K103N Mutation in Antiretroviral Therapy--Naive African Patients Infected with HIV Type 1

PAM-free diagnostics with diverse type V CRISPR-Cas systems

Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.

Demographic, clinical, and virologic characteristics of African-born persons with HIV/AIDS in a Minnesota hospital

Minnesota is currently home to the tenth largest African population and the second largest East African population in the United States. HIV is increasingly being diagnosed in African-born persons in Minnesota. A retrospective survey was conducted on all African-born patients in our HIV clinic between January 1994 and June 2005. We identified 237 patients who were African-born and HIV-positive. They constituted 12% of patients attending the clinic within the study timeframe. There was no significant difference in the ages of the African-born and non-African patients in the HIV clinic. African-born patients were more likely to be women compared with non-African patients (p < 0.001). Forty-three percent of the African-born patients presented with AIDS as defined by CD4(+) T cell counts less than 200 cells per milliliter compared to 33% of antiretroviral naïve non-African HIV patients in the clinic (p < 0.001). Most patients were infected through heterosexual contact and only 4% were diagnosed as a result of routine testing. Seven known HIV subtypes and four unique recombinant forms were identified. The most common opportunistic infection was pulmonary tuberculosis. African immigrants with HIV appear to: (1) access care at later stages of HIV disease than other patients in our clinic; (2) are often infected with non-B subtypes; (3) do not routinely get tested for HIV. Increased awareness to this growing trend is needed for health care providers and public health officials to tailor educational programs and prevention efforts for African immigrants in the United States.

The changing epidemiology of HIV/AIDS at a Minnesota hospital: impact of demographic change and viral diversity

The past decade has seen a dramatic influx of African-born immigrants and refugees into Minnesota. The impact of this on Hennepin County Medical Center (HCMC), a public teaching hospital located in Minneapolis, has been considerable, especially in the management of HIV-infected persons given that approximately 30% of newly diagnosed individuals seen at HCMC in the past 3 years acquired the virus in Africa. An ongoing and permanent alteration in the demographics of HIV/AIDS in this part of the American midwest is clearly occurring, therefore, accompanied by considerable diversification of the viral makeup of the epidemic. The following article describes currently available data on the viral characteristics of the African-born HIV-infected population of Minnesota and highlights the potential impact of this expanding viral diversity on the ability of the clinical laboratory at HCMC to provide the virologic information necessary to manage effectively patients infected with the HIV virus.