  
C. G. Ortiz ◽  
M. R. Lima ◽  
E. L. Zanella ◽  
L. Rangel ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Neospora Caninum ◽  
Pcr Amplification ◽  
Positive Control ◽  
Negative Control ◽  
Genomic Region ◽  
Sample Collection ◽  
Caninum Infection ◽  
Blood Lymphocytes ◽  
Negative Results

Neospora caninum, an intracellular protozoon, causes encephalomyelitis in dogs (Bjerkas I et al. 1984 Zentralblat fur Parasitenkunde 70, 271-274). For the past decade, neosporosis has been a main cause of abortion in dairy cattle worldwide (Anderson M et al. 2000 Anim. Reprod. Sci. 60-61, 417-431; Dubey JP 2003 Korean J. Parasitology 41, 1-16). Vertical transmission has been indicated as an important way of spreading neosporosis (Hall CA et al. 2005 Vet. Parasitology 31, 231-41); thus, we investigated whether the protozoon could be transferred by embryo production techniques. Blood samples were collected from 92 dairy cows with history of reproductive failure and abortion within the previous 90 days at 7 dairy farms in Tizayuca, Mexico. For serology evaluation, a commercial indirect ELISA kit (Civtest Bovis Neospora, Laboratories Hipra S.A, Girona, Spain), yielded 46.74% (43/92) positive results, 46.74% (43/92) negative results, and 6.52% (6/92) suspicious to N. caninum infection. Thirteen positive cows were chosen for uterine flush (UF), ovum pickup (OPU), and a blood sample collection. Lymphocytes from blood and cells within the UF and OPU collection fluids were collected after centrifugation and DNA was extracted. All samples were tested for the presence of N. caninum by PCR, using primers and protocols that amplified a 275-bp fragment of the genomic region (5-GGGTGAACCGAGGGAGTTG-3 and 5-CCTCCCAATGCGAACGAAA-3). The N. caninum vaccine (Bovilis® NeoGuard, Intervet, Santiago Tianguistenco, Mexico) was used as a positive control and water as a negative control. Uterine flush could not be obtained from 1 cow. From 13 cows seropositive to N. caninum, only 38% were positive to PCR from blood lymphocytes. In contrast, PCR amplification was obtained from OPU cell sediment in 92.31% (12/13) and in 33.33% (4/12) of UF. Of these 12 OPU- and 4 UF-positive samples, only 5 and 3 of their corresponding blood lymphocytes were positive. Our results using uterine and follicular fluid were contradictory to those published by Moskwa et al. (2008 Vet. Parasitology 158, 370-375) where oocytes and embryos were evaluated. These results indicate that N. caninum is present in the ovary and uterine lumen of the cows, suggesting a possible risk of neospora transmission during oocyte and embryo collection and transfer techniques. UNAM and UPF.

The Majority of RAS Pathway Mutations Detected in Relapsed B-Cell Precursor Acute Lymphoblastic Leukemia Are Present in Major or Minor Subclones at Diagnosis

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2397-2397 ◽  
Author(s):  
Jiangyan Yu ◽  
Esmé Waanders ◽  
Simon V. van Reijmersdal ◽  
Edwin Sonneveld ◽  
Peter M Hoogerbrugge ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Allele Frequency ◽  
Deep Sequencing ◽  
Mutant Allele ◽  
Sanger Sequencing ◽  
Lymphoblastic Leukemia ◽  
Read Depth ◽  
Cell Precursor ◽  
Ras Pathway ◽  
Mutant Allele Frequency

Abstract B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is one of the most common cancers in children. The relapse incidence varies between 15% and 25%, dependent on the treatment protocol. It has been demonstrated that the presence of mutations in the RAS pathway genes, which regulate signal transduction upon binding of ligand to a variety of membrane receptors, are frequently associated with high-risk ALL and may be relapse drivers (Zhang et al., Blood 2011 118:3080-7; Irving et al., ASH 2013). Relapses in ALL are thought to result from the outgrowth of therapy-resistant residual leukemia cells and recent studies have shown a complex, dynamic architecture of clonal diversity in ALL (Anderson et al., Nature 2011 469:356-61; Notta et al. Nature 2011 496:362-7). In this study, we have investigated the clonal origin of RAS pathway mutations in relapsed BCP-ALL. We screened 146 relapse samples from children with relapsed BCP-ALL for mutations in five RAS pathway genes using IonTorrent sequencing with a read-depth of approximately 150x. A total of 30% of relapse samples carried RAS pathway mutations, including mutations in KRAS (n=22), NRAS (n=13), PTPN11 (n=8), and FLT3 (n=2). No RAS mutations were found in 103 patients, whereas one patient had both a PTPN11 and a KRAS mutation, and another patient had two KRAS mutations. For 28 mutations we collected matched diagnosis samples and determined mutation presence using Sanger sequencing. We found that 12 of the RAS mutations were also present at diagnosis (43%) and 16 were initially not detected at diagnosis (57%). In order to gain more insight into the clonal evolution of relapse development, we performed amplicon based ultra-deep sequencing on the diagnosis samples, with an average read-depth of 50,000x for each mutation. The ultra-deep sequencing allows for sensitive and accurate detection of relapse-prone clones at diagnosis. A total of 22 mutations were identified at diagnosis samples (79%), of which 10 mutations had a low mutant allele frequency (average 3.8%), and were initially missed by Sanger sequencing (Fig.1). The 12 mutations determined using Sanger sequencing were detected at an average mutant allele frequency of 30.8%. We were unable to detect 6 mutations in the matched diagnosis samples, indicating that these mutations were newly acquired in the relapse clone at a time point after relapse. Our results indicate that cells harboring RAS pathway mutations are recurrently present in subclones at diagnosis. These cells may survive initial therapy and subsequently emerge at relapse. Patients with (minor clones with) RAS pathway mutations identified by ultra-deep sequencing, may benefit from treatment with MEK inhibitors added to the frontline therapy strategy. Figure 1. Backtracking of RAS pathway mutations by ultra-deep sequencing. A total of 22 mutations (out of 28) were detected in matched diagnosis samples. The 12 mutations (solid grey) determined by Sanger sequencing were detected at high mutant allele frequency ranging from 22% to 42%. Ten mutations (diagonally striped) were missed by Sanger sequencing but detected by ultra-deep sequencing. These mutations showed a low mutant allele frequency varying from 0.3% to 8%. Figure 1. Backtracking of RAS pathway mutations by ultra-deep sequencing. A total of 22 mutations (out of 28) were detected in matched diagnosis samples. The 12 mutations (solid grey) determined by Sanger sequencing were detected at high mutant allele frequency ranging from 22% to 42%. Ten mutations (diagonally striped) were missed by Sanger sequencing but detected by ultra-deep sequencing. These mutations showed a low mutant allele frequency varying from 0.3% to 8%. Disclosures No relevant conflicts of interest to declare.

Immunization Campaigns and Political Agendas: Retrospective from Ecuador and El Salvador

2003 ◽  
Vol 33 (1) ◽  
pp. 113-128 ◽  
Author(s):  
Stephen Gloyd ◽  
Jose Suarez Torres ◽  
Mary Anne Mercer
Keyword(s):  
El Salvador ◽  
Disease Incidence ◽  
Immunization Coverage ◽  
Polio Eradication ◽  
Short Term ◽  
Poor Countries ◽  
Vaccine Preventable Diseases ◽  
National Immunization ◽  
International Donors

Since the mid-1980s international donors have promoted vertical, campaign-based strategies to help improve immunization coverage in poor countries. National immunization days (NIDs) are currently in vogue and are prominent in the worldwide polio eradication efforts. In spite of their widespread use, campaigns that include NIDs have not been well evaluated for their effects on coverage, reduction in vaccine-preventable diseases, or effects on the health system. An assessment of the results of two such campaigns implemented in Ecuador and El Salvador shows limited impact on short-term coverage and questionable effects on long-term coverage and disease incidence. Although NIDs may have substantial short-term political benefits, the vertical approach can undermine provision of routine services by ministries of health and may be counterproductive in the long-term.

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