Over the course of the past several decades, rapid advancements in molecular technologies have revolutionized the practice of public health microbiology, and have fundamentally changed the nature, accuracy, and timeliness of laboratory data for outbreak investigation and response. Whole-genome sequencing, in particular, is becoming an increasingly feasible and cost-effective approach for near real-time high-resolution strain typing, genomic characterization, and comparative analyses. This review discusses the current state of the art in bacterial strain typing for outbreak investigation and infectious disease surveillance, and the impact of emerging genomic technologies on the field of public health microbiology.

Animal-human interspecies transmission is thought to play a significant role in influencing rotavirus strain diversity in humans. Proving this concept requires a better understanding of the complete genetic constellation of rotaviruses circulating in various animal species. However, very few whole genomes of animal rotaviruses, especially in developing countries, are available. In this study, complete genetic configuration of the first African camel rotavirus strain (RVA/Camel-wt/SDN/MRC-DPRU447/2002/G8P[11]) was assigned a unique G8-P[11]-I2-R2-C2-M2-A18-N2-T6-E2-H3 genotype constellation that has not been reported in other ruminants. It contained a novel NSP1 genotype (genotype A18). The evolutionary dynamics of the genome segments of strain MRC-DPRU447 were rather complex compared to those found in other camelids. Its genome segments 1, 3, 7-10 were closely related (>93% nucleotide identity) to those of human-animal reassortant strains like RVA/Human-tc/ITA/PA169/1988/G6P[14] and RVA/Human-wt/HUN/Hun5/1997/G6P[14], segments 4, 6 and 11 shared common ancestry (>95% nucleotide identity) with bovine rotaviruses like strains RVA/Cow-wt/CHN/DQ-75/2008/G10P[11] and RVA/Cow-wt/KOR/KJ19-2/XXXX/G6P[7], whereas segment 2 was closely related (94% nucleotide identity) to guanaco rotavirus strain RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1]. Its genetic backbone consisted of DS-1-like, AU-1-like, artiodactyl-like and a novel A18 genotype. This suggests that strain MRC-DPRU447 potentially emerged through multiple reassortment events between several mammalian rotaviruses of at least two genogroups or simply strain MRC-DPRU447 display a unique progenitor genotypes. Close relationship between some of the genome segments of strain MRC-DPRU447 to human rotaviruses suggests previous occurrence of reassortment processes combined with interspecies transmission between humans and camels. The whole genome data for strain MRC-DPRU447 adds to the much needed animal rotavirus data from Africa which is limited at the moment.

Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.

The Centers for Disease Control and Prevention Minority HIV Research Initiative (MARI) funded 8 investigators in 2016 to develop HIV prevention and treatment interventions in highly affected communities. We describe MARI studies who used community-based participatory research methods to inform the development of interventions in Black/African American and Hispanic/Latinx communities focused on sexual minority men (SMM) or heterosexual populations. Each study implemented best practice strategies for engaging with communities, informing recruitment strategies, navigating through the impacts of COVID-19, and disseminating findings. Best practice strategies common to all MARI studies included establishing community advisory boards, engaging community members in all stages of HIV research, and integrating technology to sustain interventions during the COVID-19 pandemic. Implementing community-informed approaches is crucial to intervention uptake and long-term sustainability in communities of color. MARI investigators' research studies provide a framework for developing effective programs tailored to reducing HIV-related racial/ethnic disparities.

BACKGROUND: There is marked geographic variation in cardiac rehabilitation (CR) initiation, ranging from 10% to 40% of eligible patients at the state level. The potential causes of this variation, such as patient access to CR centers, are not well studied. OBJECTIVES: The authors sought to determine how access to CR centers affects CR initiation in Medicare beneficiaries. METHODS: The authors used Medicare files to identify CR-eligible Medicare beneficiaries and calculate CR initiation rates at the hospital referral region (HRR) level. We used linear regression to evaluate the percent variation in CR initiation accounted for by CR access across HRRs. We then employed geospatial hotspot analysis to identify CR deserts, or counties in which patient load per CR center is disproportionately high. RESULTS: A total of 1,133,657 Medicare beneficiaries were eligible for CR from 2014 to 2017, of whom 263,310 (23%) initiated CR. The West North Central Census Division had the highest adjusted CR initiation rate (35.4%) and the highest density of CR programs (6.58 per 1,000 CR-eligible Medicare beneficiaries). Density of CR programs accounted for 21.2% of geographic variation in CR initiation at the HRR level. A total of 40 largely urban counties comprising 14% of the United States population age ≥65 years had disproportionately low CR access and were identified as CR deserts. CONCLUSIONS: A substantial proportion of geographic variation in CR initiation was related to access to CR programs, with a significant amount of the U.S. population living in CR deserts. These data invite further study on interventions to increase CR access.

Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (73%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (07%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (914%), moxifloxacin (916%) and ethambutol (933%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation. 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license

OBJECTIVE: Researchers at the Centers for Disease Control and Prevention monitor unplanned school closure (USC) reports through online systematic searches (OSS) to assist public health emergency responses. We counted the additional reports identified through social media along with OSS to improve USC monitoring. METHODS: Facebook and Twitter data of public-school districts and private schools in counties affected by California wildfires in October and December of 2017 and January of 2018 were retrieved. We computed descriptive statistics and performed multivariable logistic regression for both OSS and social media data. RESULTS: Among the 362 public-school districts in wildfire-affected counties, USCs were identified for 115 (32%) districts, of which OSS identified 104 (90%), Facebook, 59 (52%), and Twitter, 37 (32%). These data correspond to 4622 public schools, among which USCs were identified for 888 (19.2%) schools, of which OSS identified 722 (81.3%), Facebook, 496 (55.9%), and Twitter, 312 (35.1%). Among 1289 private schools, USCs were identified for 104 schools, of which OSS identified 47 (45.2%), Facebook, 67 (64.4%), and Twitter, 29 (27.9%). USC announcements identified via social media, in addition to those via OSS, were 11 public school districts, 166 public schools, and 57 private schools. CONCLUSION: Social media complements OSS as additional resources for USC monitoring during disasters.

Coxiella burnetii is an intracellular bacterial pathogen that can be associated with significant reproductive disease or acute mortality in livestock and wildlife. A novel marine mammal-associated strain of C. burnetii has been identified in pinnipeds of the Northwestern Pacific Ocean. Little is known about C. burnetii infection in regard to reproductive success or population status. Our objective was to characterize the severity and extent of histologic lesions in 117 opportunistically collected placentas from presumed-normal northern fur seals (Callorhinus ursinus) in July 2011 on St. Paul Island, Alaska, where a high placental prevalence of C. burnetii had been reported. Sections were examined by histology and immunohistochemistry and impression smears with modified acid-fast stain. The nature and frequency of histologic changes were compared with target COM1 PCR-confirmed C. burnetii positive and negative placentas. Overall, histologic changes were similar to placental lesions described in aborting ruminants; however, changes were variable within and between placentas. Vasculitis and occasional intracellular bacteria were seen only in C. burnetii PCR-positive placentas. Dystrophic mineralization, edema, and inflammation were seen in PCR-positive and negative placentas, although they were statistically more common in PCR-positive placentas. Results suggest that C. burnetti and associated pathologic changes are multifocal and variable in placentas from these presumably live-born pups. Therefore, multiple sections of tissue from different placental areas should be examined microscopically and screened by PCR to ensure accurate diagnosis, as the genomes per gram of placenta may not necessarily represent the severity of placental disease. These limitations should inform field biologists, diagnosticians, and pathologists how best to screen and sample for pathogens and histopathology in marine mammal placental samples.

In the United States, Dermacentor variabilis and Dermacentor andersoni are considered key vectors for Rickettsia rickettsii, the causative agent of Rocky Mountain spotted fever. Through regional surveillance, a wide diversity of Rickettsia spp. have been documented in D. variabilis, and Dermacentor spp. has been suggested as potential vectors for various other pathogens, including Babesia spp. and Ehrlichia canis. To better define the prevalence and diversity of pathogens in Dermacentor spp. across the United States, 848 ticks collected from dogs and cats in 44/50 states in 2018-2019 were tested by PCR for Rickettsia spp.-specific 17 kDa and ompA gene fragments; a subset of Dermacentor spp. was also tested with PCR, targeting fragments of the 18S and large subunit region rRNA genes of Babesia spp. and 16S rRNA genes of E. canis. Rickettsia spp. was identified in 12.5% (106/848) of ticks. Species detected include Rickettsia montanensis (n = 64 ticks), Rickettsia bellii (n = 15 ticks), Rickettsia rhipicephali (n = 13 ticks), Rickettsia peacockii (n = 8 ticks), Rickettsia amblyommatis (n = 3 ticks), Rickettsia cooleyi (n = 1 tick), and unclassified Rickettsia spp. (n = 2 ticks). Ticks with R. montanensis and R. bellii were submitted from every U.S. region; R. rhipicephali was predominantly detected in ticks from the southern half of the United States, and all R. peacockii-positive ticks were D. andersoni that originated from the Rocky Mountain states. Ehrlichia canis was not detected in any Dermacentor spp., and Babesia conradae was detected in two Dermacentor albipictus. Because most ticks had fed on dogs or cats before submission, these findings do not implicate a given Dermacentor sp. as a primary vector of these agents, but in regard to Rickettsia spp., the data do support other published work showing D. variabilis harbors a diversity of Rickettsia species with unknown implications for animal and human health.

Coronavirus disease has disproportionately affected persons in congregate settings and high-density workplaces. To determine more about the transmission patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in these settings, we performed whole-genome sequencing and phylogenetic analysis on 319 (14.4%) samples from 2,222 SARS-CoV-2-positive persons associated with 8 outbreaks in Minnesota, USA, during March-June 2020. Sequencing indicated that virus spread in 3 long-term care facilities and 2 correctional facilities was associated with a single genetic sequence and that in a fourth long-term care facility, outbreak cases were associated with 2 distinct sequences. In contrast, cases associated with outbreaks in 2 meat-processing plants were associated with multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak. Early identification and cohorting (segregating) of virus-positive persons in these settings, along with continued vigilance with infection prevention and control measures, is imperative.

BACKGROUND: Given the paucity of studies for low- or middle-income countries, we aim to provide the first ever estimations of lifetime risk of diabetes, years of life spent and lost among those with diabetes for Brazilians. Estimates of Brazil´s diabetes burden consist essentially of reports of diabetes prevalence from national surveys and mortality data. However, these additional metrics are at times more meaningful ways to characterize this burden. METHODS: We joined data on incidence of physician-diagnosed diabetes from the Brazilian risk factor surveillance system, all-cause mortality from national statistics, and diabetes mortality rate ratios from ELSA-Brasil, an ongoing cohort study. To calculate lifetime risk of developing diabetes, we applied an illness-death state model. To calculate years of life lost for those with diabetes and years lived with the disease, we additionally calculated the mortality rates for those with diabetes. RESULTS: A 35-year-old white adult had a 23.4% (95% CI = 22.5%-25.5%) lifetime risk of developing diabetes by age 80 while a same-aged black/brown adult had a 30.8% risk (95% confidence interval (CI) = 29.6%-33.2%). Men diagnosed with diabetes at age 35 would live 32.9 (95% CI = 32.4-33.2) years with diabetes and lose 5.5 (95% CI = 5.1-6.1) years of life. Similarly-aged women would live 38.8 (95% CI = 38.3-38.9) years with diabetes and lose 2.1 (95% CI = 1.9-2.6) years of life. CONCLUSIONS: Assuming maintenance of current rates, one-quarter of young Brazilians will develop diabetes over their lifetimes, with this number reaching almost one-third among young, black/brown women. Those developing diabetes will suffer a decrease in life expectancy and will generate a considerable cost in terms of medical care.

A group convened and led by the Virus Evolution Working Group of the World Health Organization reports on its deliberations and announces a naming scheme that will enable clear communication about SARS-CoV-2 variants of interest and concern. | | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has a linear, unsegmented, positive-sense RNA genome. As with all viruses, SARS-CoV-2 continuously adapts to changing environments in real time via random genome mutations that are subject to natural selection. Most mutations are neutral or detrimental to the virus; however, a small number of mutations may provide a selective advantage, such as escape from the host immune system or resistance to antiviral drugs. Such mutations may also lead to increased fitness for transmissibility. As mutated forms of viruses or variants spread from person to person, they will eventually be detected at the population level.

The effect of HIV infection on COVID-19 outcomes is unclear. Studies in South Africa (1) and the United Kingdom (2) found an independent association between HIV infection and COVID-19 mortality; however, other studies have not found an association between poor COVID-19 outcomes and either HIV status among hospitalized patients (3-5) or HIV-associated factors such as CD4 count, viral load, or type of antiretroviral therapy (ART) (6). The effect of HIV infection on COVID-19 outcomes remains an urgent question in sub-Saharan Africa, where many countries are experiencing dual HIV and COVID-19 epidemics, and capacity to treat severe COVID-19 is limited. Using data from patients with probable or confirmed COVID-19 admitted to specialized treatment centers during March-December 2020 in Zambia, the Zambian Ministry of Health and CDC assessed the relationship between HIV infection and severe COVID-19 and COVID-19-associated death. Among 443 patients included in the study, 122 (28%) were HIV-positive, and of these, 91 (89%) were receiving ART at the time of hospitalization. HIV status alone was not significantly associated with severe COVID-19 at admission or during hospitalization or with COVID-19-associated death. However, among HIV-positive persons, those with severe HIV disease were more likely to develop severe COVID-19 and were at increased risk for COVID-19-associated death. Ensuring that persons maintain HIV disease control, including maintaining ART continuity and adherence, achieving viral suppression, and addressing and managing underlying medical conditions, could help reduce COVID-19-associated morbidity and mortality in sub-Saharan Africa.

To meet the educational, physical, social, and emotional needs of children, many U.S. schools opened for in-person learning during fall 2020 by implementing strategies to prevent transmission of SARS-CoV-2, the virus that causes COVID-19 (1,2). To date, there have been no U.S. studies comparing COVID-19 incidence in schools that varied in implementing recommended prevention strategies, including mask requirements and ventilation improvements* (2). Using data from Georgia kindergarten through grade 5 (K-5) schools that opened for in-person learning during fall 2020, CDC and the Georgia Department of Public Health (GDPH) assessed the impact of school-level prevention strategies on incidence of COVID-19 among students and staff members before the availability of COVID-19 vaccines.(†) Among 169 K-5 schools that participated in a survey on prevention strategies and reported COVID-19 cases during November 16-December 11, 2020, COVID-19 incidence was 3.08 cases among students and staff members per 500 enrolled students.(§) Adjusting for county-level incidence, COVID-19 incidence was 37% lower in schools that required teachers and staff members to use masks, and 39% lower in schools that improved ventilation, compared with schools that did not use these prevention strategies. Ventilation strategies associated with lower school incidence included methods to dilute airborne particles alone by opening windows, opening doors, or using fans (35% lower incidence), or in combination with methods to filter airborne particles with high-efficiency particulate absorbing (HEPA) filtration with or without purification with ultraviolet germicidal irradiation (UVGI) (48% lower incidence). Multiple strategies should be implemented to prevent transmission of SARS-CoV-2 in schools (2); mask requirements for teachers and staff members and improved ventilation are important strategies that elementary schools could implement as part of a multicomponent approach to provide safer, in-person learning environments. Universal and correct mask use is still recommended by CDC for adults and children in schools regardless of vaccination status (2).

Cessation of kindergarten through grade 12 in-person instruction and extracurricular activities, which has often occurred during the COVID-19 pandemic, can have negative social, emotional, and educational consequences for children (1,2). Although preventive measures such as masking, physical distancing, hand hygiene, and improved ventilation are commonly used in schools to reduce transmission of SARS-CoV-2, the virus that causes COVID-19, and support in-person instruction (3-6), routine school-based COVID-19 testing has not been as widely implemented. In addition to these types of standard preventive measures, Utah health and school partners implemented two high school testing programs to sustain extracurricular activities and in-person instruction and help identify SARS-CoV-2 infections: 1) Test to Play,* in which testing every 14 days was mandated for participation in extracurricular activities; and 2) Test to Stay,(†) which involved school-wide testing to continue in-person instruction as an alternative to transitioning to remote instruction if a school crossed a defined outbreak threshold (3). During November 30, 2020-March 20, 2021, among 59,552 students tested through these programs, 1,886 (3.2%) received a positive result. Test to Play was implemented at 127 (66%) of Utah's 193 public high schools and facilitated completion of approximately 95% of scheduled high school extracurricular winter athletics competition events.(§) Test to Stay was conducted at 13 high schools, saving an estimated 109,752 in-person instruction student-days.(¶) School-based COVID-19 testing should be considered as part of a comprehensive prevention strategy to help identify SARS-CoV-2 infections in schools and sustain in-person instruction and extracurricular activities.

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2,500 COVID-19 cases associated with this variant have been detected in the United States (US) since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight that the primary ports of entry for B.1.1.7 in the US were in New York, California, and Florida. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid- to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%-50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

INTRODUCTION: Healthcare workers (HCWs) in Zambia have become infected with SARS-CoV-2, the virus that causes coronavirus disease (COVID-19). However, SARS-CoV-2 prevalence among HCWs is not known in Zambia. METHODS: We conducted a cross-sectional SARS-CoV-2 prevalence survey among Zambian HCWs in twenty health facilities in six districts in July 2020. Participants were tested for SARS-CoV-2 infection using polymerase chain reaction (PCR) and for SARS-CoV-2 antibodies using enzyme-linked immunosorbent assay (ELISA). Prevalence estimates and 95% confidence intervals (CIs), adjusted for health facility clustering, were calculated for each test separately and a combined measure for those who had PCR and ELISA performed. RESULTS: In total, 660 HCWs participated in the study, with 450 (68.2%) providing nasopharyngeal swab for PCR and 575 (87.1%) providing a blood specimen for ELISA. Sixty-six percent of participants were females and the median age was 31.5 years (interquartile range 26.2-39.8 years). The overall prevalence of the combined measure was 9.3% (95% CI 3.8%-14.7%). PCR-positive prevalence of SARS-CoV-2 was 6.6% (95% CI 2.0%-11.1%) and ELISA-positive prevalence was 2.2% (95% CI 0.5%-3.9%). CONCLUSIONS: SARS-CoV-2 prevalence among HCWs was similar to a population-based estimate (10.6%) during a period of community transmission in Zambia. Public health measures such as establishing COVID-19 treatment centers before the first cases, screening for COVID-19 symptoms among patients accessing health facilities, infection prevention and control trainings, and targeted distribution of personal protective equipment based on exposure risk might have prevented increased SARS-CoV-2 transmission among Zambian HCWs.

BACKGROUND: Between March and December, 2020, more than 20 000 laboratory-confirmed cases of SARS-CoV-2 infection were reported in Zambia. However, the number of SARS-CoV-2 infections is likely to be higher than the confirmed case counts because many infected people have mild or no symptoms, and limitations exist with regard to testing capacity and surveillance systems in Zambia. We aimed to estimate SARS-CoV-2 prevalence in six districts of Zambia in July, 2020, using a population-based household survey. METHODS: Between July 4 and July 27, 2020, we did a cross-sectional cluster-sample survey of households in six districts of Zambia. Within each district, 16 standardised enumeration areas were randomly selected as primary sampling units using probability proportional to size. 20 households from each standardised enumeration area were selected using simple random sampling. All members of selected households were eligible to participate. Consenting participants completed a questionnaire and were tested for SARS-CoV-2 infection using real-time PCR (rtPCR) and anti-SARS-CoV-2 antibodies using ELISA. Prevalence estimates, adjusted for the survey design, were calculated for each diagnostic test separately, and combined. We applied the prevalence estimates to census population projections for each district to derive the estimated number of SARS-CoV-2 infections. FINDINGS: Overall, 4258 people from 1866 households participated in the study. The median age of participants was 18·2 years (IQR 7·7-31·4) and 50·6% of participants were female. SARS-CoV-2 prevalence for the combined measure was 10·6% (95% CI 7·3-13·9). The rtPCR-positive prevalence was 7·6% (4·7-10·6) and ELISA-positive prevalence was 2·1% (1·1-3·1). An estimated 454 708 SARS-CoV-2 infections (95% CI 312 705-596 713) occurred in the six districts between March and July, 2020, compared with 4917 laboratory-confirmed cases reported in official statistics from the Zambia National Public Health Institute. INTERPRETATION: The estimated number of SARS-CoV-2 infections was much higher than the number of reported cases in six districts in Zambia. The high rtPCR-positive SARS-CoV-2 prevalence was consistent with observed community transmission during the study period. The low ELISA-positive SARS-CoV-2 prevalence might be associated with mitigation measures instituted after initial cases were reported in March, 2020. Zambia should monitor patterns of SARS-CoV-2 prevalence and promote measures that can reduce transmission. FUNDING: US Centers for Disease Control and Prevention.

INTRODUCTION: Grounded in organizational change theory, the purpose of this study was to investigate the efficacy of the Presidential Youth Fitness Program (PYFP) and its association with healthy cultures within schools. METHODS: Using a qualitative approach, data were collected through interviews, site visits and artifacts across 374 schools. An explanatory collective case study approach was used to identify key events related to implementation. RESULTS: Pivotal antecedents to organizational change included prolonged, continual PD, direct support of PYFP implementation, and recognition. Further, three key themes of leveling of the playing field, strategically overcoming barriers, and recruiting teacher fitness champions were identified. CONCLUSIONS: Creating a healthy school culture was an unexpected, but feasible outcome stemming from the implementation of the PYFP. A collective effort, led by physical education teachers and fitness champions and embraced by the administration, faculty, and community, is necessary for the school culture to unfreeze from its present status.

On December 14, 2020, the United Kingdom reported a SARS-CoV-2 variant of concern (VOC), lineage B.1.1.7, also referred to as VOC 202012/01 or 20I/501Y.V1.* The B.1.1.7 variant is estimated to have emerged in September 2020 and has quickly become the dominant circulating SARS-CoV-2 variant in England (1). B.1.1.7 has been detected in over 30 countries, including the United States. As of January 13, 2021, approximately 76 cases of B.1.1.7 have been detected in 12 U.S. states.(†) Multiple lines of evidence indicate that B.1.1.7 is more efficiently transmitted than are other SARS-CoV-2 variants (1-3). The modeled trajectory of this variant in the U.S. exhibits rapid growth in early 2021, becoming the predominant variant in March. Increased SARS-CoV-2 transmission might threaten strained health care resources, require extended and more rigorous implementation of public health strategies (4), and increase the percentage of population immunity required for pandemic control. Taking measures to reduce transmission now can lessen the potential impact of B.1.1.7 and allow critical time to increase vaccination coverage. Collectively, enhanced genomic surveillance combined with continued compliance with effective public health measures, including vaccination, physical distancing, use of masks, hand hygiene, and isolation and quarantine, will be essential to limiting the spread of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). Strategic testing of persons without symptoms but at higher risk of infection, such as those exposed to SARS-CoV-2 or who have frequent unavoidable contact with the public, provides another opportunity to limit ongoing spread.

BACKGROUND: In the summer of 2019, e-cigarette, or vaping, product use-associated lung injury (EVALI) was detected in the United States. Multiple agencies reported illicit tetrahydrocannabinol (THC)-containing e-cigarette, or vaping, products containing vitamin E acetate (VEA) as a substance of concern. METHODS: As an expansion of the Utah Department of Health's response to EVALI, the Utah Public Health Laboratory and the Utah Department of Public Safety screened 170 products from 96 seizures between October 2018 and January 2020. Using Pearson's correlation coefficient, we analyzed the temporal correlation of national, and Utah specific case counts, and the percentage of seizures indicating VEA by month. RESULTS: The findings indicate strong and significant correlations between seizures indicating VEA and both the national (r = 0.70, p = 0.002) and Utah specific (r = 0.78, p < 0.001) case counts. CONCLUSION: These findings underscore that VEA should not be added to e-cigarettes, or vaping, products and the importance of collaboration with law enforcement when responding to outbreaks associated with illicit substances.

Zambia is a landlocked, lower-middle income country in southern Africa, with a population of 17 million (1). The first known cases of coronavirus disease 2019 (COVID-19) in Zambia occurred in a married couple who had traveled to France and were subject to port-of-entry surveillance and subsequent remote monitoring of travelers with a history of international travel for 14 days after arrival. They were identified as having suspected cases on March 18, 2020, and tested for COVID-19 after developing respiratory symptoms during the 14-day monitoring period. In March 2020, the Zambia National Public Health Institute (ZNPHI) defined a suspected case of COVID-19 as 1) an acute respiratory illness in a person with a history of international travel during the 14 days preceding symptom onset; or 2) acute respiratory illness in a person with a history of contact with a person with laboratory-confirmed COVID-19 in the 14 days preceding symptom onset; or 3) severe acute respiratory illness requiring hospitalization; or 4) being a household or close contact of a patient with laboratory-confirmed COVID-19. This definition was adapted from World Health Organization (WHO) interim guidance issued March 20, 2020, on global surveillance for COVID-19 (2) to also include asymptomatic contacts of persons with confirmed COVID-19. Persons with suspected COVID-19 were identified through various mechanisms, including port-of-entry surveillance, contact tracing, health care worker (HCW) testing, facility-based inpatient screening, community-based screening, and calls from the public into a national hotline administered by the Disaster Management and Mitigation Unit and ZNPHI. Port-of-entry surveillance included an arrival screen consisting of a temperature scan, report of symptoms during the preceding 14 days, and collection of a history of travel and contact with persons with confirmed COVID-19 in the 14 days before arrival in Zambia, followed by daily remote telephone monitoring for 14 days. Travelers were tested for SARS-CoV-2, the virus that causes COVID-19, if they were symptomatic upon arrival or developed symptoms during the 14-day monitoring period. Persons with suspected COVID-19 were tested as soon as possible after evaluation for respiratory symptoms or within 7 days of last known exposure (i.e., travel or contact with a confirmed case). All COVID-19 diagnoses were confirmed using real-time reverse transcription-polymerase chain reaction (RT-PCR) testing (SARS-CoV-2 Nucleic Acid Detection Kit, Maccura) of nasopharyngeal specimens; all patients with confirmed COVID-19 were admitted into institutional isolation at the time of laboratory confirmation, which was generally within 36 hours. COVID-19 patients were deemed recovered and released from isolation after two consecutive PCR-negative test results ≥24 hours apart. A Ministry of Health memorandum was released on April 13, 2020, mandating testing in public facilities of 1) all persons admitted to medical and pediatric wards regardless of symptoms; 2) all patients being admitted to surgical and obstetric wards, regardless of symptoms; 3) any outpatient with fever, cough, or shortness of breath; and 4) any facility or community death in a person with respiratory symptoms, and 5) biweekly screening of all HCWs in isolation centers and health facilities where persons with COVID-19 had been evaluated. This report describes the first 100 COVID-19 cases reported in Zambia, during March 18-April 28, 2020.

Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread globally. Genome sequencing of SARS-CoV-2 allows reconstruction of its transmission history, although this is contingent on sampling. We have analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020 which subsequently spread locally before active community surveillance was implemented.

The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.

BACKGROUND: Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history. METHODS: A genetic strategy was applied to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal. RESULTS: Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travellers compared to travellers. CONCLUSIONS: These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement.

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, with >52,000 cases in California as of May 4, 2020. Here we investigate the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning 9 counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington State, with lack of a predominant lineage and limited transmission between communities. Lineages associated with outbreak clusters in 2 counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain SARS-CoV-2 spread in California and other states.

Background: Data on mortality burden and excess deaths attributable to diabetes are sparse and frequently unreliable, particularly in low and middle-income countries. Estimates in Brazil to date have relied on death certificate data, which do not consider the multicausal nature of deaths. Our aim was to combine cohort data with national prevalence and mortality statistics to estimate the absolute number of deaths that could have been prevented if the mortality rates of people with diabetes were the same as for those without. In addition, we aimed to estimate the increase in burden when considering undiagnosed diabetes. Methods: We estimated self-reported diabetes prevalence from the National Health Survey (PNS) and overall mortality from the national mortality information system (SIM). We estimated the diabetes mortality rate ratio (rates of those with vs without diabetes) from the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil), an ongoing cohort study. Joining estimates from these three sources, we calculated for the population the absolute number and the fraction of deaths attributable to diabetes. We repeated our analyses considering both self-reported and unknown diabetes, the latter estimated based on single point-in-time glycemic determinations in ELSA-Brasil. Finally, we compared results with diabetes-related mortality information from death certificates. Results: In 2013, 65 581 deaths, 9.1% of all deaths between the ages of 35-80, were attributable to known diabetes. If cases of unknown diabetes were considered, this figure would rise to 14.3%. In contrast, based on death certificates only, 5.3% of all death had diabetes as the underlying cause and 10.4% as any mentioned cause. Conclusions: In this first report of diabetes mortality burden in Brazil using cohort data to estimate diabetes mortality rate ratios and the prevalence of unknown diabetes, we showed marked underestimation of the current burden, especially when unknown cases of diabetes are also considered.

There is a disproportionately high HIV incidence among Black men who have sex with men (MSM) despite equal or lower levels of HIV risk behaviors compared to White MSM. Due to high levels of racial segregation in the U.S., Black MSM have an elevated likelihood of living in neighborhoods that contain psychosocial stressors, which, in turn, may increase behaviors promoting HIV infection. We examined associations between perceived neighborhood problems and sexual behaviors among Black MSM in the Deep South, a population at highest risk of HIV. Data came from the MARI Study, which included Black MSM ages 18-66 years recruited from the Jackson, MS, and Atlanta, GA, metropolitan areas (n = 377). Participants completed questions about neighborhood problems (e.g., excessive noise, heavy traffic/speeding cars and trash/litter) and sexual behaviors (e.g., condomless sex and drug use before or during sex). We used Poisson's regression model with robust standard errors to estimate the adjusted prevalence ratio (aPR; 95% confidence intervals [CI]) of neighborhood problems (coded as tertiles [tertile 1 = low neighborhood problems, tertile 2 = medium neighborhood problems, tertile 3 = high neighborhood problems] as well as continuously) with sexual behaviors, after adjustment for sociodemographic characteristics and other variables. About one-fourth of the sample reported at least one neighborhood problem, with the most common (31.6%) being no/poorly maintained sidewalks, which indicates an infrastructural problem. In multivariable models, compared to those in the lowest tertile, those reporting more neighborhood problems (tertile 2: aPR = 1.49, 95% CI = 1.04, 2.14 and tertile 3: aPR = 1.53, 95% CI = 1.05, 2.24) reported more drug use before or during sex (p for trend = .027). Neighborhood problems may promote behaviors (e.g., drug use before or during sex) conducive to HIV infection. Structural interventions could improve community infrastructure to reduce neighborhood problems (e.g., no/poorly maintained sidewalks and litter). These interventions may help to reduce HIV incidence among Black MSM in the Deep South.

Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" through more effective investigations of outbreaks of foodborne illnesses, better-targeted tuberculosis control, and more timely and granular influenza surveillance to inform the selection of vaccine strains. In this article, we describe how public health agencies have been adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given the ongoing development in sequencing and sequencing-related technologies.