Equitable access to COVID-19 diagnostics: factors associated with the uptake of rapid antigen testing in Victoria, Australia, January - February 2022.

BACKGROUND: Accessible and accurate diagnostics are critical to control communicable diseases. Uptake of COVID-19 rapid antigen (RA) testing requires physical and financial access to tests, knowledge about usage, motivation, and ability to report results. We sought to understand patterns of and factors associated with RA test uptake in Victoria during a period of high caseload, RA test promotion, and difficulty accessing RA and PCR testing. We hypothesise RA test uptake is indicated by the ratio of cases diagnosed by RA test (probable) to those diagnosed using PCR (confirmed) (p:c). METHODS: Analysing case records, trends in p:c were assessed, between regions, sex, age groups, socio-economic strata and cultural diversity. Logistic regression assessed associations between case classification, and median age, postcode-level socio-economic disadvantage, and proportion overseas-born. RESULTS: We included 591,789 cases. Mean p:c was lower in socio-economically disadvantaged areas (decile 1 + 2: 0.90 vs. decile 9 + 10: 1.10), and in postcodes where the overseas-born population was above the Victorian average (0.83 vs. 1.05). Conversely, p:c was higher in younger age groups; with no difference between sexes overall. In metropolitan Melbourne, odds of RA test usage increased as socio-economic disadvantage decreased (decile 9 + 10, aOR 1.40, 95%CI 1.37-1.43, vs. decile 1 + 2; p < .001), decreased for cases from areas with a higher overseas-born population (aOR 0.85, 0.83-0.86, p < .001), and with older age. CONCLUSIONS: Reduced uptake of RA tests in Victoria is associated with socio-economic disadvantage, cultural diversity, and older age. Equitable access to COVID-19 diagnostics requires elimination of financial barriers, and greater engagement with culturally diverse and older groups. Inequitable RA test uptake may lead to case under-ascertainment, affecting resource allocation, effective control strategy development, in turn impacting COVID-19 morbidity and mortality, and could indicate relative engagement with response initiatives.

Suppression of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) After a Second Wave in Victoria, Australia.

Countries worldwide are experiencing a second wave of coronavirus disease 2019 (COVID-19), which is proving to be difficult to control. We describe 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.

Spatial and Temporal Epidemiology of Infectious Syphilis in Victoria, Australia, 2015-2018.

ABSTRACT: 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.

Opioid Use Fueling HIV Transmission in an Urban Setting: An Outbreak of HIV Infection Among People Who Inject Drugs-Massachusetts, 2015-2018.

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.

Identification of Substance-Exposed Newborns and Neonatal Abstinence Syndrome Using ICD-10-CM - 15 Hospitals, Massachusetts, 2017.

Opioid use disorder and neonatal abstinence syndrome (NAS) increased in Massachusetts from 1999 to 2013 (1,2). In response, in 2016, the state passed a law requiring birth hospitals to report the number of newborns who were exposed to controlled substances to the Massachusetts Department of Public Health (MDPH)* by mandating monthly reporting of International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) diagnostic codes related to maternal dependence on opioids (F11.20) or benzodiazepines (F13.20) and to newborns affected by maternal use of drugs of addiction (P04.49) or experiencing withdrawal symptoms from maternal drugs of addiction (P96.1) separately.† MDPH uses these same codes for monthly, real-time crude estimates of NAS and uses P96.1 alone for official NAS state reporting.§ MDPH requested CDC's assistance in evaluating the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of either maternal or newborn codes to identify substance-exposed newborns, and of newborn exposure codes (both exposure [P04.49] or withdrawal [P96.1]) and the newborn code for withdrawal alone (P96.1) to identify infants with NAS cases related to three exposure scenarios: 1) opioids, 2) opioids or benzodiazepines, and 3) any controlled substance. Confirmed diagnoses of substance exposure and NAS abstracted from linked clinical records for 1,123 infants born in 2017 and their birth mothers were considered the diagnostic standard and were compared against hospital-reported ICD-10-CM codes. For identifying substance-exposed newborns across the three exposure scenarios, the newborn exposure codes had higher sensitivity (range = 31%-61%) than did maternal drug dependence codes (range = 16%-41%), but both sets of codes had high PPV (≥74%). For identifying NAS, for all exposure scenarios, the sensitivity for either newborn code (P04.49 or P96.1) was ≥92% and the PPV was ≥64%; for P96.1 alone the sensitivity was ≥79% and the PPV was ≥92% for all scenarios. Whereas ICD-10-CM codes are effective for NAS surveillance in Massachusetts, they should be applied cautiously for substance-exposed newborn surveillance. Surveillance for substance-exposed newborns using ICD-10-CM codes might be improved by increasing the use of validated substance-use screening tools and standardized facility protocols and improving communication between patients and maternal health and infant health care providers.

Notes from The Field: Ebola Virus Disease Cluster - Northern Sierra Leone, January 2016.

On January 14, 2016, the Sierra Leone Ministry of Health and Sanitation was notified that a buccal swab collected on January 12 from a deceased female aged 22 years (patient A) in Tonkolili District had tested positive for Ebola virus by reverse transcription-polymerase chain reaction (RT-PCR). The most recent case of Ebola virus disease (Ebola) in Sierra Leone had been reported 4 months earlier on September 13, 2015 (1), and the World Health Organization had declared the end of Ebola virus transmission in Sierra Leone on November 7, 2015 (2). The Government of Sierra Leone launched a response to prevent further transmission of Ebola virus by identifying contacts of the decedent and monitoring them for Ebola signs and symptoms, ensuring timely treatment for anyone with Ebola, and conducting an epidemiologic investigation to identify the source of infection.

Frequency and spelling of names in the Sierra Leone Ebola Database.

Although there is no published analysis of surnames and given names used in Sierra Leone, certain names are common and identical names are frequently encountered. This makes disease tracking and contact tracing difficult. During the Ebola outbreak in 2014-2016, deficiencies in public health information systems in Sierra Leone exacerbated data collection difficulties. The study objective was to examine frequency of names recorded in the Viral Hemorrhagic Fever database (VHF) component of the Sierra Leone Ebola Database (SLED). First names and surnames were standardized by a Sierra Leonean linguist. Frequencies of standardized first names, surnames, full names, and initials were analyzed. The most frequent surname was used by 18.2% of VHF records and the most frequent 20 surnames accounted for 74.1%. The most frequent male first name accounted for 5.5% of VHF records and the most frequent female first name for 4.6%. The 20 most frequent full names accounted for 12.4% of records, and the most frequent initials were used in 7.3% of VHF records. A limited number of names are used in Sierra Leone, which poses a challenge to large public health responses. Algorithms that address inconsistent spelling could be used to improve computer-based databases. Databases must also use variables other than name for identification. The lessons learned in this analysis can assist other investigations, particularly those requiring contact tracing to limit disease spread.

A qualitative study of injection and sexual risk behavior among unstably housed people who inject drugs in the context of an HIV outbreak in Northeast Massachusetts, 2018.

BACKGROUND: To investigate the underlying causes of a sudden increase in HIV among people who inject drugs (PWID) and initiate an appropriate response to the outbreak, we engaged in in-depth qualitative interviews with members of the PWID community in Lawrence and Lowell, Massachusetts. METHODS: We interviewed 34 PWID who were currently or recently unstably housed, then transcribed interviews and coded transcripts, grouping codes into categories from which we identified key themes. RESULTS: Participants described a heightened threat of overdose prompting PWID to inject together, increasing opportunities for sharing injection equipment. There were misunderstandings about safe injection practices to prevent HIV transmission and a low threshold for injection-related risk taking. Stigma regarding HIV prevented conversations about HIV status. Less thought was given to sexual risks than injection-related risks for HIV transmission. CONCLUSIONS: We found multiple facilitators of HIV transmission. Additional HIV education and prevention interventions focusing on both injection and sexual risk practices would benefit this population, in addition to structural interventions such as increased access and availability of syringe service programs.

COVID-19 in health care workers, Australia 2020.

BACKGROUND: Health care workers are at increased risk of SARS-CoV-2 infection due to potential exposure to patients or staff in health care settings. Australian health care services and health care workers experienced intense pressure to prepare for and respond to SARS-CoV-2 infections. We summarise national data on health care worker infections and associated outbreaks during 2020. METHODS: We collected aggregated data on infected health care workers and outbreaks in health care facilities from all jurisdictions. Health care workers working solely in residential aged care and outbreaks in residential aged care facilities were excluded. Jurisdictions provided data on the number of health care setting outbreaks, confirmed cases, hospitalisation, source of infection, and health care worker role. We analysed data for two periods that aligned with two distinct peaks in the epidemic relative to 1 June 2020, referred to here as the first wave (23 January - 31 May 2020) and the second wave (1 June - 18 September 2020). RESULTS: Jurisdictions reported a total of 2,163 health care worker infections with SARS-CoV-2 during the surveillance period. Source of acquisition was known for 81.0% of cases (1,667/2,059). The majority of cases in the first wave were acquired overseas, shifting to locally-acquired cases in the second wave. The odds of infection in the second wave compared to the first wave were higher for nurses/midwives (odds ratio, OR: 1.61; 95% confidence interval (95% CI): 1.32-2.00), lower for medical practitioners (OR: 0.36; 95% CI: 0.28-0.47) and did not differ for 'other' health care workers (OR: 1.07; 95% CI: 0. 87-1.32). The odds of infection in the second wave were higher in a health care setting (OR: 1.76; 95% CI: 1.28-2.41) than in the community. There were 120 outbreaks in health care settings with 1,428 cases, of which 56.7% (809/1,428) were health care workers. The majority (88/120; 73.8%) of outbreaks in health care settings occurred in the second wave of the epidemic, with 90.9% of these (80/88) occurring in Victoria. CONCLUSIONS: In the second wave of the epidemic, when there was heightened community transmission, health care workers were more likely to be infected in the workplace. Throughout the epidemic, nurses were more likely to be infected than staff in other roles.

Building the Sierra Leone Ebola Database: organization and characteristics of data systematically collected during 2014-2015 Ebola epidemic.

PURPOSE: During the 2014-2016 Ebola outbreak in West Africa, the Sierra Leone Ministry of Health and Sanitation (MoHS), the US Centers for Disease Control and Prevention, and responding partners under the coordination of the National Ebola Response Center (NERC) and the MoHS's Emergency Operation Center (EOC) systematically recorded information from the 117 Call Center system and district alert phone lines, case investigations, laboratory sample testing, clinical management, and safe and dignified burial records. Since 2017, CDC assisted MoHS in building and managing the Sierra Leone Ebola Database (SLED) to consolidate these major data sources. The primary objectives of the project were helping families to identify the location of graves of their loved ones who died at the time of the Ebola epidemic through the SLED Family Reunification Program and creating a data source for epidemiological research. The objective of this paper is to describe the process of consolidating epidemic records into a useful and accessible data collection and to summarize data characteristics, strength, and limitations of this unique information source for public health research. METHODS: Because of the unprecedented conditions during the epidemic, most of the records collected from responding organizations required extensive processing before they could be used as a data source for research or the humanitarian purpose of locating burial sites. This process required understanding how the data were collected and used during the outbreak. To manage the complexity of processing the data obtained from various sources, the Sierra Leone Ebola Database (SLED) Team used an organizational strategy that allowed tracking of the data provenance and lifecycle. RESULTS: The SLED project brought raw data into one consolidated data collection. It provides researchers with secure and ethical access to the SLED data and serves as a basis for the research capacity building in Sierra Leone. The SLED Family Reunification Program allowed Sierra Leonean families to identify location of the graves of loved ones who died during the Ebola epidemic. CONCLUSIONS: The SLED project consolidated and utilized epidemic data recorded during the Sierra Leone Ebola Virus Disease outbreak that were collected and contributed to SLED by national and international organizations. This project has provided a foundation for developing a method of ethical and secure SLED data access while preserving the host nation's data ownership. SLED serves as a data source for the SLED Family Reunification Program and for epidemiological research. It presents an opportunity for building research capacity in Sierra Leone and provides a foundation for developing a relational database. Large outbreak data systems such as SLED provide a unique opportunity for researchers to improve responses to epidemics and indicate the need to include data management preparedness in the plans for emergency response.

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study.

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 laboratory-confirmed 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. FINDINGS: Between Jan 25, 2020, and Jan 31, 2021, there were 20 451 laboratory-confirmed cases of COVID-19 in Victoria, Australia, of which 15 431 were submitted for sequencing, and 11 711 met all quality control metrics and were included in our analysis. We identified 595 genomic clusters, with a median of five cases per cluster (IQR 2-11). Overall, samples from 11 503 (98·2%) of 11 711 cases clustered with another sample in Victoria, either within a genomic cluster or transmission network. Genomic analysis revealed that 10 426 cases, including 10 416 (98·4%) of 10 584 locally acquired cases, diagnosed during the second wave (between June and October, 2020) were derived from a single incursion from hotel quarantine, with the outbreak lineage (transmission network G, lineage D.2) rapidly detected in other Australian states and territories. Phylodynamic analyses indicated that the epidemic growth rate of the outbreak lineage in Victoria during the initial growth phase (samples collected between June 4 and July 9, 2020; 47·4 putative transmission events, per branch, per year [1/years; 95% credible interval 26·0-85·0]), was similar to that of other reported variants, such as B.1.1.7 in the UK (mean approximately 71·5 1/years). Strict interventions were implemented, and the outbreak lineage has not been detected in Australia since Oct 29, 2020. Subsequent cases represented independent international or interstate introductions, with limited local spread. INTERPRETATION: Our study highlights how rapid escalation of clonal outbreaks can occur from a single incursion. However, strict quarantine measures and decisive public health responses to emergent cases are effective, even with high epidemic growth rates. Real-time genomic surveillance can alter the way in which public health agencies view and respond to COVID-19 outbreaks. FUNDING: The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.

GP Clinic: promoting access to primary health care for mental health service clients.

OBJECTIVE: To evaluate an innovative rural service offering comprehensive primary health care for mental health service clients. DESIGN: A formative evaluation using mixed methods. SETTING: A rural NSW community. PARTICIPANTS: Fifteen health care providers and 120 adult clients. INTERVENTION: A monthly clinic held in a general practice to provide primary health care for clients of the community mental health team. MAIN OUTCOME MEASURES: Client utilisation and clinic activity data. Provider views of service effectiveness, possible improvements and sustainability. RESULTS: The GP Clinic has operated successfully for 2.5 years without access block. Some 52% of clients had no physical illness and 82% were referred to other health and community services. In total, 40% continued to attend the clinic while 32% went on to consult a GP independently. Client access to care improved as did collaboration between the community mental health team and primary care providers. CONCLUSION: The GP Clinic is a straightforward and flexible service model that could be used more widely.

Quality of age data in the Sierra Leone Ebola database.

INTRODUCTION: While it is suspected that some ages were misreported during the 2014-2016 West African Ebola outbreak, an analysis examining age data quality has not been conducted. The study objective was to examine age heaping and terminal digit preference as indicators for quality of age data collected in the Sierra Leone Ebola Database (SLED). METHODS: Age data quality for adult patients was analyzed within SLED for the Viral Hemorrhagic Fever (VHF) database and the laboratory testing dataset by calculating Whipple´s index and Myers´s blended index, stratified by sex and region. RESULTS: Age data quality was low in both the VHF database (Whipple´s index for the 5-year range, 229.2) and the laboratory testing dataset (Whipple´s index for the 5-year range, 236.4). Age was reported more accurately in the Western Area and least accurately in the Eastern Province. Age data for females were less accurate than for males. CONCLUSION: Age data quality was low in adult patients during the 2014-2016 Ebola outbreak in Sierra Leone, which may reduce its use as an identifying or stratifying variable. These findings inform future analyses using this database and describe a phenomenon that has relevance in data collection methods and analyses for future outbreaks in developing countries.

National reporting of deaths after enhanced Ebola surveillance in Sierra Leone.

BACKGROUND: Sierra Leone experienced the largest documented epidemic of Ebola Virus Disease in 2014-2015. The government implemented a national tollfree telephone line (1-1-7) for public reporting of illness and deaths to improve the detection of Ebola cases. Reporting of deaths declined substantially after the epidemic ended. To inform routine mortality surveillance, we aimed to describe the trends in deaths reported to the 1-1-7 system and to quantify people's motivations to continue reporting deaths after the epidemic. METHODS: First, we described the monthly trends in the number of deaths reported to the 1-1-7 system between September 2014 and September 2019. Second, we conducted a telephone survey in April 2017 with a national sample of individuals who reported a death to the 1-1-7 system between December 2016 and April 2017. We described the reported deaths and used ordered logistic regression modeling to examine the potential drivers of reporting motivations. FINDINGS: Analysis of the number of deaths reported to the 1-1-7 system showed that 12% of the expected deaths were captured in 2017 compared to approximately 34% in 2016 and over 100% in 2015. We interviewed 1,291 death reporters in the survey. Family members reported 56% of the deaths. Nearly every respondent (94%) expressed that they wanted the 1-1-7 system to continue. The most common motivation to report was to obey the government's mandate (82%). Respondents felt more motivated to report if the decedent exhibited Ebola-like symptoms (adjusted odds ratio 2.3; 95% confidence interval 1.8-2.9). CONCLUSIONS: Motivation to report deaths that resembled Ebola in the post-outbreak setting may have been influenced by knowledge and experiences from the prolonged epidemic. Transitioning the system to a routine mortality surveillance tool may require a robust social mobilization component to match the high reporting levels during the epidemic, which exceeded more than 100% of expected deaths in 2015.

Tracking the COVID-19 pandemic in Australia using genomics.

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 (Re) 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.

The 117 call alert system in Sierra Leone: from rapid Ebola notification to routine death reporting.

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.