Epidemiological Characterization of Patients in the First Eight Weeks Following Detection of SARS-CoV-2 B.1.1.529 (omicron) Variant in Cuba.

INTRODUCTION: In November 2021, omicron-a new SARS-CoV-2 variant-was identified in South Africa and almost immediately, WHO declared it a 'variant of concern'. In view of its rapid worldwide spread and its imminent introduction in Cuba, genomic surveillance was strengthened. OBJECTIVE: Describe cases during the first eight epidemiological weeks (epiweeks) of SARS-CoV-2 infection attributable to omicron variant in Cuba by clinical and epidemiological variables. METHODS: From epiweek 48, 2021 to epiweek 4, 2022, 288 nasopharyngeal swabs were processed for sequencing of a 1836 bp fragment of the S gene. Variants were identified according to GISAID database and confirmed by phylogenetic analysis. Variants' association with clinical and epidemiological outcomes was assessed. RESULTS: The first cases of omicron variant were imported, mostly from African countries and the United States. During the period studied, omicron was detected in 83.0% (239/288) of cases processed, while the delta variant was found in 17.0% (49/288). Most persons infected with omicron were symptomatic (63.2%; 151/239) and fully vaccinated (65.3%; 156/239); severe cases and deaths occurred mainly among patients aged ≥65 years (92.9%; 13/14), and 12 of these deaths occurred in fully vaccinated persons (92.3%; 12/13). Omicron spread rapidly throughout the country (from 10% of cases in epiweek 48, 2021, to 100% by epiweek 4, 2022), displacing the formerly predominant delta variant. CONCLUSIONS: Omicron's rapid expansion in Cuba was associated with increased incidence but not with a higher case fatality rate. The relatively milder disease in those infected with this variant could be influenced by the high vaccination coverage, along with the natural immunity acquired as a consequence of previous virus infection.

Subtype-Dependent Co-receptor Tropism in Cuban HIV-1-Infected Patients: Implications for Maraviroc Treatment.

INTRODUCTION: Unlike most high-income countries where subtype B viruses predominate, the Cuban HIV-1 epidemic is characterized by a great diversity of subtypes and circulating recombinant forms. Some studies have shown that HIV variants exhibiting a preference for the CXCR4 co-receptor (X4-tropic) could have impacts on disease pathogenesis, with clinical implications for antiviral treatment plans. Determination of HIV co-receptor tropism is crucial for clinicians in deciding whether maraviroc is an appropriate antiviral. OBJECTIVE: Characterize V3 sequence variability and its relation to viral tropism across different subtypes circulating in Cuba and explore how this may affect treatment success with maraviroc. METHODS: We designed a cross-sectional study that included 72 plasma samples obtained at the Pedro Kourí Tropical Medicine Institute in Havana, Cuba. We sequenced the C2V3 env region and assessed subtype based both on env and pol sequences; tropism was predicted by Geno2pheno analysis. Additionally, 35 V3-loop Cuban sequences, obtained from a previous study, were incorporated into the analysis. Statistical associations among virological, clinical and epidemiological variables were assessed by a chi-square test. RESULTS: Tropism prediction for 72 variants revealed that CRF19_cpx was associated with dual-tropic R5X4 viruses (p = 0.034). Moreover, when 35 sequences from a former study were added, the association was significant not only for R5X4 (p = 0.019) but also for X4-tropic variants (p = 0.044). Alignment of 107 V3-loop sequences showed wide diversity among the different HIV-1 subtypes circulating in Cuba. CONCLUSIONS: In accordance with G2P, CRF19_cpx is a genetic variant with a high proportion of X4 and R5X4-tropic viruses. The results from the present study suggest that the Cuban recombinant could be a more pathogenic variant and that maraviroc may not be suitable for patients infected with CRF19_cpx.

Circulation of Human Papillomavirus and Chlamydia trachomatisin Cuban Women.

INTRODUCTION Human papillomaviruses and Chlamydia tracho-matis are the most frequent causes of sexually transmitted infec-tions. Although the association between some human papillomavirus genotypes and cervical cancer has been demonstrated and Chla-mydia trachomatis infection is the most common cause of female infertility, Cuba has no national baseline studies on the circulation and co-circulation of these agents, the synergistic effect of which may be a risk factor for occurrence and development of precancer-ous cervical lesions. Additionally, few local studies have examined risk factors for infection.OBJECTIVE Determine the frequency of infection by human papil-lomavirus and Chlamydia trachomatis and their association with sociodemographic, clinical and epidemiological variables in women seeking routine Pap smears or other medical services at the primary care level in Cuba.METHODS A cross-sectional study was conducted among 500 wom-en aged 16-67 years (100 from Havana, 200 from Villa Clara and 200 from Holguín Provinces, Cuba), from August through December 2015. Chlamydia trachomatis infection was detected by real-time polymerase chain reaction and 35 genotypes of human papillomavirus by low-density microarray. We then examined the association of infec-tion with sociodemographic, clinical and epidemiological variables.RESULTS Human papillomavirus was detected in 14.8% (74/500) of the women. Of the 29 genotypes identifi ed, 79.7% (59/74) were onco-genic high-risk types. Type 16 was the most frequently identifi ed (23%; 17/74), followed by type 31 (10.8%; 8/74) and then by types 33, 53, 61 and 66 in equal proportions (8.1%; 6/74). Infection frequency was greater in women aged ≤25 years (38.8%; 31/80), students (46.7% 7/15), single women (23.0%; 40/174) and among those who reported having more than 3 sexual partners in the last 2 years (41.5%; 17/41). Differences were found among provinces for circulating genotypes and infection-related variables. Human papillomavirus infection from genotypes 16, 31, 33, 53, 61, 66, 68 and 89 was associated with the 7.9% (30/382) of women who had positive Pap tests. Infection fromChlamydia trachomatis was positive in 1% (5/500) of women, all aged ≤25 years. Coinfection by Chlamydia trachomatis and HPV was found in one woman infected with human papillomavirus genotype 61.CONCLUSIONS Frequency of human papillomavirus is high in the three Cuban provinces studied, with greater frequency of genotype 16 and other oncogenic high-risk types. For both agents, infection is more frequent in young women and adolescents. Positive Pap tests are fre-quently associated with HPV infection. Prevalence fi ndings from this study could be used as a baseline for future research or interventions. KEYWORDS Human papillomavirus, genotypes, Chlamydia tracho-matis, neoplasms, sexually transmitted diseases, cervix Uteri, infec-tion, real-time polymerase chain reaction, women, Cuba.

HIV-1 Antiretroviral Resistance in Cuba, 2009-2014.

INTRODUCTION By the end of 2017, there were more than 28,000 individuals living with HIV in Cuba, over 80% receiving antiretroviral therapy, which dramatically reduces viral replication, improves immune status and decreases risk of transmission. These results could be jeopardized by emergence of HIV-1 drug resistance. In 2009, a test for HIV-1 genotypic resistance was introduced in routine clinical practice in Cuba. OBJECTIVE Investigate antiretroviral resistance and its relation to subtype distribution in HIV-1 treatment-naïve and previously treated patients in Cuba. METHODS Resistance and HIV-1 subtype distribution were determined in 342 antiretroviral treatment-naïve patients and 584 previously treated for HIV-1 whose blood specimens were sent to the Pedro Kourí Tropical Medicine Institute during 2009-2014. Transmitted drug resistance was determined using the Calibrated Population Resistance Tool v.6. Drug resistance analysis was conducted using the algorithm Rega v9.1.0. RESULTS Prevalence of transmitted drug resistance was 11.4%, and 41% of mutated viruses exhibited dual-class resistance to nucleoside reverse transcriptase inhibitor and non-nucleoside reverse transcriptase inhibitor. Overall, 84.9% of patients had ≥1 resistance mutation, 80% had ≥1 nucleoside reverse transcriptase inhibitor mutation, 71.4% had ≥1 non-nucleoside reverse transcriptase inhibitor mutation and 31.7% had ≥1 protease inhibitor mutation. K65R and K101E mutations were significantly more frequent in subtype C, L210W in CRF19_cpx, and M47V/I in CRF BGs (20, 23, 24). Full class resistance to nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, protease inhibitors and multidrug resistance were detected in 21.2%, 32.4%, 8% and 4.1% of patients, respectively. Average percentage resistance to nucleoside reverse transcriptase inhibitor, protease inhibitor, full class resistance to nucleoside reverse transcriptase inhibitor, protease inhibitor and multidrug resistance increased in patients failing two or more regimens. Nevertheless, after 2011, a declining trend was observed in the frequency of multidrug resistance and full class resistance to nucleoside reverse transcriptase inhibitors and protease inhibitors. CONCLUSIONS Detected levels of transmitted drug resistance highlight the need for a national surveillance study in treatment-naïve patients. Resistance prevalence is high in previously treated patients but appears to be decreasing over time. The frequency of resistance mutations in recombinant forms of HIV in Cuba needs further study. KEYWORDS Antiretroviral therapy, highly active antiretroviral therapy, HIV, anti-HIV agents, drug resistance, multiple drug resistance, Cuba.