BACKGROUND: Whole-genome sequencing of pathogens can improve resolution of outbreak clusters and define possible transmission networks. We applied high-throughput genome sequencing of SARS-CoV-2 to 75% of cases in the State of Victoria (population 6.24 million) in Australia. METHODS:Cases of SARS-CoV-2 infection were detected through active case finding and contact tracing. A dedicated SARS-CoV-2 multidisciplinary genomic response team was formed to enable rapid integration of epidemiological and genomic data. Phylodynamic analysis was performed to assess the putative impact of social restrictions. RESULTS:Between 25 January and 14 April 2020, 1,333 COVID-19 cases were reported in Victoria, with a peak in late March. After applying internal quality control parameters, 903 samples were included in genomic analyses. Sequenced samples from Australia were representative of the global diversity of SARS-CoV-2, consistent with epidemiological findings of multiple importations and limited onward transmission. In total, 76 distinct genomic clusters were identified; these included large clusters associated with social venues, healthcare facilities and cruise ships. Sequencing of sequential samples from 98 patients revealed minimal intra-patient SARS-CoV-2 genomic diversity.Phylodynamic modelling indicated a significant reduction in the effective viral reproductive number (Re) from 1.63 to 0.48 after the implementation of travel restrictions and population-level physical distancing.

Objectives. To describe and control an outbreak of HIV infection among people who inject drugs (PWID). Methods. The investigation included people diagnosed with HIV infection during 2015 to 2018 linked to 2 cities in northeastern Massachusetts epidemiologically or through molecular analysis. Field activities included qualitative interviews regarding service availability and HIV risk behaviors. Results. We identified 129 people meeting the case definition; 116 (90%) reported injection drug use. Molecular surveillance added 36 cases to the outbreak not otherwise linked. The 2 largest molecular groups contained 56 and 23 cases. Most interviewed PWID were homeless. Control measures, including enhanced field epidemiology, syringe services programming, and community outreach, resulted in a significant decline in new HIV diagnoses. Conclusions. We illustrate difficulties with identification and characterization of an outbreak of HIV infection among a population of PWID and the value of an intensive response. Public Health Implications. Responding to and preventing outbreaks requires ongoing surveillance, with timely detection of increases in HIV diagnoses, community partnerships, and coordinated services, all critical to achieving the goal of the national Ending the HIV Epidemic initiative.

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Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput genomics for SARS-CoV-2, sequencing 80% of cases in Victoria, Australia (population 6.24 million) between 6 January and 14 April 2020 (total 1,333 COVID-19 cases). We integrate epidemiological, genomic and phylodynamic data to identify clusters and impact of interventions. The global diversity of SARS-CoV-2 is represented, consistent with multiple importations. Seventy-six distinct genomic clusters were identified, including large clusters associated with social venues, healthcare and cruise ships. Sequencing sequential samples from 98 patients reveals minimal intra-patient SARS-CoV-2 genomic diversity. Phylodynamic modelling indicates a significant reduction in the effective viral reproductive number (R e) from 1.63 to 0.48 after implementing travel restrictions and physical distancing. Our data provide a concrete framework for the use of SARS-CoV-2 genomics in public health responses, including its use to rapidly identify SARS-CoV-2 transmission chains, increasingly important as social restrictions ease globally.

Background A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia.Methods In this observational, genomic epidemiological study, we did genomic sequencing of all laboratoryconfirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK.

A toll-free, nationwide phone alert system was established for rapid notification and response during the 2014–2015 Ebola epidemic in Sierra Leone. The system remained in place after the end of the epidemic under a policy of mandatory reporting and Ebola testing for all deaths, and, from June 2016, testing only in case of suspected Ebola. We describe the design, implementation and changes in the system; analyse calling trends during and after the Ebola epidemic; and discuss strengths and limitations of the system and its potential role in efforts to improve death reporting in Sierra Leone. Numbers of calls to report deaths of any cause (death alerts) and persons suspected of having Ebola (live alerts) were analysed by province and district and compared with numbers of Ebola cases reported by the WHO. Nearly 350 000 complete, non-prank calls were made to 117 between September 2014 and December 2016. The maximum number of daily death and live alerts was 9344 (October 2014) and 3031 (December 2014), respectively. Call volumes decreased as Ebola incidence declined and continued to decrease in the post-Ebola period. A national social mobilisation strategy was especially targeted to influential religious leaders, traditional healers and women’s groups. The existing infrastructure and experience with the system offer an opportunity to consider long-term use as a death reporting tool for civil registration and mortality surveillance, including rapid detection and control of public health threats. A routine social mobilisation component should be considered to increase usage.

This analysis of notified syphilis cases in Victoria, Australia between 2015 and 2018 shows that the syphilis epidemic in Victoria has become more generalized, with increases among heterosexual men and women residing in outer Melbourne suburbs-areas that differ from those of gay men.I ncreases in syphilis among gay men were observed in the early 2000s in high-income countries, including the United States, the United Kingdom, Australia, and Europe. 1 More recently, syphilis cases have increased among heterosexuals in several countries, including North America, Japan, and Australia. [2][3][4][5][6][7] In Victoria, Australia, the number of cases in women has increased rapidly since 2015, 8 and congenital syphilis infections have reemerged for the first time since the last reported case in 2004. 9 What has driven the increase among women in Victoria is not fully understood. Australian surveillance data only report infectious syphilis cases by sex but not sexual orientation, making it difficult to track and understand the pattern of the epidemic between heterosexuals and gay men. In this study, we aimed to improve our understanding of the epidemiology of syphilis in Victoria by examining the demographic and clinical characteristics of notified syphilis cases by risk group and by mapping area of residence. Understanding the geographical distribution of syphilis by risk group would help inform the design and targeting of interventions aimed at improving control. METHODSSyphilis is a notifiable disease in Victoria, Australia. 10 Routinely collected syphilis notification data were obtained from the Victorian Government Department of Health: age, gender, country of birth, Aboriginal and Torres Strait Islander status, postcode of residence, gender of sex partners, presence or absence of symptoms, reasons for syphilis testing, and the source of notification. 10 The source of notification was categorized as follows: high caseload clinic (public sexual health clinics and general practices with a large clientele of gay men, sexually transmitted infections [STIs] and human immunodeficiency virus [HIV]); low caseload general practice (minimal STIs focus); hospitals; prisons; and laboratory.Deidentified and aggregated data on all infectious syphilis cases (primary, secondary, and early latent <2 years) 11 notified to the Victorian Department of Health between 2015 and 2018 were extracted. Late latent syphilis cases and those with unknown staging were excluded. Postcode of residence of the case was categorized by local government area based on Australian Standard Geography Classification. 12 Cases were categorized into four risk groups based on gender and sexual practices: "gay men"-men who have sex with men only, "heterosexual men"-men who have sex with women only, "bisexual men"-men who have sex with both men and women, and "women"-women who have sex with men and/or women. 13 Reinfection with syphilis was classified by the person notifying the case.Statistical analysis was conducted using IBM SPSS Statistics for Windows, Version ...

Countries around the world are experiencing a second wave of COVID-19 which is proving to be difficult to control. This report describes the combination of physical distancing, mandatory mask wearing, movement restrictions and enhanced test, trace and isolation efforts that can be used to successfully suppress community transmission to zero.