Identifying SARS-CoV-2 regional introductions and transmission clusters in real time

The unprecedented SARS-CoV-2 global sequencing effort has suffered from an analytical bottleneck. Many existing methods for phylogenetic analysis are designed for sparse, static datasets and are too computationally expensive to apply to densely sampled, rapidly expanding datasets when results are needed immediately to inform public health action. For example, public health is often concerned with identifying clusters of closely related samples, but the sheer scale of the data prevents manual inspection and the current computational models are often too expensive in time and resources. Even when results are available, intuitive data exploration tools are of critical importance to effective public health interpretation and action. To help address this need, we present a phylogenetic summary statistic which quickly and efficiently identifies newly introduced strains in a region, resulting clusters of infected individuals, and their putative geographic origins. We show that this approach performs well on simulated data and is congruent with a more sophisticated analysis performed during the pandemic. We also introduce Cluster Tracker (https://clustertracker.gi.ucsc.edu/), a novel interactive web-based tool to facilitate effective and intuitive SARS-CoV-2 geographic data exploration and visualization. Cluster-Tracker is updated daily and automatically identifies and highlights groups of closely related SARS-CoV-2 infections resulting from inter-regional transmission across the United States, streamlining public health tracking of local viral diversity and emerging infection clusters. The combination of these open-source tools will empower detailed investigations of the geographic origins and spread of SARS-CoV-2 and other densely-sampled pathogens.

Living through the COVID-19 Pandemic: Impact and Lessons on Dietary Behavior and Physical Well-Being

The aim of this review is to highlight the spectrum on which human behavior has been affected by blanket restriction measures and on a wider scale, the COVID-19 pandemic. Some of the human behaviors that have been impacted by the COVID-19 lockdown are dietary behavior and nutrition, food options and food delivery usage, physical activity and sedentary behaviors. This is important in planning effective public health strategies with minimal detriment to all subsets of society as well as improving the distribution of government aid to populations that are more severely affected. Our main purpose is to present the literature from a rapidly growing pool of scientific research to hopefully enable a better and more comprehensive understanding of the effects of this pandemic and the lessons learnt from the accompanying restrictions, as well as policy recommendations that can be made in national pandemic responses in the future.

The epidemiological impact of the Canadian COVID Alert App

We analyzed the effectiveness of the Canadian COVID Alert app on reducing COVID-19 infections and deaths due to the COVID-19 virus using two separate, but complementary approaches, were taken. First, we undertook a comparative study to assess how the adoption and usage of the COVID Alert app compared to those of similar apps deployed in other regions. Next, we used data from the COVID Alert server and a range of plausible parameter values to estimate the numbers of infections and deaths averted in Canada using a model that combines information on number of notifications, secondary attack rate, expected fraction of transmissions that could be prevented, quarantine effectiveness, and expected size of the full transmission chain in the absence of exposure notification. The comparative analysis revealed that the COVID Alert app had among the lowest adoption levels among apps that reported usage. Our model indicates that use of the COVID Alert app averted between 6,284 and 10,894 infections across the six Canadian provinces where app usage was highest during the March - July 2021 period. This range is equivalent to 1.6%-2.9% of the total recorded infections across Canada in that time. Using province-specific case fatality rates, 57-101 deaths were averted during the same period. The number of cases and deaths averted was greatest in Ontario, whereas the proportion of cases and death averted was greatest in Newfoundland and Labrador. App impact measures were reported so rarely and so inconsistently by other countries that the relative assessment of impact is inconclusive. While the nationwide rates are low, provinces with widespread adoption of the app showed high ratios of averted cases and deaths (upper bound was greater than 60% of averted cases). Our findings suggest that the COVID Alert app, when adopted at sufficient levels, can be an effective public health tool for combatting a pandemic such as COVID-19.

Sampling bias in Brazilian studies on transgender and gender diverse populations: the two-step measure for assessing gender identity in surveys

Correctly recognizing gender identity in population-based surveys is essential to develop effective public health strategies to improve the living conditions of transgender and gender-diverse populations, as well as to adequately collect data on cisgender individuals. This study aims to present the two-step measure as the best strategy for assessing gender identity in Brazilian surveys, thus we performed two separate analyses. Firstly, we conducted a systematic review concerning HIV-related care among Brazilian transgender and gender-diverse populations to assess the strategy used to identify participants’ gender identity. Secondly, we re-analyzed data from a recent survey that included Brazilian transgender populations, comparing characteristics and health outcomes from the sample identified by single-item and by the two-step measure. Concerning the systematic review, from 6,585 references, Brazilian research teams published seven articles, and only one study used the two-step measure. Regarding this survey, the two-step measure recognized 567 cisgender and 773 transgender and gender diverse participants among the 1,340 participants who answered the questionnaire, whereas the single-item measure was able to recognize only 540 transgender and gender diverse people. Furthermore, 31 transgender women self-identified as “transgender men” on the single-item measure. Therefore, although scarcely used in Brazil, the two-step measure is a more accurate strategy to recognize gender identity.

Knowledge, Attitude and Practices of Breastfeeding Among Mothers of Children Under 6 Months of Age in Suva, Fiji

Breastfeeding is a cost-effective public health approach that decreases infant and child morbidity and mortality. Fiji's exclusive breastfeeding rate was 40 percent compared to the global target of 50 percent. The research aims to evaluate mothers’ breastfeeding infants' level of knowledge, attitudes, and practice less than 6 months of age in Suva. A descriptive quantitative cross-sectional study was carried out in 3 randomly selected medical areas in Suva, Fiji. Knowledge, attitude, and practice (KAP) questionnaire was used to gather data from 415 mothers. The overall mean scores for breastfeeding knowledge of mothers were 12.9, the attitude was 33.7, and practice 7.20. Results showed that mothers were generally found to have good levels of knowledge and practice but a fair attitude. Knowledge was associated with the number of children that mothers had and ethnicity. Attitude had a positive correlation with household income. The practice was positively correlated with the mother's status of employment, the number of children, ethnicity, marital status, and household income. To improve breastfeeding knowledge, attitude and practices of mothers, awareness and education should be strengthened in all health facilities. Improvement in health education materials and advocacy is required.

Lessons from Covid-19: A Plan for Action (Pages 59-67) in Journal of the Harvard Club of India

The need for a National Public Health Agency in India is of crucial relevance today. Along with a responsive public health system, we need to focus on preventive healthcare and the promotion of healthy lifestyles. The country, as it marks its 75th year of Independence, must remember that it is essential to bring in structural change for effective public health governance.

Considerations for the Safe Operation of Schools During the Coronavirus Pandemic

During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing safe in-person schooling has been a dynamic process balancing evolving community disease burden, scientific information, and local regulatory requirements with the mandate for education. Considerations include the health risks of SARS-CoV-2 infection and its post-acute sequelae, the impact of remote learning or periods of quarantine on education and well-being of children, and the contribution of schools to viral circulation in the community. The risk for infections that may occur within schools is related to the incidence of SARS-CoV-2 infections within the local community. Thus, persistent suppression of viral circulation in the community through effective public health measures including vaccination is critical to in-person schooling. Evidence suggests that the likelihood of transmission of SARS-CoV-2 within schools can be minimized if mitigation strategies are rationally combined. This article reviews evidence-based approaches and practices for the continual operation of in-person schooling.

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening about 10 000 genomes, over 400 000 metagenomes and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available.

Point-of-Care Diagnostic Tools for Surveillance of SARS-CoV-2 Infections

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a recently emerged and highly contagious virus that causes coronavirus disease 2019 (COVID-19). As of August 24, 2021, there were more than 212 million confirmed COVID-19 cases and nearly 4.4 million deaths reported globally. Early diagnosis and isolation of infected individuals remains one of the most effective public health interventions to control SARS-CoV-2 spread and for effective clinical management of COVID-19 cases. Currently, SARS-CoV-2 infection is diagnosed presumptively based on clinical symptoms and confirmed by detecting the viral RNA in respiratory samples using reverse transcription polymerase chain reaction (RT-PCR). Standard RT-PCR protocols are time consuming, expensive, and technically demanding, which makes them a poor choice for large scale and point-of-care screening in resource-poor settings. Recently developed isothermal nucleic acid amplification tests (iNAAT), antigen and/or serological tests are cost-effective to scale COVID-19 testing at the point-of-care (PoC) and for surveillance activities. This review discusses the development of rapid PoC molecular tools for the detection and surveillance of SARS-CoV-2 infections.