Toward a pan-SARS-CoV-2 vaccine targeting conserved epitopes on spike and non-spike proteins for potent, broad and durable immune responses.

BACKGROUND: The SARS-CoV-2 non-Spike (S) structural protein targets on nucleocapsid (N), membrane (M) and envelope (E), critical in the host cell interferon response and memory T-cell immunity, are grossly overlooked in COVID vaccine development. The current Spike-only vaccines bear an intrinsic shortfall for promotion of a fuller T cell immunity. Vaccines designed to target conserved epitopes could elicit strong cellular immune responses that would synergize with B cell responses and lead to long-term vaccine success. We pursue a universal (pan-SARS-CoV-2) vaccine against Delta, Omicrons and ever-emergent new mutants. METHODS AND FINDINGS: We explored booster immunogenicity of UB-612, a multitope-vaccine that contains S1-RBD-sFc protein and sequence-conserved promiscuous Th and CTL epitope peptides on the Sarbecovirus N, M and S2 proteins. To a subpopulation (N = 1,478) of infection-free participants (aged 18-85 years) involved in a two-dose Phase-2 trial, a UB-612 booster (third dose) was administered 6-8 months after the second dose. The immunogenicity was evaluated at 14 days post-booster with overall safety monitored until the end of study. The booster induced high viral-neutralizing antibodies against live Wuhan WT (VNT50, 1,711) and Delta (VNT50, 1,282); and against pseudovirus WT (pVNT50, 11,167) vs. Omicron BA.1/BA.2/BA.5 variants (pVNT50, 2,314/1,890/854), respectively. The lower primary neutralizing antibodies in the elderly were uplifted upon boosting to approximately the same high level in young adults. UB-612 also induced potent, durable Th1-oriented (IFN-γ+-) responses (peak/pre-boost/post-boost SFU/106 PBMCs, 374/261/444) along with robust presence of cytotoxic CD8+ T cells (peak/pre-boost/post-boost CD107a+-Granzyme B+, 3.6%/1.8%/1.8%). This UB-612 booster vaccination is safe and well tolerated without SAEs. CONCLUSIONS: By targeting conserved epitopes on viral S2, M and N proteins, UB-612 could provide potent, broad and long-lasting B-cell and T-cell memory immunity and offers the potential as a universal vaccine to fend off Omicrons and new VoCs without resorting to Omicron-specific immunogens. TRIAL REGISTRATION: ClinicalTrials.gov ID: NCT04773067; ClinicalTrials.gov ID: NCT05293665; ClinicalTrials.gov ID: NCT05541861.

Taiwan's Response to Influenza: A Seroepidemiological Evaluation of Policies and Implications for Pandemic Preparedness.

OBJECTIVES: To evaluate class suspension and mass vaccination implemented among Taipei schoolchildren during the 2009 influenza pandemic and investigate factors affecting antibody responses. METHODS: We conducted 2 cohort studies on: (1) 972 schoolchildren from November 2009-March 2010 to evaluate pandemic policies and (2) 935 schoolchildren from November 2011-March 2012 to verify factors in antibody waning. Anti-influenza H1N1pdm09 hemagglutination inhibition antibodies (HI-Ab) were measured from serum samples collected before vaccination, and at 1 and 4 months after vaccination. Factors affecting HI-Ab responses were investigated through logistic regression and generalized estimating equation. RESULTS: Seroprevalence of H1N1pdm09 before vaccination was significantly higher among schoolchildren who experienced class suspensions than those who did not (59.6% vs 47.5%, p<0.05). Participating in after-school activities (adjusted odds ratio [aOR]=2.47, p=0.047) and having ≥3 hours per week of exercise (aOR=2.86, p=0.019) were significantly correlated with H1N1pdm09 infection. Two doses of the H1N1pdm09 vaccine demonstrated significantly better antibody persistence than 1 dose (HI-Ab geometric mean titer: 132.5 vs 88.6, p=0.047). Vaccine effectiveness after controlling for preexisting immunity was 86% (32%-97%). Exercise ≥3 hours per week and preexisting immunity were significantly associated with antibody waning/maintenance. CONCLUSIONS: This study is the first to show that exercise and preexisting immunity may affect antibody waning. Further investigation is needed to identify immune correlates of protection.

A multitope SARS-CoV-2 vaccine provides long-lasting B cell and T cell immunity against Delta and Omicron variants.

BackgroundThe Delta and Omicron variants of SARS-CoV-2 are currently responsible for breakthrough infections due to waning immunity. We report phase I/II trial results of UB-612, a multitope subunit vaccine containing S1-RBD-sFc protein and rationally designed promiscuous peptides representing sarbecovirus conserved helper T cell and cytotoxic T lymphocyte epitopes on the nucleocapsid (N), membrane (M), and spike (S2) proteins.MethodWe conducted a phase I primary 2-dose (28 days apart) trial of 10, 30, or 100 µg UB-612 in 60 healthy young adults 20 to 55 years old, and 50 of them were boosted with 100 µg of UB-612 approximately 7 to 9 months after the second dose. A separate placebo-controlled and randomized phase II study was conducted with 2 doses of 100 µg of UB-612 (n = 3,875, 18-85 years old). We evaluated interim safety and immunogenicity of phase I until 14 days after the third (booster) dose and of phase II until 28 days after the second dose.ResultsNo vaccine-related serious adverse events were recorded. The most common solicited adverse events were injection site pain and fatigue, mostly mild and transient. In both trials, UB-612 elicited respective neutralizing antibody titers similar to a panel of human convalescent sera. The most striking findings were long-lasting virus-neutralizing antibodies and broad T cell immunity against SARS-CoV-2 variants of concern (VoCs), including Delta and Omicron, and a strong booster-recalled memory immunity with high cross-reactive neutralizing titers against the Delta and Omicron VoCs.ConclusionUB-612 has presented a favorable safety profile, potent booster effect against VoCs, and long-lasting B and broad T cell immunity that warrants further development for both primary immunization and heterologous boosting of other COVID-19 vaccines.Trial RegistrationClinicalTrials.gov: NCT04545749, NCT04773067, and NCT04967742.FundingUBI Asia, Vaxxinity Inc., and Taiwan Centers for Disease Control, Ministry of Health and Welfare.

Emerged HA and NA mutants of the pandemic influenza H1N1 viruses with increasing epidemiological significance in Taipei and Kaohsiung, Taiwan, 2009-10.

The 2009 influenza pandemic provided an opportunity to observe dynamic changes of the hemagglutinin (HA) and neuraminidase (NA) of pH1N1 strains that spread in two metropolitan areas--Taipei and Kaohsiung. We observed cumulative increases of amino acid substitutions of both HA and NA that were higher in the post-peak than in the pre-peak period of the epidemic. About 14.94% and 3.44% of 174 isolates had one and two amino acids changes, respective, in the four antigenic sites. One unique adaptive mutation of HA2 (E374K) was first detected three weeks before the epidemic peak. This mutation evolved through the epidemic, and finally emerged as the major circulated strain, with significantly higher frequency in the post-peak period than in the pre-peak (64.65% vs 9.28%, p<0.0001). E374K persisted until ten months post-nationwide vaccination without further antigenic changes (e.g. prior to the highest selective pressure). In public health measures, the epidemic peaked at seven weeks after oseltamivir treatment was initiated. The emerging E374K mutants spread before the first peak of school class suspension, extended their survival in high-density population areas before vaccination, dominated in the second wave of class suspension, and were fixed as herd immunity developed. The tempo-spatial spreading of E374K mutants was more concentrated during the post-peak (p = 0.000004) in seven districts with higher spatial clusters (p<0.001). This is the first study examining viral changes during the naïve phase of a pandemic of influenza through integrated virological/serological/clinical surveillance, tempo-spatial analysis, and intervention policies. The vaccination increased the percentage of E374K mutants (22.86% vs 72.34%, p<0.001) and significantly elevated the frequency of mutations in Sa antigenic site (2.36% vs 23.40%, p<0.001). Future pre-vaccination public health efforts should monitor amino acids of HA and NA of pandemic influenza viruses isolated at exponential and peak phases in areas with high cluster cases.

Nasopharyngeal carriage of Streptococcus pneumoniae in Taiwan before and after the introduction of a conjugate vaccine.

BACKGROUND: The heptavalent pneumococcal conjugate vaccine was introduced in Taiwan in October 2005. To evaluate the effect of the vaccination, we conducted an active, prospective, large-scale, long-term, and multicenter study to assess the prevalence of nasopharyngeal Streptococcus pneumoniae carriage in Taiwanese children. METHODS: This study was performed at three tertiary teaching hospitals in northern, central, and southern Taiwan. Questionnaires provided demographic, family/household, and medical history data. Pneumococcal isolates were tested for their susceptibility to various antimicrobial agents and serotypes. In addition, influenza virus and Staphylococcus aureus were recovered from nasopharyngeal and nasal swabs, respectively. RESULTS: Between July 2005 and July 2008, 857 pneumococcal strains were recovered from a total of 6057 children aged >2 months to 5 years (carriage rate, 14.1%). Carriage rates differed geographically and varied with subject age. In a multivariate analysis, having at least one sibling, attendance at day-care centers, a history of otitis media, and history of upper respiratory tract infection in the previous 2 weeks were each associated with a higher risk of pneumococcal colonization of the nasopharynx. Staphylococcus aureus nasal colonization was inversely associated with nasopharyngeal carriage of pneumococcus (p=0.000; odds ratio [OR]: 0.48; 95% CI: 0.39-0.58). Daycare attendance was the only risk factor for carriage of penicillin non-susceptible S. pneumoniae (OR: 2.37; 95% CI: 1.22-4.88). Although vaccination rates rose from 2005 to 2008, no concomitant decrease in S. pneumoniae carriage occurred. The rate of penicillin resistance among S. pneumoniae isolates was 92.8% (using the meningitis criteria). The prevalence of cefotaxime resistance (21.6%) was higher than that of penicillin (6.9%; non-meningitis criteria). Slightly more than half (57.4%) of the isolates belonged to strains covered by the heptavalent pneumococcal conjugate vaccine when both vaccine and vaccine-related serotypes were included. CONCLUSIONS: Although vaccination rates rose from 2005 to 2008, no concomitant decrease occurred in S. pneumoniae carriage. Interaction between S. aureus and S. pneumoniae may influence vaccination efficacy. These findings provide baseline data to further compare pneumococcal carriage rates and antibiotic resistance patterns in Taiwanese children as vaccination rates continue to increase.

Clinical implications, risk factors and mortality following community-onset bacteremia caused by extended-spectrum ß-lactamase (ESBL) and non-ESBL producing Escherichia coli.

BACKGROUND/PURPOSE: Infections caused by extended-spectrum ß-lactamase (ESBL)-producing bacteria have become a serious clinical concern worldwide. The occurrence of ESBLs in Taiwan has been well-documented and is reviewed in recent publications. However, studies comparing community-onset bacteremia caused by ESBL- and non-ESBL-producing Escherichia coli are limited. METHODS: We retrospectively reviewed the medical records of patients with E. coli bacteremia who visited the emergency department of Kaohsiung Chang Gung Memorial Hospital from January 2005 to December 2006. Clinical data were collected to compare the clinical features of patients with ESBL-producing E. coli with those of patients with non-ESBL-producers and to identify the risk factors associated with ESBL-producing E. coli bacteremia. RESULTS: There were 404 episodes of community-onset E. coli bacteremia. The overall 30-day mortality rate was 11.4% (46/404) and the mortality rate of healthcare-associated infections was significantly higher than that of community-acquired infections [4/13 (30.8%) vs. 42/391 (10.7%); p= 0.049] Nonurinary focus was independently associated with an increased risk of fatality [47/178 (26.4%) vs. 4/226 (1.8%); p < 0.001]. The frequency of ESBL producers was 4.7% (19/404). Of these, four (21.1%) were associated with a long-term care facility. Significant risk factors associated with ESBL-producing E. coli bacteremia included recent antibiotic exposure (within 30 days) and urinary catheter placement. Although the trend was towards higher mortality in patients with ESBL-producing E. coli bacteremia, the difference did not reach statistical significance compared with the mortality of patients with non-ESBL E. coli bacteremia. CONCLUSION: Fewer than 5% of community-onset E. coli bacteremia episodes in Southern Taiwan were due to ESBL-producers. Prior antibiotic use within 30 days and urinary catheter placement were independently associated with ESBL-producing E. coli bacteremia.

Activity of ertapenem, ciprofloxacin, ceftriaxone, piperacillin-tazobactam, and ampicillin-sulbactam against 12 common clinical isolates of community-acquired bacteremia.

BACKGROUND AND PURPOSE: To compare the antimicrobial activities of ertapenem, ciprofloxacin, ceftriaxone, piperacillin-tazobactam, and ampicillin-sulbactam against 12 common organisms that cause community-acquired bacteremia and to identify the most active agents for the treatment of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae. METHODS: 1200 blood specimens from patients with community-acquired bacteremia were collected at Chang Gung Memorial Hospital, Kaohsiung, Taiwan. All isolates were identified by the API system, and each culture's antimicrobial susceptibility was determined by the standard disk-diffusion method. The minimal inhibitory concentrations of the antibiotics were detected by the Epsilimeter test. RESULTS: The in vitro susceptibilities of 11 of the 12 common pathogens to ertapenem were 100%. The frequency of ESBL-producing E. coli and K. pneumoniae was 6.2% and 9.5%, respectively. Only 48% and 50% of E. coli and K. pneumoniae, respectively, were susceptible to ciprofloxacin. These data infer that ciprofloxacin should not be given for ESBL-producing E. coli and K. pneumoniae. Ceftriaxone and piperacillin-tazobactam had high activity against the most common pathogens isolated. CONCLUSIONS: ESBL E. coli and K. pneumoniae are highly resistant to ciprofloxacin, so this antibiotic should be avoided for patients with community-acquired bacteremia. ESBL E. coli and K. pneumoniae are highly susceptible to ertapenem.

Clinical implications and risk factors of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae infection in children: a case-control retrospective study in a medical center in southern Taiwan.

BACKGROUND AND PURPOSE: Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacilli constitute a growing problem worldwide. However, studies focusing on children are limited. METHODS: We have observed an increase in cases of ESBL-producing Klebsiella pneumoniae (ESBL-KP) infections in the past 6 years in our hospital in southern Taiwan. Using a case-control study design, we compared the clinical characteristics between 54 patients infected by ESBL-KP and 54 frequency-matched controls infected by non-ESBL-producing isolates. RESULTS: Risk factors associated with the infection of ESBL-KP were mainly longer pre-infection hospital stay and recent antibiotic exposure (within 30 days before the episode). Other potential risk factors included recent surgery, the application of mechanical ventilation, nasogastric tubes and central venous catheter insertion. ESBL-KP-related infection cases had a longer hospital stay than controls, and also had a higher mortality rate, although not significantly so. CONCLUSIONS: Recent antibiotic exposure was by far the most important predisposing factor associated with infection of ESBL-KP. Unnecessary antibiotic use should be avoided both in the hospital and community, especially ceftazidime, vancomycin/teicoplanin, aminoglycosides and ampicillin. In our study, carbapenem antibiotics remained the most active drugs against ESBL-KP in pediatric patients, while flomoxef and ciprofloxacin were suitable alternative choices.

Complicated parapneumonic effusion and empyema in children.

BACKGROUND AND PURPOSE: Parapneumonic effusion and empyema are recognized complications of bacterial pneumonia. Optimal management in children, especially the duration of parenteral antibiotics and the role of surgery, is controversial. This study analyzed the clinical characteristics, management, outcome, and bacterial etiology of 59 patients with complicated parapneumonic effusion and empyema treated at a single medical center in Kaohsiung from January 1995 to March 2004. METHODS: The diagnosis of complicated parapneumonic effusion was based on the specific characteristics of pleural fluid, computed tomography or ultrasound findings, or direct visualization of loculations during the surgical procedure. RESULTS: Causative agents were culture-confirmed in 42% of the cases. Streptococcus pneumoniae was the leading pathogen in this series (20% of cases). None of the S. pneumoniae isolates were susceptible to penicillin. Mycoplasma pneumoniae accounted for 19% of cases based on immunoglobulin M assay. CONCLUSIONS: An initial combination therapy regimen consisting of cefotaxime or ceftriaxone plus macrolide provided reasonable activity against 80% of the pathogens isolated in this series. This study also revealed that prolonged parenteral antibiotic treatment resulted in longer length of hospital stay.