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Vaccine escape recombinants emerge after pneumococcal vaccination in the United States.

ABSTRACT: The heptavalent pneumococcal conjugate vaccine (PCV7) was introduced in the United States (US) in 2000 and has significantly reduced invasive pneumococcal disease; however, the incidence of nonvaccine serotype invasive disease, particularly due to serotype 19A, has increased. The serotype 19A increase can be explained in part by expansion of a genotype that has been circulating in the US prior to vaccine implementation (and other countries since at least 1990), but also by the emergence of a novel "vaccine escape recombinant" pneumococcal strain. This strain has a genotype that previously was only associated with vaccine serotype 4, but now expresses a nonvaccine serotype 19A capsule. Based on prior evidence for capsular switching by recombination at the capsular locus, the genetic event that resulted in this novel serotype/genotype combination might be identifiable from the DNA sequence of individual pneumococcal strains. Therefore, the aim of this study was to characterise the putative recombinational event(s) at the capsular locus that resulted in the change from a vaccine to a nonvaccine capsular type. Sequencing the capsular locus flanking regions of 51 vaccine escape (progeny), recipient, and putative donor pneumococci revealed a 39 kb recombinational fragment, which included the capsular locus, flanking regions, and two adjacent penicillin-binding proteins, and thus resulted in a capsular switch and penicillin nonsusceptibility in a single genetic event. Since 2003, 37 such vaccine escape strains have been detected, some of which had evolved further. Furthermore, two new types of serotype 19A vaccine escape strains emerged in 2005. To our knowledge, this is the first time a single recombinational event has been documented in vivo that resulted in both a change of serotype and penicillin nonsusceptibility. Vaccine escape by genetic recombination at the capsular locus has the potential to reduce PCV7 effectiveness in the longer term.

SUBMITTER: Brueggemann AB

PROVIDER: S-EPMC2077903 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:IntroductionNational reports suggest that Hispanic patients may underutilize influenza and pneumococcal vaccination, although studies sometimes conflict on this point. A clearer picture of adult immunization utilization in older Hispanic patients is necessary to ensure equity in adult vaccinations.MethodsUsing electronic health records from 648 community health centers (CHCs) across 21 states, we compared English-preferring Hispanic patients, Spanish-preferring Hispanic patients, and Non-Hispanic White (NHW) adults aged ≥50 years across five outcomes between 2012-2017: (1) Odds of ever receiving pneumococcal vaccination after age 65, (2) Odds of ever receiving ≥2 pneumococcal vaccinations for those ≥65, (3) odds of vaccination between the ages of 50 and 64 for those with diabetes or heart disease, (4) odds of influenza vaccine, and (5) annual rate of influenza vaccination.ResultsOf our total study sample (N = 143,869), 85,562 were age 50-64 during the entire study period, and 65,977 were ≥65 at some point during the study period. In patients aged 50-64, Spanish-preferring Hispanic patients were more likely to have ever had an influenza vaccination (covariate-adjusted odds ratio [aOR] = 1.33, 95% CI = 1.29-1.37), had higher rates of annual influenza vaccination (covariate-adjusted rate ratio [aRR] = 1.41, 95% CI = 1.38-1.44), and higher odds of pneumococcal vaccination (aOR = 1.87, 95% CI = 1.76-1.98) than NHW patients. These findings were similar in Spanish-preferring Hispanic patients ≥65. English-preferring Hispanics ≥65 were less likely than NHW patients to ever have an influenza vaccination (aOR = 0.91, 95% CI = 0.85-0.98) and to have ever received at least one (aOR = 0.92, 95% CI = 0.86-0.99) or two (aOR = 0.86, 95% CI = 0.77-0.95) pneumococcal vaccine doses.ConclusionsIn a multistate CHC network, Spanish-preferring Hispanic patients were more likely to receive influenza and pneumococcal vaccinations than NHW patients; older English-preferring Hispanic patients were often less likely than NHW patients to receive these vaccinations. In vaccine initiatives, English-preferring Hispanic patients may be at higher risk of vaccination inequity.

Project description:Recently, the SARS-CoV-2 variants from the United Kingdom (UK), South Africa, and Brazil have received much attention for their increased infectivity, potentially high virulence, and possible threats to existing vaccines and antibody therapies. The question remains if there are other more infectious variants transmitted around the world. We carry out a large-scale study of 506,768 SARS-CoV-2 genome isolates from patients to identify many other rapidly growing mutations on the spike (S) protein receptor-binding domain (RBD). We reveal that essentially all 100 most observed mutations strengthen the binding between the RBD and the host angiotensin-converting enzyme 2 (ACE2), indicating the virus evolves toward more infectious variants. In particular, we discover new fast-growing RBD mutations N439K, S477N, S477R, and N501T that also enhance the RBD and ACE2 binding. We further unveil that mutation N501Y involved in United Kingdom (UK), South Africa, and Brazil variants may moderately weaken the binding between the RBD and many known antibodies, while mutations E484K and K417N found in South Africa and Brazilian variants, L452R and E484Q found in India variants, can potentially disrupt the binding between the RBD and many known antibodies. Among these RBD mutations, L452R is also now known as part of the California variant B.1.427. Finally, we hypothesize that RBD mutations that can simultaneously make SARS-CoV-2 more infectious and disrupt the existing antibodies, called vaccine escape mutations, will pose an imminent threat to the current crop of vaccines. A list of most likely vaccine escape mutations is given, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S. Mutation T478K appears to make the Mexico variant B.1.1.222 the most infectious one. Our comprehensive genetic analysis and protein-protein binding study show that the genetic evolution of SARS-CoV-2 on the RBD, which may be regulated by host gene editing, viral proofreading, random genetic drift, and natural selection, gives rise to more infectious variants that will potentially compromise existing vaccines and antibody therapies.

Project description:To investigate the differences in vaccine hesitancy and preference of the currently available COVID-19 vaccines between two countries, namely, China and the United States (U.S.). A cross-national survey was conducted in both China and the United States, and discrete choice experiments, as well as Likert scales, were utilized to assess vaccine preference and the underlying factors contributing to vaccination acceptance. Propensity score matching (PSM) was performed to enable a direct comparison between the two countries. A total of 9077 (5375 and 3702 from China and the United States, respectively) respondents completed the survey. After propensity score matching, over 82.0% of respondents from China positively accepted the COVID-19 vaccination, while 72.2% of respondents from the United States positively accepted it. Specifically, only 31.9% of Chinese respondents were recommended by a doctor to have COVID-19 vaccination, while more than half of the U.S. respondents were recommended by a doctor (50.2%), local health board (59.4%), or friends and families (64.8%). The discrete choice experiments revealed that respondents from the United States attached the greatest importance to the efficacy of COVID-19 vaccines (44.41%), followed by the cost of vaccination (29.57%), whereas those from China held a different viewpoint, that the cost of vaccination covered the largest proportion in their trade-off (30.66%), and efficacy ranked as the second most important attribute (26.34%). Additionally, respondents from China tended to be much more concerned about the adverse effect of vaccination (19.68% vs. 6.12%) and have a lower perceived severity of being infected with COVID-19. Although the overall acceptance and hesitancy of COVID-19 vaccination in both countries are high, underpinned distinctions between these countries were observed. Owing to the differences in COVID-19 incidence rates, cultural backgrounds, and the availability of specific COVID-19 vaccines in the two countries, vaccine rollout strategies should be nation-dependent.

Project description:Understanding the epidemiology of pneumococcal co-colonization is important for monitoring vaccine effectiveness and the occurrence of horizontal gene transfer between pneumococcal strains. In this study we aimed to evaluate the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal co-colonization among Portuguese children. Nasopharyngeal samples from children up to 6 years old yielding a pneumococcal culture were clustered into three groups: pre-vaccine era (n?=?173), unvaccinated children of the vaccine era (n?=?169), and fully vaccinated children (4 doses; n?=?150). Co-colonization, serotype identification, and relative serotype abundance were detected by analysis of DNA of the total bacterial growth of the primary culture plate using the plyNCR-RFLP method and a molecular serotyping microarray-based strategy. The plyNCR-RFLP method detected an overall co-colonization rate of 20.1%. Microarray analysis confirmed the plyNCR-RFLP results. Vaccination status was the only factor found to be significantly associated with co-colonization: co-colonization rates were significantly lower (p?=?0.004; Fisher's exact test) among fully vaccinated children (8.0%) than among children from the pre-PCV7 era (17.3%) or unvaccinated children of the PCV7 era (18.3%). In the PCV7 era there were significantly less non-vaccine type (NVT) co-colonization events than would be expected based on the NVT distribution observed in the pre-PCV7 era (p?=?0.024). In conclusion, vaccination with PCV7 resulted in a lower co-colonization rate due to an asymmetric distribution between NVTs found in single and co-colonized samples. We propose that some NVTs prevalent in the PCV7 era are more competitive than others, hampering their co-existence in the same niche. This result may have important implications since a decrease in co-colonization events is expected to translate in decreased opportunities for horizontal gene transfer, hindering pneumococcal evolution events such as acquisition of antibiotic resistance determinants or capsular switch. This might represent a novel potential benefit of conjugate vaccines.

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Vaccine escape recombinants emerge after pneumococcal vaccination in the United States.

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