Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand.

New Zealand's COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.

The Global Epidemiology of RSV in Community and Hospitalized Care: Findings From 15 Countries.

BACKGROUND: Respiratory syncytial virus (RSV) is one of the leading causes of acute respiratory tract infections. To optimize control strategies, a better understanding of the global epidemiology of RSV is critical. To this end, we initiated the Global Epidemiology of RSV in Hospitalized and Community care study (GERi). METHODS: Focal points from 44 countries were approached to join GERi and share detailed RSV surveillance data. Countries completed a questionnaire on the characteristics of their surveillance system. RESULTS: Fifteen countries provided granular surveillance data and information on their surveillance system. A median (interquartile range) of 1641 (552-2415) RSV cases per season were reported from 2000 and 2020. The majority (55%) of RSV cases occurred in the <1-year-olds, with 8% of cases reported in those aged ≥65 years. Hospitalized cases were younger than those in community care. We found no age difference between RSV subtypes and no clear pattern of dominant subtypes. CONCLUSIONS: The high number of cases in the <1-year-olds indicates a need to focus prevention efforts in this group. The minimal differences between RSV subtypes and their co-circulation implies that prevention needs to target both subtypes. Importantly, there appears to be a lack of RSV surveillance data in the elderly.

Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand.

Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. During that outbreak, New Zealand used genomic sequencing in a primary role, leading to a second elimination of the virus. We generated genomes from 78% of the laboratory-confirmed samples of SARS-CoV-2 from the second outbreak and compared them with the available global genomic data. Genomic sequencing rapidly identified that virus causing the second outbreak in New Zealand belonged to a single cluster, thus resulting from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.

Temporal Variations in Respiratory Syncytial Virus Epidemics, by Virus Subtype, 4 Countries.

Temporal variation of respiratory syncytial virus (RSV) epidemics was recently reported to be determined by the dominant RSV subtype. However, when we repeated the analysis for 4 countries in the Northern and Southern Hemispheres, the dominant subtype did not seem to affect temporal variation of RSV epidemics.

Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing.

Since the first wave of coronavirus disease in March 2020, citizens and permanent residents returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days and mandatory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of October 20, 2020, of 62,698 arrivals, testing of persons in MIQ had identified 215 cases of SARS-CoV-2 infection. Among 86 passengers on a flight from Dubai, United Arab Emirates, that arrived in New Zealand on September 29, test results were positive for 7 persons in MIQ. These passengers originated from 5 different countries before a layover in Dubai; 5 had negative predeparture SARS-CoV-2 test results. To assess possible points of infection, we analyzed information about their journeys, disease progression, and virus genomic data. All 7 SARS-CoV-2 genomes were genetically identical, except for a single mutation in 1 sample. Despite predeparture testing, multiple instances of in-flight SARS-CoV-2 transmission are likely.

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide 'lockdown' of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during the 'first wave', representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.

Assessment of fish iridoviruses using a novel cell line GS-1, derived from the spleen of orange-spotted grouper Epinephelus coioides (Hamilton) and susceptible to ranavirus and megalocytivirus.

A new cell line (GS-1) was developed from the spleen tissue of the orange-spotted grouper, Epinephelus coioides applied for viral infection studies of fish ranavirus and megalocytivirus. The cells proficiently multiplied in Leibovitz's L-15 medium supplemented with 10% fetal bovine serum at temperatures between 20°C and 32°C. Morphologically, the cell line comprised fibroblast-like cells, and this was confirmed by immunostaining with vimentin, fibronectin, and desmin antibodies. The optimal temperature for grouper iridovirus (GIV) and infectious spleen and kidney necrosis virus (ISKNV) proliferation in GS-1 cells was 25°C, and the highest titer of GIV was 108.4 TCID50/ml, and the highest titer of ISKNV was 105.2 TCID50/ml. Electron micrographs showed that the mean diameter of GIV virions was 180-220 nm, which was larger than ISKNV virions (160-200 nm). Negatively stained GIV particles possessed an envelope structure that was assembled by the three-layered structure with an inner electron-dense core surrounded by a lighter coat (mean diameter, 27 ± 3 nm). The highest GIV-induced mortality of groupers occurred at 25°C, whereas the highest ISKNV-induced mortality occurred at 30°C. In summary, GS-1 cell line is a valuable tool for isolating and investigating fish ranavirus and megalocytivirus in the same host system.

Distribution of influenza virus types by age using case-based global surveillance data from twenty-nine countries, 1999-2014.

BACKGROUND: Influenza disease burden varies by age and this has important public health implications. We compared the proportional distribution of different influenza virus types within age strata using surveillance data from twenty-nine countries during 1999-2014 (N=358,796 influenza cases). METHODS: For each virus, we calculated a Relative Illness Ratio (defined as the ratio of the percentage of cases in an age group to the percentage of the country population in the same age group) for young children (0-4 years), older children (5-17 years), young adults (18-39 years), older adults (40-64 years), and the elderly (65+ years). We used random-effects meta-analysis models to obtain summary relative illness ratios (sRIRs), and conducted meta-regression and sub-group analyses to explore causes of between-estimates heterogeneity. RESULTS: The influenza virus with highest sRIR was A(H1N1) for young children, B for older children, A(H1N1)pdm2009 for adults, and (A(H3N2) for the elderly. As expected, considering the diverse nature of the national surveillance datasets included in our analysis, between-estimates heterogeneity was high (I2>90%) for most sRIRs. The variations of countries' geographic, demographic and economic characteristics and the proportion of outpatients among reported influenza cases explained only part of the heterogeneity, suggesting that multiple factors were at play. CONCLUSIONS: These results highlight the importance of presenting burden of disease estimates by age group and virus (sub)type.

Pandemic Seasonal H1N1 Reassortants Recovered from Patient Material Display a Phenotype Similar to That of the Seasonal Parent.

UNLABELLED: We have previously shown that 11 patients became naturally coinfected with seasonal H1N1 (A/H1N1) and pandemic H1N1 (pdm/H1N1) during the Southern hemisphere winter of 2009 in New Zealand. Reassortment of influenza A viruses is readily observed during coinfection of host animals and in vitro; however, reports of reassortment occurring naturally in humans are rare. Using clinical specimen material, we show reassortment between the two coinfecting viruses occurred with high likelihood directly in one of the previously identified patients. Despite the lack of spread of these reassortants in the community, we did not find them to be attenuated in several model systems for viral replication and virus transmission: multistep growth curves in differentiated human bronchial epithelial cells revealed no growth deficiency in six recovered reassortants compared to A/H1N1 and pdm/H1N1 isolates. Two reassortant viruses were assessed in ferrets and showed transmission to aerosol contacts. This study demonstrates that influenza virus reassortants can arise in naturally coinfected patients. IMPORTANCE: Reassortment of influenza A viruses is an important driver of virus evolution, but little has been done to address humans as hosts for the generation of novel influenza viruses. We show here that multiple reassortant viruses were generated during natural coinfection of a patient with pandemic H1N1 (2009) and seasonal H1N1 influenza A viruses. Though apparently fit in model systems, these reassortants did not become established in the wider population, presumably due to herd immunity against their seasonal H1 antigen.

Strengthening the influenza vaccine virus selection and development process: Report of the 3rd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at WHO headquarters, Geneva, Switzerland, 1-3 April 2014.

Despite long-recognized challenges and constraints associated with their updating and manufacture, influenza vaccines remain at the heart of public health preparedness and response efforts against both seasonal and potentially pandemic influenza viruses. Globally coordinated virological and epidemiological surveillance is the foundation of the influenza vaccine virus selection and development process. Although national influenza surveillance and reporting capabilities are being strengthened and expanded, sustaining and building upon recent gains has become a major challenge. Strengthening the vaccine virus selection process additionally requires the continuation of initiatives to improve the timeliness and representativeness of influenza viruses shared by countries for detailed analysis by the WHO Global Influenza Surveillance and Response System (GISRS). Efforts are also continuing at the national, regional, and global levels to better understand the dynamics of influenza transmission in both temperate and tropical regions. Improved understanding of the degree of influenza seasonality in tropical countries of the world should allow for the strengthening of national vaccination policies and use of the most appropriate available vaccines. There remain a number of limitations and difficulties associated with the use of HAI assays for the antigenic characterization and selection of influenza vaccine viruses by WHOCCs. Current approaches to improving the situation include the more-optimal use of HAI and other assays; improved understanding of the data produced by neutralization assays; and increased standardization of serological testing methods. A number of new technologies and associated tools have the potential to revolutionize influenza surveillance and response activities. These include the increasingly routine use of whole genome next-generation sequencing and other high-throughput approaches. Such approaches could not only become key elements in outbreak investigations but could drive a new surveillance paradigm. However, despite the advances made, significant challenges will need to be addressed before next-generation technologies become routine, particularly in low-resource settings. Emerging approaches and techniques such as synthetic genomics, systems genetics, systems biology and mathematical modelling are capable of generating potentially huge volumes of highly complex and diverse datasets. Harnessing the currently theoretical benefits of such bioinformatics ("big data") concepts for the influenza vaccine virus selection and development process will depend upon further advances in data generation, integration, analysis and dissemination. Over the last decade, growing awareness of influenza as an important global public health issue has been coupled to ever-increasing demands from the global community for more-equitable access to effective and affordable influenza vaccines. The current influenza vaccine landscape continues to be dominated by egg-based inactivated and live attenuated vaccines, with a small number of cell-based and recombinant vaccines. Successfully completing each step in the annual influenza vaccine manufacturing cycle will continue to rely upon timely and regular communication between the WHO GISRS, manufacturers and regulatory authorities. While the pipeline of influenza vaccines appears to be moving towards a variety of niche products in the near term, it is apparent that the ultimate aim remains the development of effective "universal" influenza vaccines that offer longer-lasting immunity against a broad range of influenza A subtypes.

Seasonal influenza vaccine policies, recommendations and use in the World Health Organization's Western Pacific Region.

OBJECTIVE: Vaccination is the most effective way to prevent seasonal influenza and its severe outcomes. The objective of our study was to synthesize information on seasonal influenza vaccination policies, recommendations and practices in place in 2011 for all countries and areas in the Western Pacific Region of the World Health Organization (WHO). METHODS: Data were collected via a questionnaire on seasonal influenza vaccination policies, recommendations and practices in place in 2011. RESULTS: Thirty-six of the 37 countries and areas (97%) responded to the survey. Eighteen (50%) reported having established seasonal influenza vaccination policies, an additional seven (19%) reported having recommendations for risk groups for seasonal influenza vaccination only and 11 (30%) reported having no policies or recommendations in place. Of the 25 countries and areas with policies or recommendations, health-care workers and the elderly were most frequently recommended for vaccination; 24 (96%) countries and areas recommended vaccinating these groups, followed by pregnant women (19 [76%]), people with chronic illness (18 [72%]) and children (15 [60%]). Twenty-six (72%) countries and areas reported having seasonal influenza vaccines available through public funding, private market purchase or both. Most of these countries and areas purchased only enough vaccine to cover 25% or less of their populations. DISCUSSION: In light of the new WHO position paper on influenza vaccines published in 2012 and the increasing availability of country-specific data, countries and areas should consider reviewing or developing their seasonal influenza vaccination policies to reduce morbidity and mortality associated with annual epidemics and as part of ongoing efforts for pandemic preparedness.

The impact of autophagic processes on the intracellular fate of Helicobacter pylori: more tricks from an enigmatic pathogen?

Helicobacter pylori is a Gram-negative pathogen that colonizes the gastric epithelium of 50-60% of the world's population. Approximately one-fifth of the infected individuals manifest severe diseases such as peptic ulcers or gastric cancer. H. pylori infection has proven difficult to cure despite intensive antibiotic treatment. One possible reason for the relatively high resistance to antimicrobial therapy is the ability of H. pylori to reside inside host cells. Although considered by most as an extracellular pathogen, H. pylori can invade both gastric epithelial cells and immunocytes to some extent. The intracellular survival of H. pylori has been implicated in its ability to persist in the stomach, evade host immune responses and resist eradication by membrane-impermeable antibiotics. Interestingly, recent evidence suggests that macroautophagy, a cellular self-degradation process characterized by the formation of double-membraned autophagosomes, plays an important role in determining the intracellular fate of H. pylori. Detailed understanding of the interaction between H. pylori and host cell autophagic processes is anticipated to provide novel insights into the molecular mechanisms of macroautophagy and H. pylori pathogenesis, opening new avenues for the therapeutic intervention of autophagy-related and H. pylori-related disorders.

Genetic analysis of fish iridoviruses isolated in Taiwan during 2001-2009.

To investigate the genetic relationships between field strains of iridoviruses gathered from various fish species in Taiwan, viruses that were collected from 2001 to 2009 were analyzed. Open reading frames encoding the viral major capsid protein (MCP) and adenosine triphosphatase (ATPase) were sequenced for phylogenetic analysis. Our results indicated that iridoviruses from Taiwan aquaculture fishes could be classified into two groups: prior to 2005, the viruses were closely related to members of the genus Ranavirus; and after 2005, they were similar to members of the genus Megalocytivirus. Based on the analysis of MCP amino acid sequences, virus isolates were divided into 4 major genotypes that were related to ISKNV, RSIV, FLIV, and GIV, respectively. Pairwise comparisons of MCP genes showed that the ranavirus was an epidemic pathogen for economically important species in the major production regions and cultured marine fish, while the megalocytivirus isolates were sensitive to host range. In addition, the distribution of synonymous and non-synonymous changes in the MCP gene revealed that the iridoviruses were evolving slowly, and most of the variations were synonymous mutations. The Ka/Ks values were lower than one, and hence, the viruses were under negative selection.

Pandemic (H1N1) 2009 and seasonal influenza A (H1N1) co-infection, New Zealand, 2009.

Co-infection with seasonal influenza A (H1N1) and pandemic (H1N1) 2009 could result in reassortant viruses that may acquire new characteristics of transmission, virulence, and oseltamivir susceptibility. Results from oseltamivir-sensitivity testing on viral culture suggested the possibility of co-infections with oseltamivir-resistant (seasonal A [H1N1]) and -susceptible (pandemic [H1N1] 2009) viruses.

Gabapentin: a pooled analysis of adverse events from three clinical trials in patients with postherpetic neuralgia.

BACKGROUND: Gabapentin has been shown to be well tolerated and effective in the management of the pain associated with postherpetic neuralgia (PHN). It is assumed that adverse events occurring with gabapentin are dose related, their frequency and severity increasing with increasing doses. OBJECTIVE: The aim of this study was to assess the dose dependence of adverse events with gabapentin by determining the relationship between increasing doses of gabapentin and the onset and/or worsening of adverse events in patients with PHN. METHODS: Data were pooled from 3 randomized, double-blind, placebo-controlled, parallel-group studies of gabapentin that focused on or included patients with PHN. Gabapentin was initiated at 300 mg/d and titrated to maintenance doses of 1800 to 3600 mg/d by day 12 to 24. The analysis of adverse events was based on 3 distinct groups: patients who received gabapentin <1800 mg/d, those who received gabapentin >or=1800 mg/d, and those who received placebo. Patients who were given higher doses of gabapentin had already received lower doses. An adverse event was recorded at the dose of its first onset and recorded again if its severity worsened at a higher dose. RESULTS: This study included data from 603 patients with PHN: 358 patients (196 [54.7%] women, 162 [45.3%] men; mean [SD] age, 72.3 [10.3] years) received gabapentin, and 245 (133 [54.3%] women, 112 [45.7%] men; mean [SD] age, 73.3 [10.7] years) received placebo. The 3 most common adverse events were dizziness, somnolence, and peripheral edema. Patients receiving gabapentin >or=1800 mg/d had a higher incidence of peripheral edema (7.5%) than those receiving gabapentin <1800 mg/d (1.4%) or placebo (1.6%) (P<0.002, gabapentin >or=1800 mg/d vs placebo). In contrast, the incidence of dizziness and somnolence was not higher in patients receiving gabapentin >or=1800 mg/d compared with those in the other groups. Compared with placebo recipients, patients receiving gabapentin <1800 mg/d reported a significantly greater frequency of dizziness (20.2% gabapentin <1800 mg/d vs 7.4% placebo; P<0.002) and somnolence (14.9% vs 5.8%, respectively; P=0.005). However, at >or=1800 mg/d, rates of dizziness (9.7%) and somnolence (6.9%) were comparable to those with placebo. Discontinuation rates were comparable between patients receiving gabapentin and those receiving placebo. CONCLUSIONS: In this pooled analysis of adverse-event data from 3 clinical trials in patients with PHN, the incidence of peripheral edema was increased when gabapentin was titrated to >or=1800 mg/d. Dizziness and somnolence, the other most commonly occurring adverse events, were transient and did not occur more frequently or worsen with titration to >or=1800 mg/d. Based on these findings, it does not appear that safety concerns should limit titration of gabapentin to achieve optimal efficacy.

Pessary reduction and postoperative cure of retention in women with anterior vaginal wall prolapse.

This study aimed to determine whether preoperative pessary reduction of anterior vaginal wall prolapse in patients with elevated postvoid residual (PVR) volumes relieves urinary retention, and if reconstructive pelvic surgery in these patients cures urinary retention. The records of all women with symptomatic anterior vaginal wall and urinary retention (PVR >or=100 cc) who underwent evaluation and surgical repair of the anterior vaginal wall at our institution between 1996 and 1999 were retrospectively reviewed. All patients underwent a detailed urogynecologic and urodynamic evaluation and had a pessary trial prior to surgery. Cure of urinary retention was defined as PVR <100 cc at 3 months postoperatively. Sensitivity, specificity, positive and negative predictive values for pessary reduction testing were calculated. Twenty-four patients met the inclusion criteria. Two patients (8%) had stage 2, eleven (46%) stage 3, and eleven (46%) stage 4 anterior vaginal wall prolapse. Preoperatively, the use of pessary was associated with relief of urinary retention in 75% patients. In predicting postoperative cure of urinary retention, pessary testing had a sensitivity of 89%, specificity of 80%, positive predictive value of 94%, and negative predictive value of 67%. Nineteen of 24 patients had a PVR <100 cc postoperatively, indicating a 79% cure rate for urinary retention. In women with symptomatic anterior vaginal wall prolapse and urinary retention, use of a pessary is associated with relief of retention in the majority of patients. Furthermore, pessary reduction testing has good sensitivity, specificity, and positive predictive value for postoperative voiding function.

FT-Raman spectroscopic investigation of lens proteins of tilapia treated with dietary vitamin E.

FT-Raman spectroscopy was employed to explore the structural changes of lens proteins in Tilapia lenses affected by dietary vitamin E supplementation. The microenvironment of major lens constituents including thiol compounds, tyrosine, and tryptophan exhibited significant change upon vitamin E treatment, while the protein secondary structure was unaltered and remained as an antiparallel beta-pleated sheet. These structures in the cortex were more susceptible to vitamin E treatment than in the nucleus. Protein sulfhydryls in the cortex were predominantly in the reduced form, while in the nucleus both the oxidized and reduced forms coexisted as evidenced by the vibrational mode of SH (2580 cm(-1)) and SS (507 cm(-1)), respectively. Both tyrosine and tryptophan were more accessible to water or more exposed in the cortex than in the nucleus. The symmetrically inverse response of vitamin E, between Raman intensity of 1090 cm(-1) and the glutathione level, was consistent with a close relationship of GSH and vitamin E in defending the lens from external insults.

Characteristics of NADH-dependent lipid peroxidation in sarcoplasmic reticulum of white shrimp, Litopenaeus vannamei, and freshwater prawn, Macrobrachium rosenbergii.

The iron-catalyzed NADH-dependent lipid peroxidation system in sarcoplasmic reticulum (SR) of cultured white shrimp, Litopenaeus vannamei and freshwater prawn, Macrobrachium rosenbergii was characterized. Production of thiobarbituric acid reactive substances was used to measure the activity of lipid peroxidation. In both species, the system preferred NADH to NADPH as the reducing agent. Lipid peroxidation activities of SR from both species increased when reaction temperatures increased from 6 to 26 degrees C. At 66 degrees C, the reaction was no longer NADH-dependent. Acidic pH amplified the lipid peroxidation activity. Sarcoplasmic reticular lipid peroxidation activity in white shrimp was always greater than in freshwater prawn. Fatty acid composition of SR lipids could be a major factor for this outcome. The proportion of n-3 highly unsaturated fatty acids, such as C20:5 and C22:6, in sarcoplasmic reticular lipids of white shrimp was twice of that in freshwater prawn. The results of this study provide important tools required for anti-oxidative nutrient study at sub-cellular level.