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    Tracing household transmission of SARS-CoV-2 in New Zealand using genomics
    (Springer Nature Limited, 2024-06-03) Jelley L; Aminisani N; O’Neill M; Jennings T; Douglas J; Utekar S; Johnston H; Welch D; Hadfield J; SHIVERS Investigation Team; de Ligt J; Winter D; French N; Thomas PG; Webby RJ; Huang S; Geoghegan JL
    By early 2022, the highly transmissible Omicron variant of SARS-CoV-2 had spread across most of the world. For the first time since the pandemic began, New Zealand was experiencing high levels of community transmission of SARS-CoV-2. We enroled a cohort of households to better understand differences in transmission dynamics among subvariants of Omicron. We enroled 71 households, comprising 289 participants, and aimed to use viral genomes to gain a clearer understanding of variant-specific differences in epidemiological parameters affecting transmission dynamics. Approximately 80% of the households enroled experienced transmission of BA.2, while most of the remaining households had infections with BA.1 or BA.5. Using a logistic regression generalised linear mixed model, we found no difference in household secondary infection rate between Omicron subvariants BA.1, BA.2 and BA.5. Of the households recruited, the vast majority (92%) experienced a single chain of transmission with one inferred introduction. Further, we found that in 48% of the households studied, all household participants became infected following an index case. Most household participants tested positive within a week following an introduction, supporting the seven-day isolation requirement for household contacts that was in place in New Zealand at the time. By integrating genomic and epidemiological data, we show that viral transmission dynamics can be investigated with a higher level of granularity than with epidemiological data alone. Overall, households are a high risk setting for viral transmission in New Zealand.
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    Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic.
    (Cold Spring Harbor Laboratory, 2024-07-17) Jelley L; Douglas J; O'Neill M; Berquist K; Claasen A; Wang J; Utekar S; Johnston H; Bocacao J; Allais M; de Ligt J; Ee Tan C; Seeds R; Wood T; Aminisani N; Jennings T; Welch D; Turner N; McIntyre P; Dowell T; Trenholme A; Byrnes C; SHIVERS investigation team; Webby R; French N; Winter D; Huang QS; Geoghegan JL
    Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.
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    Validation of Persian Version of the Telephone Interview for Cognitive Status-modified Questionnaire Among Iranian Adults
    (Mazandaran University of Medical Sciences and Health Services, 2022-06) Aminisani N; Shamshirgaran M; Laghousi D; Javadpour A; Gholamnezhad Z; Gilani N; Alpass F
    Background: Dementia is a growing public health problem worldwide, and its early detection can help to manage the disease more effectively. This study aimed to validate the Persian version of the Telephone Interview for Cognitive Status-modified (TICS-m) questionnaire in older adults in the northeast of Iran. Methods: This cross-sectional study was accomplished as part of the Neyshabur Longitudinal Study on Ageing (NeLSA) from January to May 2019. The translated Persian version of TICS-m was tested for content and face validity. The construct validity of the questionnaire was also assessed using exploratory factor analysis (EFA) with the extraction method of principal component analysis (PCA) and Oblimin rotation. Results: A total of 210 community-dwelling adults (aged ≥ 50; mean age: 59.6 ± 6.8 years) were registered in the NeLSA. The content validity ratio (CVR) of all items in the TICS-m questionnaire was higher than 0.62. The content validity index (CVI) of the three items was less than 0.78; so, these items were revised and replaced with alternative words. The face validity of the questionnaire was also confirmed. According to the results of EFA, the six extracted factors accounted for 68.8% of the total variance. Conclusions: Our results revealed that the construct validity of the Persian version of the TICS-m is satisfactory.
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    The concurrent accuracy of the modified telephone interview for cognitive status and mini-mental state examination tools in detection of cognitive impairment among older adults
    (Scientific Electronic Library Online, 2022-09) Laghousi D; Aminisani N; Shamshirgaran SM; Javadpour A; Gholamnezhad Z; Gilani N; Asghari-Jafarabadi M; Alpass F
    Due to the need for face-to-face administration of many cognitive screening tests, it is not always feasible to screen large-scale samples. Objective: This study aimed to assess the discriminant validity of the Persian version of Telephone Interview for Cognitive Status (P-TICS-m) and Mini-Mental State Examination in the middle-aged Iranian population. Methods: The P-TICS-m and MMSE were administered to 210 randomly selected middle-aged community-dwelling adults who had been registered in the Neyshabur Longitudinal Study on Ageing. Participants also underwent psychological examination by two neurologists to assess cognitive impairment based on the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-V) criteria. To evaluate the discriminant validity of P-TICS-m and MMSE with DSM-V criteria, the sensitivity, specificity, positive and negative predictive values (PPV and NPV), and positive and negative likelihood ratios (LR+ and LR−) were calculated. Results: The mean age of the participants was 59.6±6.8 years. The TICS and MMSE were highly correlated (r=0.635, p<0.001). The sensitivity, specificity, PPV, NPV, LR+, and LR− to discriminate cognitive impairment were, respectively, 83%, 92%, 68%, 96%, 10, and 0.182 for MMSE and 100%, 13%, 19%, 100%, 1.16, and 0 for TICS-m. The receiver operating characteristic curve analysis results showed no statistically significant differences between P-TICS-m and MMSE. Conclusions: Our findings indicate that the TICS-m test can be used as a screening tool instead of the MMSE. Due to the low specificity and low PPV of the TICS-m compared to MMSE, the diagnosis should be confirmed using definitive diagnostic tests when a subject is classified as having cognitive impairment.