Molecular epidemiology of silent introduction and sustained transmission of wild poliovirus type 1, Israel, 2013

Poliovirus vaccine coverage in Israel is over 90%. The last nine birth cohorts have been vaccinated exclusively with inactivated polio vaccine (IPV). However, between February and July 2013 type 1 wild poliovirus (WPV1) was detected persistently in 10 and intermittently in 8 of 47 environmental surveillance sites in southern and central Israel and in 30 stool samples collected during July from healthy individuals in southern Israel. We report results of sequence and phylogenetic analyses of genes encoding capsid proteins to determine the source and transmission mode of the virus. WPV1 capsid protein 1 nucleotide sequences were most closely related to South Asia (SOAS) cluster R3A polioviruses circulating in Pakistan in 2012 and isolated from Egyptian sewage in December 2012. There was no noticeable geographical clustering within WPV1-positive sites. Uniform codon usage among isolates from Pakistan, Egypt and Israel showed no signs of optimisation or deoptimisation. Bayesian phylogenetic time clock analysis of the entire capsid coding region (2,643 nt) with a 1.1% evolutionary rate indicated that Israeli and Egyptian WPV1-SOAS lineages diverged in September 2012, while Israeli isolates split into two sub-branches after January 2013. This suggests one or more introduction events into Israel with subsequent silent circulation despite high population immunity.

Download Full-text

Recent Transposition of an LTR-Retrotransposon in the Gene Coding for S Receptor Kinase is Responsible for a Novel Self-Compatible Phenotype of Radish (Raphanus Sativus L.)

10.21203/rs.3.rs-884506/v1 ◽

2021 ◽

Author(s):

So-Hyeon Bong ◽

Ganghee Cho ◽

Dong-Seon Kim ◽

Sunggil Kim

Keyword(s):

Raphanus Sativus ◽

Phylogenetic Analyses ◽

Ltr Retrotransposon ◽

Nucleotide Polymorphisms ◽

Receptor Kinase ◽

Coding Region ◽

Single Nucleotide ◽

Breeding Lines ◽

Gene Coding ◽

Genes Encoding

Abstract Self-incompatibility (SI) responses of radish (Raphanus sativus L.) are determined by two tightly linked genes encoding an S receptor kinase (SRK) and an S-locus cysteine-rich protein/S locus protein 11 (SCR/SP11), respectively. A radish showing an almost self-compatible (SC) phenotype was identified in this study. Inheritance patterns showed that this SC phenotype was dominant over an SI phenotype. In addition, this SC phenotype co-segregated with an S haplotype in an F2 population. This SC radish contained an RsS-26 haplotype in which duplicate SRK-like genes were previously identified. Full-length sequences of two SRK-like genes of 18,133-bp and 6,200-bp in length were obtained from radish with the RsS-26 haplotype (designated as RsSRK-26-1 and RsSRK-26-2, respectively). Duplicate SCR/SP11-like genes were also identified in the radish with the RsS-26 haplotype. Phylogenetic analyses indicated that both duplicate SRK-like and SCR/SP11-like genes were closely related to other known SRK and SCR/SP11 genes, respectively. No critical mutation was found in the coding region of SRK-like or SCR/SP11-like gene. However, a 4,146-bp intact LTR-retrotransposon was identified in the third intron of RsSRK-26-1 of the SC radish. Interestingly, this LTR-retrotransposon was not detected in three other breeding lines containing the same RsS-26 haplotype. Except for this LTR-retrotransposon, only two single nucleotide polymorphisms (SNPs) were identified in intronic regions between normal and mutant RsSRK-26-1 alleles. While normal transcription was observed for radish showing RsSRK-26-1 and SI phenotypes in these three breeding lines, no transcript of RsSRK-26-1 was detected in the SC radish, suggesting that recent transposition of an LTR-retrotransposon in the RsSRK-26-1 gene might be responsible for the SC phenotype of radish.

Download Full-text

Controlling polio outbreak due to imported wild poliovirus in Indonesia: A success story

Paediatrica Indonesiana ◽

10.14238/pi49.4.2009.234-43 ◽

2009 ◽

Vol 49 (4) ◽

pp. 234 ◽

Cited By ~ 1

Author(s):

Sumarmo Poorwo Soedarmo ◽

Sidik Utoro

Keyword(s):

Acute Flaccid Paralysis ◽

Polio Eradication ◽

Outbreak Response ◽

Success Story ◽

Wild Poliovirus ◽

First Case ◽

Supplementary Immunization Activities ◽

Stool Samples ◽

Outbreak Response Immunization

Background As a WHO member state, Indonesia is committed toGlobal Polio Eradication. The last indigenous polio case was found in 1995. However, we faced a big challenge with the occurrence of polio outbreak, beginning with a polio case caused by imported wild poliovirus (WPV) type 1 in Sukabumi in 2005. The virus was originated from Sudan and imported to Indonesia through Saudi Arabia. The outbreak ended with totally 305 cases throughout the country. The last one occurred on 20 February 2006 in Aceh Tenggara District, Nanggroe Aceh Darussalam Province. In addition and separated from the WPV type 1 outbreak, in August 2005, four Acute Flaccid Paralysis (AFP) cases with type 1 Vaccine Derived Poliovirus (VDPV) in stool samples were identified in Madura, East Java Province. The first case was on 9 June 2005 and ended with 45 cases in Madura and another case in Probolinggo District, East Jawa.Objective To report a success of controlling outbreak of importedWPV in Indonesia.Methods Outbreak Response Immunization (ORI) and mopup immunization were conducted immediately. To completelystop the transmission, three rounds of National ImmunizationDays (NIDs) were conducted in 2005 (August, September, andNovember). Some more Supplementary Immunization Activities(SIAs) were conducted in 2006 (mop up in January, NIDs inFebruary and early April, mop ups in June and August 2006).For the VDPV outbreak, ORI of 18,880 children in 83 villagestook place during the first week of August, beside three roundsofNIDs in 2005.Results All activities resulted in satisfactorily coverage, whereeach round always exceeded 95%.Conclusions Those activities were conducted successfully andproven to be effective to stop the outbreak. Then again, Indonesia can be a polio free country in the coming years.

Download Full-text

Population immunity to polioviruses in the context of a large-scale wild poliovirus type 1 outbreak in Tajikistan, 2010

Vaccine ◽

10.1016/j.vaccine.2013.06.106 ◽

2013 ◽

Vol 31 (42) ◽

pp. 4911-4916 ◽

Cited By ~ 11

Author(s):

Nino Khetsuriani ◽

Mark A. Pallansch ◽

Shamsiddin Jabirov ◽

Nargis Saparova ◽

M. Steven Oberste ◽

...

Keyword(s):

Large Scale ◽

Poliovirus Type ◽

Wild Poliovirus ◽

Population Immunity

Download Full-text

Genetic Epidemiology Reveals 3 Chronic Reservoir Areas With Recurrent Population Mobility Challenging Poliovirus Eradication in Pakistan

Clinical Infectious Diseases ◽

10.1093/cid/ciz1037 ◽

2019 ◽

Vol 71 (7) ◽

pp. e58-e67 ◽

Cited By ~ 3

Author(s):

Ribqa Akhtar ◽

Nayab Mahmood ◽

Muhammad Masroor Alam ◽

Muhammad Naeem ◽

Syed Sohail Zahoor Zaidi ◽

...

Keyword(s):

Genetic Relatedness ◽

Immunization Coverage ◽

Polio Eradication ◽

Genomic Diversity ◽

Environmental Surveillance ◽

Population Mobility ◽

Coding Region ◽

Wild Poliovirus ◽

Effective Combination

Abstract Background Pakistan is among 3 countries endemic for wild poliovirus type 1 (WPV1) circulation that are still struggling for eradication of poliomyelitis. Active clinical and environmental surveillance with meticulous laboratory investigations provide insights into poliovirus transmission patterns and genomic diversity to inform decisions for strategic operations required to achieve eradication. Methods We analyzed epidemiological and virological data to comprehend the current epidemiological status of WPV1 in Pakistan during 2015–2017. Stool specimens of patients with acute flaccid paralysis (AFP) and sewage samples collected from 60 environmental sites were tested. Viral culturing, intratypic differentiation by real-time polymerase chain reaction, and nucleic acid sequencing of the VP1 region of the poliovirus genome to determine genetic relatedness among WPV1 strains were applied. Results Poliovirus isolates were grouped into 11 distinct clusters, which had ≥95% nucleotide homology in the VP1 coding region. Most of the poliovirus burden was shared by 3 major reservoirs: Karachi, Peshawar, and Quetta block (64.2% in 2015, 75.4% in 2016, and 76.7% in 2017). Conclusions Environmental surveillance reveals importations and pockets of unimmunized children that dictate intensive target mop-up campaigns to contain poliovirus transmission. A decrease in the number of orphan isolates reflects effective combination of AFP and environmental surveillance in Pakistan. The genetic data reflect sustained transmission within reservoir areas, further expanded by periodic importations to areas of high immunity reflected by immediate termination of imported viruses. Improved immunization coverage with high-quality surveillance is vital for global certification of polio eradication.

Download Full-text

Natural Genetic Exchanges between Vaccine and Wild Poliovirus Strains in Humans

Journal of Virology ◽

10.1128/jvi.74.18.8434-8443.2000 ◽

2000 ◽

Vol 74 (18) ◽

pp. 8434-8443 ◽

Cited By ~ 146

Author(s):

Sophie Guillot ◽

Valérie Caro ◽

Nancy Cuervo ◽

Ekaterina Korotkova ◽

Mariana Combiescu ◽

...

Keyword(s):

Paralytic Poliomyelitis ◽

Nucleotide Sequencing ◽

Wild Type ◽

Coding Region ◽

Wild Poliovirus ◽

Type 3 ◽

Recombinant Genome ◽

Natural Means

ABSTRACT In a previous study of poliovirus vaccine-derived strains isolated from patients with vaccine-associated paralytic poliomyelitis (VAPP) (9, 11), we reported that a high proportion (over 50%) of viruses had a recombinant genome. Most were intertypic vaccine/vaccine recombinants. However, some had restriction fragment length polymorphism (RFLP) profiles different from those of poliovirus vaccine strains. We demonstrate here that five such recombinants, of 88 VAPP strains examined, carried sequences of wild (nonvaccine) origin. To identify the parental wild donor of these sequences, we used RFLP profiles and nucleotide sequencing to look for similarity in the 3D polymerase-coding region of 61 wild, cocirculating poliovirus isolates (43 type 1, 16 type 2, and 2 type 3 isolates). In only one case was the donor identified, and it was a wild type 1 poliovirus. For the other four vaccine/wild recombinants, the wild parent could not be identified. The possibility that the wild sequences were of a non-poliovirus-enterovirus origin could not be excluded. Another vaccine/wild recombinant, isolated in Belarus from a VAPP case, indicated that the poliovirus vaccine/wild recombination is not an isolated phenomenon. We also found wild polioviruses (2 of 15) carrying vaccine-derived sequences in the 3′ moiety of their genome. All these results suggest that genetic exchanges with wild poliovirus and perhaps with nonpoliovirus enteroviruses, are also a natural means of evolution for poliovirus vaccine strains.

Download Full-text

Genetic Analysis and Characterization of Wild Poliovirus Type 1 During Sustained Transmission in a Population With >95% Vaccine Coverage, Israel 2013

Clinical Infectious Diseases ◽

10.1093/cid/ciu1136 ◽

2014 ◽

Vol 60 (7) ◽

pp. 1057-1064 ◽

Cited By ~ 21

Author(s):

Lester M. Shulman ◽

Javier Martin ◽

Danit Sofer ◽

Cara C. Burns ◽

Yossi Manor ◽

...

Keyword(s):

Genetic Analysis ◽

Vaccine Coverage ◽

Poliovirus Type ◽

Wild Poliovirus

Download Full-text

Renal Tubular Dysgenesis Associated with Compound Heterozygous ACE Mutations

Journal of Clinical and Nursing Research ◽

10.26689/jcnr.v5i2.1923 ◽

2021 ◽

Vol 5 (2) ◽

Author(s):

Yiran Liu ◽

Xueyan Wang

Keyword(s):

Autosomal Recessive Disorder ◽

Compound Heterozygous ◽

Renal Tubules ◽

Coding Region ◽

Renal Tubular Dysgenesis ◽

Frameshift Deletion ◽

Genes Encoding ◽

Renal Tubular ◽

Compound Heterozygous State

Inherited renal tubular dysgenesis(RTD), a rare, autosomal recessive disorder is caused by mutations in the genes encoding components of the renin-angiotensin pathway: angiotensinogen(AGT), renin (REN), angiotensin-converting enzyme(ACE), and angiotensin ?? receptor type 1(AGTR1). It characterized by the absence or poor development of renal tubules, and associated with oligohydramnios, Potter sequence and neonatal death due to renal or respiratory failure. We report a family with two mutations in the coding region of the ACE gene: a nonsense mutation in exon4 (c.538C>T) and a frameshift deletion at nucleotide 3073 and nucleotide 3074 in exon20(c.3073_3074delTC). The mutations were in the compound heterozygous state causing disease, because each parent had their own mutation.

Download Full-text

Sequence of the human glycogen-associated regulatory subunit of type 1 protein phosphatase and analysis of its coding region and mRNA level in muscle from patients with NIDDM

Diabetes ◽

10.2337/diabetes.43.10.1234 ◽

1994 ◽

Vol 43 (10) ◽

pp. 1234-1241 ◽

Cited By ~ 26

Author(s):

Y. H. Chen ◽

L. Hansen ◽

M. X. Chen ◽

C. Bjorbaek ◽

H. Vestergaard ◽

...

Keyword(s):

Protein Phosphatase ◽

Mrna Level ◽

Regulatory Subunit ◽

Coding Region

Download Full-text

Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽

10.3390/v13040545 ◽

2021 ◽

Vol 13 (4) ◽

pp. 545

Author(s):

Gédéon Prince Manouana ◽

Paul Alvyn Nguema-Moure ◽

Mirabeau Mbong Ngwese ◽

C.-Thomas Bock ◽

Peter G. Kremsner ◽

...

Keyword(s):

Genetic Diversity ◽

Preventive Measures ◽

Phylogenetic Analyses ◽

Enteric Viruses ◽

Study Cohort ◽

Viral Agent ◽

A Genome ◽

Stool Samples ◽

Pcr Techniques ◽

High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

Download Full-text

Inferring Numbers of Wild Poliovirus Excretors Using Quantitative Environmental Surveillance

Vaccines ◽

10.3390/vaccines9080870 ◽

2021 ◽

Vol 9 (8) ◽

pp. 870

Author(s):

Yuri Perepliotchikov ◽

Tomer Ziv-Baran ◽

Musa Hindiyeh ◽

Yossi Manor ◽

Danit Sofer ◽

...

Keyword(s):

Oral Polio Vaccine ◽

Turnaround Time ◽

Quantitative Detection ◽

Environmental Surveillance ◽

Wild Poliovirus ◽

Polio Vaccine ◽

Kinetic Information ◽

Using Data ◽

Number Of Individuals

Response to and monitoring of viral outbreaks can be efficiently focused when rapid, quantitative, kinetic information provides the location and the number of infected individuals. Environmental surveillance traditionally provides information on location of populations with contagious, infected individuals since infectious poliovirus is excreted whether infections are asymptomatic or symptomatic. Here, we describe development of rapid (1 week turnaround time, TAT), quantitative RT-PCR of poliovirus RNA extracted directly from concentrated environmental surveillance samples to infer the number of infected individuals excreting poliovirus. The quantitation method was validated using data from vaccination with bivalent oral polio vaccine (bOPV). The method was then applied to infer the weekly number of excreters in a large, sustained, asymptomatic outbreak of wild type 1 poliovirus in Israel (2013) in a population where >90% of the individuals received three doses of inactivated polio vaccine (IPV). Evidence-based intervention strategies were based on the short TAT for direct quantitative detection. Furthermore, a TAT shorter than the duration of poliovirus excretion allowed resampling of infected individuals. Finally, the method documented absence of infections after successful intervention of the asymptomatic outbreak. The methodologies described here can be applied to outbreaks of other excreted viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), where there are (1) significant numbers of asymptomatic infections; (2) long incubation times during which infectious virus is excreted; and (3) limited resources, facilities, and manpower that restrict the number of individuals who can be tested and re-tested.

Download Full-text