Jimmy Whitworth

The effect of human immunodeficiency virus (HIV) type 1 envelope subtypes A and D on disease progression was investigated in 1045 adults in Uganda. At enrollment and every 6 months, a clinical history, examination, and laboratory investigations that included CD4 cell counts were done. HIV-1 envelope subtype was assessed mainly by peptide serology supplemented by heteroduplex mobility assay and DNA sequencing. A multivariate analysis of survival was performed to assess the prognostic value of HIV-1 subtype on death. A marginal general linear model also determined the effect of subtype on CD4 cell count during follow-up. Subtype D was associated with faster progression to death (relative risk, 1.29; 95% confidence interval, 1.07-1.56; P=.009) and with a lower CD4 cell count during follow-up (P=.001), compared with subtype A, after adjusting for CD4 cell count at enrollment. In Africa, envelope subtype D is associated with faster disease progression, compared with subtype A.

the World Health Organization (WHO) office in China received a report of 29 pneumonia cases of unknown aetiology in Wuhan city in Hubei province, central China. Within 1 week it became clear that the initial cases were associated with a seafood market where live poultry and wild animals were also sold. The virus was quickly identified as a novel beta-coronavirus and the genetic sequence was shared on 12 January 2020. The infection is now officially termed COVID-19 and the virus SARS-CoV-2. News of this outbreak gave many public health officials an involuntary shudder as they recalled the parallels with the severe acute respiratory syndrome (SARS) outbreak that arose in China in November 2002. That outbreak was also caused by a novel coronavirus spilling over from an animal reservoir and transmitted by respiratory droplets. SARS spread to many parts of the world through international air travel, caused more than 8000 cases and 774 deaths and cost in the region US$20 billion to control.

Despite continued efforts to improve health systems worldwide, emerging pathogen epidemics remain a major public health concern. Effective response to such outbreaks relies on timely intervention, ideally informed by all available sources of data. The collection, visualization and analysis of outbreak data are becoming increasingly complex, owing to the diversity in types of data, questions and available methods to address them. Recent advances have led to the rise of outbreak analytics, an emerging data science focused on the technological and methodological aspects of the outbreak data pipeline, from collection to analysis, modelling and reporting to inform outbreak response. In this article, we assess the current state of the field. After laying out the context of outbreak response, we critically review the most common analytics components, their inter-dependencies, data requirements and the type of information they can provide to inform operations in real time. We discuss some challenges and opportunities and conclude on the potential role of outbreak analytics for improving our understanding of, and response to outbreaks of emerging pathogens. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.

BACKGROUND: Uptake of HIV test results from an annual serosurvey of a population study cohort in rural southwestern Uganda had never exceeded 10% in any given year since inception in 1989. An intervention offering counselling and HIV results at home was conducted in four study villages following the 2001 serosurvey round, and followed by a qualitative evaluation exploring nature of demand and barriers to knowing HIV status. METHODS: Data from annual serosurveys and counsellor records are analyzed to estimate the impact of the intervention on uptake of HIV test results. Textual data are analyzed from 21 focus group discussions among counsellors, and men and women who had received HIV test results, requested but not yet received, and never requested; and 34 in-depth interviews equally divided among those who had received test results either from counselling offices and homes. RESULTS: Offering HIV results at home significantly increased uptake of results from 10 to 37% for all adults aged 15 (p<0.001), and 46% of those age 25 to 54. Previous male advantage in uptake of test results was effectively eliminated. Focus group discussions and in-depth interviews highlight substantial non-monetary costs of getting HIV results from high-visibility public facilities prior to intervention. Inconvenience, fear of stigmatization, and emotional vulnerability of receiving results from public facilities were the most common explanations for the relative popularity of home-based voluntary counselling and testing (VCT). It is seen as less appropriate for youth and couples with conflicting attitudes toward testing. CONCLUSIONS: Home delivery of results revealed significantly higher demand to know HIV status than stubbornly low uptake figures from the past would suggest. Integrating VCT into other services, locating testing centres in less visible surroundings, or directly confronting stigma surrounding testing may be less expensive ways to reproduce increased uptake with home VCT.

About 30 million people in Africa are estimated to be living with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS), yet data about the natural history of infection on the continent are sparse. We reviewed the literature on the natural history of HIV-1 and HIV-2 infections among African adults. Only one study, conducted in rural Uganda, has reported on survival from the time of HIV-1 seroconversion: the median was 9.8 years, which is similar to that reported in developed countries in the early stages of the epidemic and consistent with the findings from the follow-up of individuals identified by serological testing during community-based prevalence studies from Africa. Progression to symptomatic disease was faster in Uganda than in developed countries, due largely to the high background level of morbidity. Various studies suggest that people infected with HIV-2 survive longer and the course of the disease is possibly more variable than in people infected with HIV-1. However no studies have investigated survival from time of seroconversion among people infected with HIV-2. The majority of patients in hospital in Africa with either HIV-1 or HIV-2 have the clinical features of AIDS just before they die, and many are severely immunosuppressed. This is similar to the situation in developed countries before the introduction of highly active antiretroviral therapy (HAART). Potentially preventable infections are the leading causes of death among individuals infected with HIV-1. Prophylactic regimens and better treatments could have some effect on survival, but major improvements in life expectancy will require HAART.