Seroprevalence and Genotype Diversity of Hepatitis C Virus in the Caribbean-A Review.

Hepatitis C (HCV) continues to present a global public health challenge, with no vaccine available for prevention. Despite the availability of direct-acting antivirals (DAAs) to cure HCV, it remains prevalent in many regions including the Caribbean. As efforts are made to eliminate HCV from the region, existing barriers, such as the high cost of DAAs and lack of an established database of HCV cases within the Caribbean, must be addressed. This review seeks to assess epidemiologic trends (seroprevalence and genotypic diversity) of HCV in the Caribbean and identify gaps in surveillance of the disease. The literature for the period 1 January 2005 to October 2022 was reviewed to gather country-specific data on HCV across the Caribbean. References were identified through indexed journals accessed through established databases using the following keywords: Caribbean, genotype distribution, and general epidemiologic characteristics. The usage pattern of HCV drugs was determined from information obtained from pharmacists across the Caribbean including Jamaica. The prevalence of HCV in the Caribbean was 1.5%; the region should therefore be considered an area of moderate HCV prevalence. The prevalence of HCV among intravenous drug users (21.9-58.8%), persons living with HIV/AIDS (0.8 to 58.5%), prisoners (32.8-64%), and men who have sex with men (MSM) (0.8-6.9%) was generally higher than in the general population (0.8-2.3%). Genotype 1 (83%) was most prevalent followed by genotypes 2 (7.2%) and 3 (2.1%), respectively. Less than 50% of countries in the Caribbean have reliable or well-curated surveillance data on HCV. Drugs currently being used for treatment of HCV infections across the Caribbean include Epclusa (sofosbuvir/velpatasvir) and Harvoni (ledipasvir/sofosbuvir). Some of these drugs are only available in the private sector and are sourced externally whenever needed. While trends point to a potentially higher prevalence of HCV, it will require well-designed random surveys to obtain better estimates of the infection seroprevalence, supported by strong public health laboratory systems. DAAs that are pan-genotypic should translate into treatments that are affordable, accessible, and available to improve cure rates and reduce the HCV burden in the population.

The multifaceted genomic history of Ashaninka from Amazonian Peru.

Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.

Prevalence of SARS-CoV-2 antibodies after the Omicron surge, Kingston, Jamaica, 2022.

A cross-sectional SARS-CoV-2 serosurvey was conducted after the Omicron surge in Jamaica using 1,540 samples collected during March - May 2022 from persons attending antenatal, STI and non-communicable diseases clinics in Kingston, Jamaica. SARS-CoV-2 spike receptor binding domain (RBD) and/or nucleocapsid IgG antibodies were detected for 88.4% of the study population, with 77.0% showing evidence of previous SARS-CoV-2 infection. Of persons previously infected with SARS-CoV-2 and/or with COVID-19 vaccination, 9.6% were negative for spike RBD IgG, most of which were unvaccinated previously infected persons. Amongst unvaccinated previously infected people, age was associated with testing spike RBD IgG negative. When considering all samples, median spike RBD IgG levels were 131.6 BAU/mL for unvaccinated persons with serological evidence of past infection, 90.3 BAU/mL for vaccinated persons without serological evidence of past infection, and 896.1 BAU/mL for vaccinated persons with serological evidence of past infection. Our study of the first reported SARS-CoV-2 serosurvey in Jamaica shows extensive SARS-CoV-2 population immunity, identifies a substantial portion of the population lacking spike RBD IgG, and provides additional evidence for increasing COVID-19 vaccine coverage in Jamaica.

Genomic evidence for ancient human migration routes along South America's Atlantic coast.

An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.

Prevalence of SARS-CoV-2 Antibodies after the Omicron Surge, Kingston, Jamaica, 2022.

A cross-sectional SARS-CoV-2 serosurvey was conducted after the Omicron surge in Jamaica using 1,540 samples collected during March â€" May 2022 from persons attending antenatal, STI and non-communicable diseases clinics in Kingston, Jamaica. SARS-CoV-2 spike receptor binding domain (RBD) and/or nucleocapsid IgG antibodies were detected for 88.4% of the study population, with 77.0% showing evidence of previous SARS-CoV-2 infection. Of persons previously infected with SARS-CoV-2 and/or with COVID-19 vaccination, 9.6% were negative for spike RBD IgG, most of which were unvaccinated previously infected persons. Amongst unvaccinated previously infected people, age was associated with testing spike RBD IgG negative. When considering all samples, median spike RBD IgG levels were 131.6 BAU/mL for unvaccinated persons with serological evidence of past infection, 90.3 BAU/mL for vaccinated persons without serological evidence of past infection, and 896.1 BAU/mL for vaccinated persons with serological evidence of past infection. Our study of the first reported SARS-CoV-2 serosurvey in Jamaica shows extensive SARS-CoV-2 population immunity, identifies a substantial portion of the population lacking spike RBD IgG, and provides additional evidence for increasing COVID-19 vaccine coverage in Jamaica.

The genomic prehistory of the Indigenous peoples of Uruguay.

The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former Indigenous ethnic diversity into the narrative of a singular people that all but died out. Here, we present the first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, from an archaeological site in eastern Uruguay that dates from 2,000 years before present. We find a surprising connection to ancient individuals from Panama and eastern Brazil, but not to modern Amazonians. This result may be indicative of a migration route into South America that may have occurred along the Atlantic coast. We also find a distinct ancestry previously undetected in South America. Though this work begins to piece together some of the demographic nuance of the region, the sequencing of ancient individuals from across Uruguay is needed to better understand the ancient prehistory and genetic diversity that existed before European contact, thereby helping to rebuild the history of the Indigenous population of what is now Uruguay.

Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics.

The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.

Successful extraction and PCR amplification of Giardia DNA from formalin-fixed stool samples.

Extracting genomic DNA of pathogenic agents from formalin-fixed specimens is inherently difficult. Storage of samples in formalin results in nucleic acid cross-linking and DNA fragmentation. In this study, DNA was extracted from 45 Giardia-positive stool samples stored in formalin and subjected to PCR amplification targeting the triose phosphate isomerase (tpi), beta gardin (bg) and glutamate dehydrogenase (gdh) genes. Samples were rehydrated by using a descending alcohol series before DNA extraction using a commercial kit. This was followed by EDTA-mediated inhibition of DNase activity and prolonged treatment with proteinase K to digest contaminating proteins. DNA was amplified at rates of 64.4% (29/45) at the tpi, 40% (18/45) at the bg and 20% (9/45) at the gdh loci as seen on nested PCR. DNA quality was subsequently tested in a genotyping experiment which produced high-quality sequences at the tpi (41.2%; 12/29) bg (50%; 9/18), and gdh (22.2%; 2/9) loci and enabled differentiation of Giardia strains at the subtype level. The modified extraction protocol was effective at removing inhibitors and reversing cross-linking of DNA. However, PCR amplification was limited to short fragments of DNA which resulted in highest success rate on amplification of the shortest (334 bp) gene fragment tested.

Molecular epidemiology of human papillomavirus genotypes in oral rinses from HIV-positive and HIV-negative Jamaican patients.

AIM: Human papillomavirus (HPV) has been reported to be associated with oral and oropharyngeal cancer. However, little information is available about the epidemiology of oral HPV infection in Jamaica. The purpose of the present study was to assess the prevalence of oral HPV strains using the oral rinse method in HIV and non-HIV Jamaican patients, as well as to determine the association of HPV with sexual practices, smoking, and alcohol use. METHODS: A cross-sectional study was conducted on patients attending The University of the West Indies Mona Dental Polyclinic and the Centre for HIV/AIDS Research and Education Services. Salivary samples were tested through molecular analysis for 37 HPV genotypes using the linear array HPV genotyping test. A survey questionnaire was used to obtain demographic details, smoking history, alcohol practice, sexual practice, and history of HPV testing. RESULTS: The HPV prevalence was 8.65% in 18-64 y olds (N = 104), with a slight female predilection (55%). No high-risk HPV types were found. HPV-84 was the most common type in both HIV and non-HIV patients; 66.7% of HPV-positive participants reported that they had six or more lifetime sexual partners. CONCLUSION: The prevalence of oral HPV was similar to that in other countries. No statistically-significant relationship was observed between the prevalence of HPV and either the number of sexual partners, smoking, or alcohol history. A nationwide study on oral HPV detection might be helpful in developing a HPV vaccination policy in Jamaica.

Evaluation of OneStep Dengue NS1 RapiDip™ InstaTest and OneStep Dengue Fever IgG/IgM RapiCard™ InstaTest during the course of a dengue type 1 epidemic.

We determined the diagnostic performance of the OneStep NS1 and the OneStep IgG/IgM RDT kits against a panel of samples which comprised of 174 dengue positive and 165 dengue negative sera characterized by three reference enzyme-linked immunosorbent assays (ELISAs). The diagnostic sensitivities of the OneStep kits for the detection of individual biomarkers of NS1, IgM and IgG were 90% (95% CI: 82.1-94.7), 32.4% (95% CI: 24.8-40.8) and 44.4% (95% CI: 38.2-50.7), respectively. The combination of the OneStep IgG/IgM kit with the OneStep NS1 kit demonstrated significantly higher sensitivities for the combined NS1/IgM (96.8%; 95% CI: 90.9-99.3) and NS1/IgM/IgG (99.5%; 95% CI: 97.1-99.9)(P<0.001). In conclusion, the OneStep NS1 kit has high sensitivity and specificity and is highly recommended for use. The low sensitivities for IgG (44.4%) and for IgM (32.4%) of the OneStep IgG/IgM kit when used alone suggest it is best used in combination with the OneStep NS1 kit to enhance its overall diagnostic performance.

Molecular epidemiology and multilocus sequence analysis of potentially zoonotic Giardia spp. from humans and dogs in Jamaica.

Giardia spp. are the causative agents of intestinal infections in a wide variety of mammals including humans and companion animals. Dogs may be reservoirs of zoonotic Giardia spp.; however, the potential for transmission between dogs and humans in Jamaica has not been studied. Conventional PCR was used to screen 285 human and 225 dog stool samples for Giardia targeting the SSU rDNA gene followed by multilocus sequencing of the triosephosphate isomerase (tpi), glutamate dehydrogenase (gdh), and ß-giardin (bg) genes. Prevalence of human infections based on PCR was 6.7 % (19/285) and canine infections 19.6 % (44/225). Nested PCR conducted on all 63 positive samples revealed the exclusive presence of assemblage A in both humans and dogs. Sub-assemblage A-II was responsible for 79.0 % (15/19) and 70.5 % (31/44) of the infections in humans and dogs, respectively, while sub-assemblage A-I was identified at a rate of 15.8 % (3/19) and 29.5 % (13/44) in humans and dogs, respectively. The predominance of a single circulating assemblage among both humans and dogs in Jamaica suggests possible zoonotic transmission of Giardia infections.

Vannellid Species Isolated from Freshwater Source in a Park in Jamaica, West Indies.

Free-living amoebae (FLA) occupy a wide range of freshwater, marine, and soil habitats, and are opportunistic pathogens in human beings. While Acanthamoeba spp., Naegleria fowleri, and Balamuthia mandrillaris are well-known opportunistic organisms, Vannella epipetala is nonpathogenic. Sediments were collected from a freshwater source from a park in Jamaica to investigate the presence of FLA. Acanthamoeba and Naegleria spp. were not recovered; however, a Vannellid species identified by microscopy and PCR analysis as V. epipetala was isolated. These nonpathogens pose a threat to human beings as they may act as Trojan horses for microsporidian parasites and other pathogens, thereby facilitating their transmission to human beings.

A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d.

Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete mitogenomes were studied, additional substitutions were found in the coding region of the mitochondrial genome. Using a complete ancient mitogenome and three modern mitogenomes, we aim to clarify the ancestral state of subhaplogroup C1d3 and to better understand the peopling of the region of the Río de la Plata basin, as well as of the builders of the mounds from which the ancient individuals were recovered. The ancient mitogenome, belonging to a female dated to 1,610±46 years before present, was identical to the mitogenome of one of the modern individuals. All individuals share the mutations defining subhaplogroup C1d3. We estimated an age of 8,974 (5,748-12,261) years for the most recent common ancestor of C1d3, in agreement with the initial peopling of the geographic region. No individuals belonging to the defined lineage were found outside of Uruguay, which raises questions regarding the mobility of the prehistoric inhabitants of the country. Moreover, the present study shows the continuity of Native lineages over at least 6,000 years.

Isolation and molecular characterization of Acanthamoeba genotypes in recreational and domestic water sources from Jamaica, West Indies.

Free living amoebae (FLA) are amphizoic protozoa that are ubiquitous in nature. Infection with FLA may result in neurological, ocular and skin infections. Exposure to Acanthamoeba occurs frequently through water contact and knowledge of the presence of the organisms in water sources is important in understanding transmission dynamics. The distribution of Acanthamoeba was studied in recreational and domestic water samples collected from across Jamaica. Morphological assessment and polymerase chain reaction revealed Acanthamoeba spp. isolates in 50.6% (42/83) and 17.3% (14/81) of recreational and domestic water, respectively. Sequencing of the DF3 region of the 18S rDNA resulted in the identification of genotypes T3, T4, T5, T10 and T11 corresponding to Acanthamoeba spp: A. griffini, A. triangularis, A. lenticulata, A. culbertsoni and A. hatchetti. Moreover, T4 was the most frequently isolated genotype in both recreational and domestic water. Thermotolerance and osmotolerance assays indicated that most isolates were potentially pathogenic. This is the first report of T3 and T10 genotypes in the Caribbean and the first report of these Acanthamoeba spp. in Jamaican waters. The study shows that there is potential risk of infection to contact wearers who practise poor lens care. Further, Acanthamoeba should be considered as a cause of neurological infections in Jamaica.

The performance of the SD BIOLINE Dengue DUO® rapid immunochromatographic test kit for the detection of NS1 antigen, IgM and IgG antibodies during a dengue type 1 epidemic in Jamaica.

BACKGROUND: Dengue is an important mosquito-borne viral infection that affects millions of persons worldwide. Early diagnosis is necessary to effect appropriate management and decrease mortality. Immunochromatographic tests are advantageous in producing dengue test results within 30 min but these results should be sensitive and specific. In this study we evaluated the diagnostic performance of the SD BIOLINE Dengue DUO® rapid immunochromatographic test kit. A panel of 309 dengue and 30 non-dengue single serum samples characterized by using reference enzyme-linked immunosorbent assays (ELISAs) was used. These samples were received in the virology laboratory for routine testing during a dengue type 1 outbreak between October to December, 2012. RESULTS: The overall diagnostic sensitivities of the SD BIOLINE Dengue DUO® rapid testfor IgM, IgG and NSI were 49.3% (95% CI: 41.3-57.4), 39.1% (95% CI: 33.3-45.2) and 90% (95% CI: 82.1-94.7), respectively. The IgM and IgG detection rates were significantly lower than that of the NSI (p < 0.001). However the combination of the IgM detection with NS1 detection or both NS1 and IgG resulted in a significant (p < 0.001) increase in sensitivity to 97.5% (95 % CI: 92.9-99.2) and 98.9% (95 % CI: 96.0-99.7), respectively. These higher sensitivities were achieved without any decrease in specificities. CONCLUSIONS: This study revealed that combining two or more parameters of the SD BIOLINE Dengue DUO® rapid kit significantly improved the sensitivity of diagnosis of dengue virus infection and supports its usefulness in the Jamaican setting.

Isolation and genotyping of acanthamoeba strains from soil sources from Jamaica, West Indies.

Acanthamoeba spp. are opportunistic pathogens that are ubiquitous in nature. Many species of this genus are responsible for a fatal encephalitis and keratitis in humans and other animals. Seventy-two soil samples were collected from the parishes across Jamaica and assessed for the presence of Acanthamoeba spp. Cultivation was carried out on non-nutrient agar plates seeded with heat killed Escherichia coli. PCR and sequencing of the DF3 region were carried out in order to genotype the isolated strains of Acanthamoeba. Thermotolerance and osmotolerance assays were utilized to investigate the pathogenic potential of the Acanthamoeba isolates. Acanthamoeba spp. was isolated from 63.9% of soil samples. Sequencing of the DF3 region of the 18S rDNA resulted in the identification of genotypes T4, T5, and T11. T4 genotype was most frequently isolated. Most isolates were thermotolerant or both thermotolerant and osmotolerant, indicating that they may present the potential to cause disease in humans and other animals.

Severe eosinophilic meningitis owing to Angiostrongylus cantonensis in young Jamaican children: case report and literature review.

Eosinophilic meningitis caused by Angiostrongylus cantonensis is an endemic and emerging disease that affects adults and children in Jamaica. Most cases resolve without sequelae, but young children are at high risk of neurological damage and death. Treatment with corticosteroids and albendazole is considered safe for adults and children, but protocols for its use in children have not been established. A 19-month-old infant with permanent neurological sequlae caused by Angiostrongylus cantonensis meningitis is reported, and five other Jamaican cases are summarized. A review of the literature of children with permanent neurological sequlae and death is presented. Children <5 years (especially <2) were at increased risk of incomplete recovery and death if they presented with bulbar signs, flaccid paresis and coma. None of the severe or fatal cases received early intervention with anthelminthics, and disease progression was not altered with corticosteroids. In view of the pathophysiology, necropsy reports and animal studies, it seems that the early use of larvicidals may change the course of severe presentations.

Leptospirosis and malaria as causes of febrile illness during a dengue epidemic in Jamaica.

BACKGROUND: Epidemics of febrile illnesses are often associated with rainy seasons in the tropics. During 2007-2008 an epidemic of dengue was identified in Jamaica based on serological testing of sera. METHODS: A subset of 3165 of 5400 sera submitted for dengue analysis was tested for Leptospira IgM and malaria IgG using ELISA to determine their role in causing epidemic fever. FINDINGS: Seropositivity for dengue, leptospirosis, and malaria were 38·4 and 6·0 and 6·5%, respectively, indicative of three concurrent epidemics. Mixed exposure to all three diseases was rare (0·1%), as were mixed dengue/malaria (2·4%); dengue/leptospirosis (1·6%), and leptospirosis/malaria (0·03%) exposure. Exposure to dengue and malaria appeared to occur most frequently among children while leptospirosis was more common among adults. CONCLUSION: While serological diagnosis definitively established that dengue was the main cause of the epidemic febrile illness, the data suggested that there may be other causes of fever, which may occur simultaneously. Consequently, leptospirosis and malaria should be considered as causes of fever during epidemics of dengue in endemic areas.

Trichosporon asahii among intensive care unit patients at a medical center in Jamaica.

We investigated an increase in Trichosporon asahii isolates among inpatients. We identified 63 cases; 4 involved disseminated disease. Trichosporon species was recovered from equipment cleaning rooms, washbasins, and fomites, which suggests transmission through washbasins. Patient washbasins should be single-patient use only; adherence to appropriate hospital disinfection guidelines was recommended.

Informed consent from patients participating in medical education: a survey from a university hospital in Jamaica.

BACKGROUND: Medical students at the University of the West Indies receive clinical training by passing through a series of hospital rotations at the University Hospital of the West Indies (UHWI). Many of these patients are unaware that medical students may be involved in their care. We performed this study to determine patient awareness and their willingness to participate in research and teaching activities. FINDINGS: All consecutive patients admitted to the UHWI between May 1, 2006 and May 29, 2006 who required elective or emergency surgical procedures were prospectively identified These patients were interviewed using a standardised pre-tested questionnaire about their knowledge and willingness to have medical students participate in the delivery of their hospital care. Data was analyzed using SPSS Version 12.0. There were 83 (39.5%) males and 127 (60.5%) females interviewed. The patients were unaware of the grade of the medical professional performing their interview/examination at admission in 157 (74.8%) cases or the grade of medical professional performing their operations in 101 (48.1%) cases. Only 14 (6.7%) patients were specifically asked to allow medical students to be present during their clinical evaluation and care. When specifically asked, 1 patient declined. Had they been asked, 196 (93.3%) patients would have voluntarily allowed medical student involvement. Only 90 (42.9%) patients were made aware that they were admitted to an academic centre with research interests. Only 6 (6.7%) patients declined. Had they been asked, 84 (93.3%) patients would be willing to participate in teaching or research projects. CONCLUSIONS: As medical educators, we are responsible to adhere to ethical and legal guidelines when we interact with patients. It is apparent that there is urgent need for policy development at the UWI to guide clinicians and students on their interactions with patients.