Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba

Detection of Polish cases of highly virulent subtype B of HIV-1 originating in the Netherlands

Infection with the human immunodeficiency virus type 1 (HIV-1) subtype B is most commonly acquired in Poland through men who have sex with men (MSM) comparable to the HIV epidemic in the Netherlands. Following a paper by Chris Wymant et al. on February 4, 2022 in Science on a highly virulent variant of HIV-1 subtype-B (VB-variant) in the Netherlands raised concerns about the possibility of the variant dissemination to other European countries. We aim to report the spread of HIV-1 VB-variant, recently identified in the Netherlands, into other European regions. Subtype B pol gene fragments of protease (P), reverse transcriptase (RT), and integrase (IN) from our laboratory supplemented with publicly available sequences were inferred with VB samples from the Netherlands. For positively clustering samples, clinical observations were compiled. Between May 2009 and August 2014, three cases of VB sequences of Polish origin and one additional from Belgium were identified. Patients presented with elevated viral loads and fast CD4 decline as original characteristics. The mean number of base substitutions per site within the clade versus interclade variability showed a high intragroup sequence similarity, reflecting an ongoing MSM transmission cluster for Polish sequences. The sampling period coincides with the ongoing Dutch VB-variant spread reported between 2003 and 2014. This study informs on phylogenetic descriptions, and clinical symptoms from the rare and emerging VBs placed in Poland. VB is not expanding since 2014 and the Inviduals infected with the VB virus can be treated successfully. Studies on the propagation of novel and potentially virulent virus variants in the undersampled regions add to the understanding of the pan-European HIV-1 transmission dynamics.

Cost analysis of implementing HIV drug resistance testing in Kenya: a case study of a service delivery site at a tertiary level hospital in Kenya

Background: HIV drug resistance (HIVDR) threatens progress achieved in response to the HIV epidemic. Understanding the costs of implementing HIVDR testing programs for patient management and surveillance in resource-limited settings is critical in optimizing resource allocation. Here, we estimate the unit cost of HIVDR testing and identify major cost drivers while documenting challenges and lessons learnt in implementation of HIVDR testing at a tertiary level hospital in Kenya. Methods: We employed a mixed costing approach to estimate the costs associated with performing a HIVDR test from the provider's perspective. Data collection involved a time and motion study of laboratory procedures and interviewing laboratory personnel and the management personnel. Cost analysis was based on estimated 1000 HIVDR tests per year. Data entry and analysis were done using Microsoft Excel and costs converted to US dollars (2019). Results: The estimated unit cost for a HIVDR test was $271.78 per test. The main cost drivers included capital ($102.42, 37.68%) and reagents (101.50, 37.35%). Other costs included: personnel ($46.81, 17.22%), utilities ($14.69, 5.41%), equipment maintenance costs ($2.37, 0.87%) and quality assurance program ($4, 1.47%). Costs in relation to specific laboratory processes were as follows: sample collection ($2.41, 0.89%), RNA extraction ($22.79, 8.38%), amplification ($56.14, 20.66%), gel electrophoresis ($10.34, 3.80%), sequencing ($160.94, 59.22%), and sequence analysis ($19.16, 7.05%). A user-initiated modification of halving reagent volumes for some laboratory processes (amplification and sequencing) reduced the unit cost for a HIVDR test to $233.81 (13.97%) reduction.  Conclusions: Capital expenditure and reagents remain the most expensive components of HIVDR testing. This cost is bound to change as the sequencing platform is utilized towards maximum capacity or leveraged for use with other tests. Cost saving in offering HIVDR testing services is also possible through reagent volume reduction without compromising on the quality of test results.

National survey of pre-treatment HIV drug resistance in Cuban patients

Background

The World Health Organization (WHO) recommends a method to estimate nationally representative pretreatment HIV drug resistance (PDR) in order to evaluate the effectiveness of first -line treatments. The objective of the present study was to determine the prevalence of PDR in Cuban adults infected with HIV-1.

Materials and methods

A cross-sectional study in Cuban adults infected with HIV-1 over 18 years was conducted. The probability proportional to size method for the selection of municipalities and patients without a prior history of antiretroviral treatment during the period from January 2017 to June 2017 was used. The plasma from 141 patients from 15 municipalities for the determination of viral subtype and HIV drug resistance was collected. Some clinical and epidemiological variables were evaluated.

Results

80. 9% of the patients corresponded to the male sex and 76.3% were men who have sex with other men (MSM). The median CD4 count was 371 cells / mm³ and the median viral load was 68000 copies / mL. The predominant genetic variants were subtype B (26.9%), CRF19_cpx (24.1%), CRF 20, 23, 24_BG (23.4%) and CRF18_cpx (12%). Overall, the prevalence of PDR was 29.8% (95%, CI 22.3–38.1). The prevalence was 12.8% (95%, CI 6.07–16.9) for any nucleoside reverse transcriptase inhibitor (NRTI), 23.4% (95%, CI 16.7–31.3) for any non-reverse transcriptase inhibitor (NNRTI) and 1.4% (95%, CI 0.17–5.03) for any protease inhibitor (PI). The most frequent mutations detected were K103N (12.9%), G190A (6.4%) and Y181C (4.8%).

Conclusions

The NNRTI prevalence above 10% in our study indicates that the first-line antiretroviral therapy in Cuba may be less effective and supports the need to look for new treatment options that contribute to therapeutic success and help the country achieve the global goals 90-90-90 set forth by UNAIDS.