Towards Targeted Screening for Acute HIV Infections in British Columbia

Background: Our objective was to describe the characteristics of acute and established HIV infections diagnosedin the Canadian province of British Columbia. Province-wide HIV testing and surveillance data were analyzed toinform recommendations for targeted use of screening algorithms to detect acute HIV infections.Methods: Acute HIV infection was defined as a confirmed reactive HIV p24 antigen test (or HIV nucleic acid test), anon-reactive or reactive HIV EIA screening test and a non-reactive or indeterminate Western Blot. Characteristics ofunique individuals were identified from the British Columbia HIV/AIDS Surveillance System. Primary drug resistanceand HIV subtypes were identified by analyzing HIV pol sequences from residual sera from newly infectedindividuals.Results: From February 2006 to October 2008, 61 individuals met the acute HIV infection case definition,representing 6.2% of the 987 newly diagnosed HIV infections during the analysis period. Acute HIV infection caseswere more likely to be men who have sex with men (crude OR 1.71; 95% CI 1.01-2.89], to have had a documentedprevious negative HIV test result (crude OR 2.89; 95% CI 1.52-5.51), and to have reported a reason for testing dueto suspected seroconversion symptoms (crude OR 5.16; 95% CI 2.88-9.23). HIV subtypes and rates of transmitteddrug resistance across all classes of drugs were similar in persons with both acute and established HIV infections.Conclusions: Targeted screening to detect acute HIV infection is a logical public health response to the HIVepidemic. Our findings suggest that acute HIV infection screening strategies, in our setting, are helpful for earlydiagnosis in men who have sex with men, in persons with seroconversion symptoms and in previously negativerepeat testers

Detection of Early Sero-Conversion HIV Infection Using the INSTITM HIV-1 Antibody Point-of-Care Test

We compared the INSTITM HIV-1 Antibody Point-of-Care (POC) Test to laboratory-based tests for detection of early sero-conversion (i.e. acute) HIV infections. Fifty-three (53) individuals with early HIV infection, (i.e. 3rd generation anti-HIV EIA non-reactive or reactive, HIV-1 Western Blot non-reactive or indeterminate and HIV-1 p24 antigen reactive) were tested by INSTITM. The INSTITM test was reactive for 34/49 (sensitivity 69.4%; 95% confidence interval 54.6-81.8%) early-infected individuals whose laboratory-based 3rd generation HIV EIA test was reactive. Four (4) were non-reactive by both the laboratory-based EIA and INSTITM tests, but were p24 antigen reactive. The INSTITM POC test performs well compared with other POC tests for the detection of early sero-conversion HIV infection, but it may miss 20% to 30% of those detected by laboratory-based 3rd generation anti-HIV tests. Both POC and laboratory-based anti-HIV tests will fail to detect a proportion of infected individuals in the first weeks after infection

Modeling Control Strategies of Respiratory Pathogens

Contact network epidemiology can provide quantitative input even before pathogen is fully characterized

BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies

A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit’s taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases of Klebsiella pneumoniae and Neisseria gonorrhoeae infection, BugSplit’s taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available at: https://bugseq.com/academic

Hepatitis C cross-genotype immunity and implications for vaccine development.

While about a quarter of individuals clear their primary hepatitis C (HCV) infections spontaneously, clearance (spontaneous or treatment-induced) does not confer sterilizing immunity against a future infection. Since successful treatment does not prevent future infections either, an effective vaccine is highly desirable in preventing HCV (re)infection. However, development of an effective vaccine has been complicated by the diversity of HCV genotypes, and complexities in HCV immunological responses. Smaller studies on humans and chimpanzees reported seemingly opposing results regarding cross-neutralizing antibodies. We report a lack of cross-genotype immunity in the largest cohort of people to date. In the adjusted Cox proportional hazards model, reinfection with a heterologous HCV genotype (adjusted Hazard Ratio [aHR]: 0.45, 95% CI: 0.25-0.84) was associated with a 55% lower likelihood of re-clearance. Among those who cleared their first infection spontaneously, the likelihood of re-clearance was 49% lower (aHR: 0.51, 95% CI: 0.27-0.94) when reinfected with a heterologous HCV genotype. These findings indicate that immunity against a particular HCV genotype does not offer expanded immunity to protect against subsequent infections with a different HCV genotype. A prophylactic HCV vaccine boosted with multiple HCV genotype may offer a broader and more effective protection

Characteristics of gay, bisexual and other men who have sex with men with multiple diagnoses of infectious syphilis in British Columbia, Canada, 2005-2014

Background: Infectious syphilis has increased substantially over the past decade. Targeting limited public health resources toward subpopulations with multiple reinfections may have a large impact in reducing onward transmission within a community. Methods: A chart review was conducted for individuals with 4 or more infectious syphilis diagnoses between 2005 and 2014 (the top 1% of all syphilis diagnoses in British Columbia, Canada). We characterized the sociodemographics, partner notification outcomes and social network. Results: Between 2005 and 2014, there were 30 individuals with 4 or more syphilis diagnoses, accounting for 139 diagnoses. All were men who have sex with men and 29 (96%) were human immunodeficiency virus–positive. Of the 139 diagnoses, 65% occurred in the early latent stage of infection, 22% in the secondary stage, and 14% in the primary stage. The median number of sexual partners per diagnosis was 5 (range, 1–50). Among the 838 partners reported, 79% were notifiable, 53% were notified, and 23% were reported to be tested or treated. Sexual network mapping showed that almost half of the members of this group could be linked to one another either directly or indirectly via partners over 10 years. Social network mapping demonstrated high connectivity, with 4 venues associated with almost two thirds of the study population. Conclusions: The connectivity and recurrent diagnoses in this study population suggest potential benefits of targeted interventions to individuals with multiple diagnoses and their partners. Our study highlights the need for enhanced care, increased syphilis testing frequency, and exploring alternative preventative methods among individuals with syphilis rediagnoses to reduce syphilis incidence

As Omicron Takes Hold and Other New Variants Arise, COVID-19 Testing Remains the Universally Agreed Tool to Effect Transition From Pandemic to Endemic State

The COVID-19 pandemic has caused more than 448 million cases and 6 million deaths worldwide to date. Omicron is now the dominant SARS-CoV-2 variant, making up more than 90% of cases in countries reporting sequencing data. As the pandemic continues into its third year, continued testing is a strategic and necessary tool for transitioning to an endemic state of COVID-19. Here, we address three critical topics pertaining to the transition from pandemic to endemic: defining the endemic state for COVID-19, highlighting the role of SARS-CoV-2 testing as endemicity is approached, and recommending parameters for SARS-CoV-2 testing once endemicity is reached. We argue for an approach that capitalizes on the current public health momentum to increase capacity for PCR-based testing and whole genome sequencing to monitor emerging infectious diseases. Strategic development and utilization of testing, including viral panels in addition to vaccination, can keep SARS-CoV-2 in a manageable endemic state and build a framework of preparedness for the next pandemic

Human Illness from Avian Influenza H7N3, British Columbia

Avian influenza that infects poultry in close proximity to humans is a concern because of its pandemic potential. In 2004, an outbreak of highly pathogenic avian influenza H7N3 occurred in poultry in British Columbia, Canada. Surveillance identified two persons with confirmed avian influenza infection. Symptoms included conjunctivitis and mild influenzalike illness