Pharmacogenetics of induction therapy-related toxicities in childhood acute lymphoblastic leukemia patients treated with UKALL 2003 protocol

Chemotherapy related toxicities have been the major factor limiting the success of acute lymphoblastic leukemia (ALL) induction therapy. Several factors, including the pharmacogenetics of asparaginase and anthracyclines, could contribute to difference in treatment outcome in ALL. We investigated the significance of variations in genes involved in hepatic and cardiac toxicity in acute lymphoblastic leukemia (ALL). Genotyping of SOD2 (rs4880), PNPL3 (rs738409) and ABCC1 (rs4148350), CBR1 (rs9024) and ABCG2 (rs2231142) was performed by Tetra-ARMS PCR-based technique to evaluate the genotype–phenotype correlation. Our results showed only minor allele G of SOD2 rs4880 increase the risk of hepatic toxicity [OR 2.63 (1.42–4.84), P = < 0.05] while minor alleles of other SNPs showed protective impact. However, the genetic contrast analysis showed a recessive form of SOD2 rs4880 [OR 7.82 (3.86–15.85), P = < 0.05] and PNPLA3 I148M [OR 5.82 (3.43–9.87), P = < 0.05] variants whereas dominant genotype of ABCC1 rs4148350 [OR 2.52 (1.55–4.10), P = < 0.05] significantly predisposes hepatotoxicity. Furthermore, heterozygous form of ABCG2 rs2231142 [OR 5.25 (1.84–14.95), P = < 0.05] and recessive genotype of 3′UTR variant CBR1 rs9024 [OR 2.31 (1.31–4.07), P = < 0.05] were strongly associated with cardiotoxicity. The information obtained from these genetic variations could offer biomarkers for individualization of therapeutic intervention in ALL.

Comparative Analysis of New Zealand Campylobacter Isolates Using MLST, PFGE and flaA PCR RFLP Genotyping

<p>Campylobacter jejuni and Campylobacter coli are the most commonly identified sources of campylobacteriosis in New Zealand, yet little is known about the distribution of genotypes within the respective population structures. Using multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and flaA genotyping, the current study identified the distribution of genotypes within New Zealand C. jejuni and C. coli isolates from an outbreak situation, as well as isolates present in the ESR Campylobacter collection. Although the most commonly identified MLST genotypes were similar to international genotypes, a number of internationally rare, or unique to New Zealand genotypes were observed. One rare dominant genotype, ST-474, arising from a point source outbreak, was found to cause a large proportion of human campylobacteriosis cases in New Zealand. A unique cluster of New Zealand genotypes were isolated only from river water, identifying a potentially water adapted C. jejuni strain. Frequent homologous recombination and horizontal gene transfer events were identified within the seven housekeeping genes characterised in the New Zealand sample and the MLST C. jejuni/C. coli database. The identified genetic instability within the current study questions the legitimacy of bacterial species boundaries, especially when examining closely related species such as C. jejuni and C. coli.</p>

Comparative Analysis of New Zealand Campylobacter Isolates Using MLST, PFGE and flaA PCR RFLP Genotyping

<p>Campylobacter jejuni and Campylobacter coli are the most commonly identified sources of campylobacteriosis in New Zealand, yet little is known about the distribution of genotypes within the respective population structures. Using multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and flaA genotyping, the current study identified the distribution of genotypes within New Zealand C. jejuni and C. coli isolates from an outbreak situation, as well as isolates present in the ESR Campylobacter collection. Although the most commonly identified MLST genotypes were similar to international genotypes, a number of internationally rare, or unique to New Zealand genotypes were observed. One rare dominant genotype, ST-474, arising from a point source outbreak, was found to cause a large proportion of human campylobacteriosis cases in New Zealand. A unique cluster of New Zealand genotypes were isolated only from river water, identifying a potentially water adapted C. jejuni strain. Frequent homologous recombination and horizontal gene transfer events were identified within the seven housekeeping genes characterised in the New Zealand sample and the MLST C. jejuni/C. coli database. The identified genetic instability within the current study questions the legitimacy of bacterial species boundaries, especially when examining closely related species such as C. jejuni and C. coli.</p>

Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks

Transmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The presence of bottlenecks within individual hosts and their potential impacts on evolutionary pathways taken during infection and subsequent transmission are poorly understood. To address this knowledge gap, we created highly diverse IAV libraries bearing molecular barcodes on two independent gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in “islands” of infection in lung lobes, each with genetically distinct populations. We performed site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and tracked viral diversity as infection spread to the trachea and lungs. We observed compartmentalized replication of discrete barcoded populations within the lobes of the lung. Bottlenecks stochastically sampled individual viruses from the upper respiratory tract or the trachea that became the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with no evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation.

Genetic Diversity of Dengue Virus in Clinical Specimens from Bangkok, Thailand, during 2018–2020: Co-Circulation of All Four Serotypes with Multiple Genotypes and/or Clades

Dengue is an arboviral disease highly endemic in Bangkok, Thailand. To characterize the current genetic diversity of dengue virus (DENV), we recruited patients with suspected DENV infection at the Hospital for Tropical Diseases, Bangkok, during 2018–2020. We determined complete nucleotide sequences of the DENV envelope region for 111 of 276 participant serum samples. All four DENV serotypes were detected, with the highest proportion being DENV-1. Although all DENV-1 sequences were genotype I, our DENV-1 sequences were divided into four distinct clades with different distributions in Asian countries. Two genotypes of DENV-2 were identified, Asian I and Cosmopolitan, which were further divided into two and three distinct clades, respectively. In DENV-3, in addition to the previously dominant genotype III, a cluster of 6 genotype I viruses only rarely reported in Thailand was also observed. All of the DENV-4 viruses belonged to genotype I, but they were separated into three distinct clades. These results indicated that all four serotypes of DENV with multiple genotypes and/or clades co-circulate in Bangkok. Continuous investigation of DENV is warranted to further determine the relationship between DENV within Thailand and neighboring countries in Southeast Asia and Asia.

Impact of SOD2, PNPLA3, ABCC1, CBR1 And ABCG2 Variants Upon Toxicities of Induction Therapy In Childhood Acute Lymphoblastic Leukemia

Chemotherapy related toxicities have been the major factor limiting the success of acute lymphoblastic leukemia (ALL) induction therapy. Several factors, including the pharmacogenetics of asparagenase and anthracyclines, could contribute to difference in treatment outcome in ALL. We investigated the significance of variations in genes that are involved in hepatic toxicity and cardiotoxicity in acute lymphoblastic leukemia (ALL). Genotyping of SOD2 (rs4880), PNPL3 (rs738409) and ABCC1 (rs4148350), CBR1 (rs9024) and ABCG2 (rs2231142) was performed by Tetra-ARMS PCR-based technique to evaluate the genotype-phenotype correlation. Our results showed only the minor allele G of SOD2 rs4880 increase the risk of hepatic toxicity [OR=2.63 (1.42-4.84), P=<.05] while minor alleles of other SNPs showed protective impact. However, the genetic contrast analysis showed a recessive form of SOD2 rs4880 [OR=7.82 (3.86-15.85), P=<0.05] and PNPLA3 I148M [OR=5.82 (3.43-9.87), P=<0.05] variants whereas dominant genotype of ABCC1 rs4148350 [OR=2.52 (1.55-4.10), P=<0.05] significantly predisposes hepatotoxicity. Furthermore, heterozygous form of ABCG2 rs2231142 [OR=5.25 (1.84-14.95), P=<0.05] and recessive genotype of 3′UTR variant CBR1 rs9024 [OR=2.31 (1.31-4.07), P=<0.05] were strongly associated with cardiotoxicity. The information obtained from these genetic variations could offer biomarkers for individualization of therapeutic intervention in ALL.

Long-term dynamics of Norovirus transmission in Japan, 2005–2019

Norovirus continues to evolve, adjusting its pathogenesis and transmissibility. In the present study, we systematically collected datasets on Norovirus outbreaks in Japan from 2005 to 2019 and analyzed time-dependent changes in the asymptomatic ratio, the probability of virus detection, and the probability of infection given exposure. Reports of 1,728 outbreaks were published, and feces from all involved individuals, including those with asymptomatic infection, were tested for virus in 434 outbreaks. We found that the outbreak size did not markedly change over this period, but the variance in outbreak size increased during the winter (November–April). Assuming that natural history parameters did not vary over time, the asymptomatic ratio, the probability of virus detection, and the probability of infection given exposure were estimated to be 18.6%, 63.3% and 84.5%, respectively. However, a model with time-varying natural history parameters yielded better goodness-of-fit and suggested that the asymptomatic ratio varied by year. The asymptomatic ratio was as high as 25.8% for outbreaks caused by genotype GII.4 noroviruses. We conclude that Norovirus transmissibility has not changed markedly since 2005, and that yearly variation in the asymptomatic ratio could potentially be explained by the circulating dominant genotype.

Angiotensin-converting enzyme-1 gene insertion/deletion polymorphism may be associated with COVID-19 clinical severity: a prospective cohort study

BACKGROUND: Angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism may play a role in the pathogenesis of coronavirus-19 disease (COVID-19). OBJECTIVES: Investigate the relationship between ACE I/D polymorphism and the clinical severity of COVID-19. DESIGN: Prospective cohort study. SETTING: Tertiary care hospital. PATIENTS AND METHODS: The study included COVID-19 patients with asymptomatic, mild, and severe disease with clinical data and whole blood samples collected from 1 April 2020 to 1 July 2020. ACE I/D genotypes were determined by polymerase chain reaction and agarose gel electrophoresis. MAIN OUTCOME MEASURE: ACE DD, DI and II genotypes frequencies. SAMPLE SIZE: 90 cases, 30 in each disease severity group. RESULTS: Age and the frequency of general comorbidity increased significantly from the asymptomatic disease group to the severe disease group. Advanced age, diabetes mellitus and presence of ischemic heart disease were independent risk factors for severe COVID-19 [OR and 95 % CI: 1.052 (1.021-1.083), 5.204 (1.006-26.892) and 5.922 (1.109-31.633), respectively]. The ACE II genotype was the dominant genotype (50%) in asymptomatic patients, while the DD genotype was the dominant genotype (63.3 %) in severe disease. The ACE II geno-type was protective against severe COVID-19 [OR and 95% CI: .323 (.112-.929)]. All nine patients (8.9%) who died had severe disease. CONCLUSIONS: The clinical severity of COVID-19 infection may be associated with the ACE I/D polymorphism. LIMITATIONS: Small sample size and single center. CONFLICT OF INTEREST: None.

Characterisation of a G2P[4] Rotavirus Outbreak in Western Australia, Predominantly Impacting Aboriginal Children

In May 2017, an outbreak of rotavirus gastroenteritis was reported that predominantly impacted Aboriginal children ≤4 years of age in the Kimberley region of Western Australia. G2P[4] was identified as the dominant genotype circulating during this period and polyacrylamide gel electrophoresis revealed the majority of samples exhibited a conserved electropherotype. Full genome sequencing was performed on representative samples that exhibited the archetypal DS-1-like genome constellation: G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and phylogenetic analysis revealed all genes of the outbreak samples were closely related to contemporary Japanese G2P[4] samples. The outbreak samples consistently fell within conserved sub-clades comprised of Hungarian and Australian G2P[4] samples from 2010. The 2017 outbreak variant was not closely related to G2P[4] variants associated with prior outbreaks in Aboriginal communities in the Northern Territory. When compared to the G2 component of the RotaTeq vaccine, the outbreak variant exhibited mutations in known antigenic regions; however, these mutations are frequently observed in contemporary G2P[4] strains. Despite the level of vaccine coverage achieved in Australia, outbreaks continue to occur in vaccinated populations, which pose challenges to regional areas and remote communities. Continued surveillance and characterisation of emerging variants are imperative to ensure the ongoing success of the rotavirus vaccination program in Australia.

Genetic Evolution Characteristics of Genotype G57 Virus, A Dominant Genotype of H9N2 Avian Influenza Virus

This study aimed to investigate the genetic evolution of the H9N2 avian influenza virus (AIV). Whole genome phylogenetic trees were constructed based on 306 H9N2 avian influenza strains collected in China from 2014 to 2019. The results showed that eight gene sequences were clustered separately according to their dominant clades, and a total of 10 genotypes were identified (seven of which were novel types). Among them, G57 genotype was confirmed as the most prevalent genotype with a frequency of 94%. In China, the G57 genotype of H9N2 first emerged in 2007, and then became the most common genotype in 2013. Therefore, the nucleotide substitution rates of G57 genotype in HA and NA genes collected from 2007 to 2019 were estimated, and the positive selection pressure sites in the same data set were measured. Taking 2013 as the boundary, the time period was divided into two periods: 2007–2012 and 2013–2019. From 2007 to 2012, multiple genotypes coexisted and could bear the pressures from both nature and environment; while G57 genotype was still in the adaptation stage, subjected to less selection pressure and in the process of slow evolution. However, from 2013 to 2019, G57 became the dominant genotype, and most of the external pressure reacted on it. Moreover, G57 genotype showed better adaptability than other genotypes. From 2013 to 2019, the nucleotide substitution rates of the HA gene were increased, and the positive selection pressures on HA and NA genes were stronger compared to those from 2007 to 2012. To sum up, the absolutely dominant G57 genotype exhibited a relatively constant genotype frequency and experienced adaptive evolution and natural selection simultaneously during the monitoring period. Therefore, urgent attention and diligent surveillance of H9N2 avian influenza virus are becoming increasingly important.