Estimating prevalence and modelling correlates of HIV test positivity among female sex workers, men who have sex with men, people who inject drugs, transgender people and prison inmates in Sierra Leone, 2021.

Key populations (KPs) are particularly vulnerable to HIV infection and efforts to prevent HIV infections among KPs have been less successful, largely due to existing laws and legislation that classify the groups as illegal. Understanding the HIV infection pathway and the burden of HIV infection among Female Sex Workers (FSWs), Transgender people (TG), Men who have sex with Men (MSM), People who Inject Drugs (PWID), and Prison Inmates (PIs) is critical to combatting the HIV epidemic globally. This study aims to estimate HIV prevalence and model the risk factors of HIV positivity rate among the aforementioned KPs in Sierra Leone. This study used Time Location Sampling, Respondent Driven Sampling (RDS), and Conventional cluster Sampling designs to generate a representative sample of FSWs, MSM, TG, PI, and PWID. HIV prevalence and the corresponding 95% confidence intervals among each KP were estimated by adjusting for sampling weight using the logit-transformed confidence intervals. To determine correlates of HIV test positivity among KPs, a multivariable modified Poisson regression model that adjusts for RDS survey weights was used and sensitivity analysis was conducted using a multivariable logistic regression model with cluster robust standard errors. The prevalence of HIV among FSWs in the six regional headquarter towns was estimated to be 11.8% (95% CI: 7.9-17.1); MSM was 3.4% [95% CI: 1.9-5.8]; TGs was 4.2% (95% CI: 2.9-6.1); PWIDs was 4.2% (95% CI: 2.7-6.4) and PI was 3.7% (95% CI: 1.4-9.6). The correlates of HIV test positivity among KPs and PIs include HIV-related knowledge, marital status, district, income, age and sex of KP, level of education, alcohol intake, injecting drugs, and use of lubricants. HIV prevalence is relatively high among FSWs, MSMs, PWID, and TGs as compared to the previous estimate of the general population. There is a need to scale up and strengthen evidence-based HIV prevention interventions such Pre-Exposure Prophylaxis and needle and syringe exchange programmes targeting KPs, including prison inmates. Government must scale up both non-clinical and clinical routine HIV and STI testing and counseling services at the correctional center and drop-in centers for KPs screening/testing, and ensure that services are responsive to the needs of KP.

Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa.

BACKGROUND: West Africa has recorded a relatively higher proportion of asymptomatic coronavirus disease 2019 (COVID-19) cases than the rest of the world, and West Africa-specific host factors could play a role in this discrepancy. Here, we assessed the association between COVID-19 severity among Ghanaians with their immune profiles and ABO blood groups. METHODS: Plasma samples were obtained from Ghanaians PCR-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive individuals. The participants were categorized into symptomatic and asymptomatic cases. Cytokine profiling and antibody quantification were performed using Luminex™ multiplex assay whereas antigen-driven agglutination assay was used to assess the ABO blood groups. Immune profile levels between symptomatic and asymptomatic groups were compared using the two-tailed Mann-Whitney U test. Multiple comparisons of cytokine levels among and between days were tested using Kruskal-Wallis with Dunn's post hoc test. Correlations within ABO blood grouping (O's and non-O's) and between cytokines were determined using Spearman correlations. Logistic regression analysis was performed to assess the association of various cytokines with asymptomatic phenotype. RESULTS: There was a trend linking blood group O to reduced disease severity, but this association was not statistically significant. Generally, symptomatic patients displayed significantly (p < 0.05) higher cytokine levels compared to asymptomatic cases with exception of Eotaxin, which was positively associated with asymptomatic cases. There were also significant (p < 0.05) associations between other immune markers (IL-6, IL-8 and IL-1Ra) and disease severity. Cytokines' clustering patterns differ between symptomatic and asymptomatic cases. We observed a steady decrease in the concentration of most cytokines over time, while anti-SARS-CoV-2 antibody levels were stable for at least a month, regardless of the COVID-19 status. CONCLUSIONS: The findings suggest that genetic background and pre-existing immune response patterns may in part shape the nature of the symptomatic response against COVID-19 in a West African population. This study offers clear directions to be explored further in larger studies.

Core encoding sequences of Hepatitis C virus in Ghanaian blood donors are predominantly mosaics of different genotype 2 strains and cannot distinguish subtypes.

BACKGROUND: Distribution of Hepatitis C virus (HCV) genotypes varies significantly worldwide. Genomic diversity between genotypes has implications for treatment, vaccine development and optimal design of HCV diagnostic assays. Molecular characterization of HCV in different geographical areas is therefore very essential for management and public health control of HCV infection. This study investigated the molecular epidemiology and characteristics of HCV genotypes in healthy individuals in Accra, Ghana. METHODS: An experimental study was carried out on blood samples obtained from voluntary blood donors. Two hundred samples were initially screened for HCV antibodies and infection was confirmed by RNA detection through RT-PCR of the 5'-untranslated region (5'UTR). The core gene sequences were analysed for HCV genotype determination by genotype-specific PCR; and then by cloning and direct sequencing followed by phylogenetic analysis. The sequences were further analysed in detail by similarity plotting. RESULTS: Molecular diagnosis confirmed the presence of HCV RNA in 2 out of 200 (1%) blood donors. Initial genotyping by genotype-specific PCR identified all two infections as subtypes 2a and 2b of genotype 2. Extensive evolutionary and genetic analyses indicated two epidemiological profiles. First, phylogenetic tree topologies clearly showed that, collectively, the core sequences of the Ghanaian HCV isolates belong to a single, distinct genetic group within HCV genotype 2 cluster, with high genetic similarity and rapid sequence variation in a single individual. Second, the sequences are mosaics comprising 2e and other genotype 2 subtype fragments. The analyses underscore a unique and complex HCV genotype 2 core sequence profile of the Ghanaian isolates. CONCLUSIONS: Analysis of HCV core encoding sequences from Ghanaian blood donors in Accra confirmed predominance of genotype 2 HCV among healthy individuals. However, the isolates could not be classified into subtypes, possibly due to their complex sequence pattern that might suggest high mutability of the prevailing genotype. The core region of Ghanaian HCV therefore may not be suitable for distinguishing subtypes. These findings extend those from previous studies and thus underscore the need to search for subtype-informative region of Ghanaian HCV to elucidate the genetic diversity and factors determining outcome of HCV infections in Ghana.

Emergence of HIV-1 drug resistance mutations in mothers on treatment with a history of prophylaxis in Ghana.

BACKGROUND: Antiretrovirals have been available in Ghana since 2003 for HIV-1 positive pregnant women for prevention of mother-to-child transmission (PMTCT). Suboptimal responses to treatment observed post-PMTCT interventions necessitated the need to investigate the profile of viral mutations generated. This study investigated HIV-1 drug resistance profiles in mothers in selected centres in Ghana on treatment with a history of prophylaxis. METHODS: Genotypic Drug Resistance Testing for HIV-1 was carried out. Subtyping was done by phylogenetic analysis and Stanford HIV Database programme was used for drug resistance analysis and interpretation. To compare the significance between the different groups and the emergence of drug resistance mutations, p values were used. RESULTS: Participants who had prophylaxis before treatment, those who had treatment without prophylaxis and those yet to initiate PMTCT showed 32% (8), 5% (3) and 15% (4) HIV-1 drug resistance associated mutations respectively. The differences were significant with p value < 0.05. Resistance Associated Mutations (RAMs) were seen in 14 participants (35%) to nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). The most common NRTI mutation found was M184 V; K103 N and A98G were the most common NNRTI mutations seen. Thymidine Analogue Mutations (TAMs) such as M41 L, K70R and T215Y were found in all the groups; the most common of the TAMs found were M41 L and T215Y. Majority of the subtypes were CRF02_AG (82%). CONCLUSION: In Ghana initiation of uninterrupted treatment upon diagnosis, coupled with drug resistance testing, would produce a better treatment outcome for HIV-1 positive pregnant women.

Migration, sexual networks, and HIV in Agbogbloshie, Ghana.

BACKGROUND: HIV is spread through structured sexual networks, which are influenced by migration patterns, but network-oriented studies of mobility and HIV risk behavior have been limited. OBJECTIVE: We present a comprehensive description and initial results from our Migration & HIV in Ghana (MHG) study in Agbogbloshie, an urban slum area within Accra, Ghana. METHODS: The MHG study was a population-based cross-sectional study of adults aged 18-49 in Agbogbloshie in 2012. We used a one-year retrospective relationship history calendar to collect egocentric network data on sexual partners as well as migration and short-term mobility, and tested for prevalent HIV-1/2 infection. RESULTS: HIV prevalence was 5.5%, with prevalence among women (7.2%) over twice that of men (2.8%). Three-quarters of residents were born outside the Greater Accra region, but had lived in Agbogbloshie an average of 10.7 years. Only 7% had moved housing structures within the past year. However, short-term mobility was common. Residents had an average of 7.3 overnight trips in the last year, with women reporting more travel than men. Thirty-seven percent of men and 9% of women reported more than one sexual partner in the last year. CONCLUSIONS: Population-based surveys of migration and sexual risk behavior using relationship history calendars in low-resource settings can produce high quality data. Residents in Agbogbloshie are disproportionately affected by HIV, and have high levels of short-term mobility. HIV prevention interventions targeted to highly mobile populations in high prevalence settings may have far-reaching and long-term implications.

Pre-vaccination seroprevalence of SARS-CoV-2 antibodies in the Volta Region, Ghana.

Objectives: Before administration of the first dose of the AstraZeneca 2019 SARS-CoV-2 vaccine to selected prioritized groups in the Volta regional capital of Ghana, we determined the pre-vaccination status of prospective recipients and established the baseline exposure status 1 year after the first case was reported. Methods: After informed consent, blood samples were collected for the detection of SARS-CoV-2 immunoglobulin (Ig) M/IgG antibodies using rapid diagnostic test kits. A total of 409 individuals (mean age 27 years) consented and participated in the study, comprising 70% students and others were health staff and educators who presented themselves for vaccination. Results: The overall exposure rate of SARS-CoV-2 was 12.7% (95% confidence interval [CI] 9.6-16.3). The prevalence of SARS-CoV-2 IgM and IgG were 4.2% (95% CI 2.4-6.6) and 5.6% (95% CI 3.6-8.3), respectively. IgM and IgG were detected in 2.9% (95% CI 1.5-5.1) of the respondents. The exposure rates were higher in participants over 40 years old (15.5%). Participants without a history of COVID-19-like symptoms had an exposure rate of 13.0% and those without any chronic diseases was 13.2%. Conclusion: Pre-vaccination exposure was relatively low and underscored the need for vaccination i to increase protection in communities and disease outcomes.

Longitudinal analysis of microbiome composition in Ghanaians living with HIV-1.

Human immunodeficiency virus (HIV) 1 infection is known to cause gut microbiota dysbiosis. Among the causes is the direct infection of HIV-1 in gut-resident CD4+ T cells, causing a cascade of phenomena resulting in the instability of the gut mucosa. The effect of HIV infection on gut microbiome dysbiosis remains unresolved despite antiretroviral therapy. Here, we show the results of a longitudinal study of microbiome analysis of people living with HIV (PLWH). We contrasted the diversity and composition of the microbiome of patients with HIV at the first and second time points (baseline_case and six months later follow-up_case, respectively) with those of healthy individuals (baseline_control). We found that despite low diversity indices in the follow-up_case, the abundance of some genera was recovered but not completely, similar to baseline_control. Some genera were consistently in high abundance in PLWH. Furthermore, we found that the CD4+ T-cell count and soluble CD14 level were significantly related to high and low diversity indices, respectively. We also found that the abundance of some genera was highly correlated with clinical features, especially with antiretroviral duration. This includes genera known to be correlated with worse HIV-1 progression (Achromobacter and Stenotrophomonas) and a genus associated with gut protection (Akkermansia). The fact that a protector of the gut and genera linked to a worse progression of HIV-1 are both enriched may signify that despite the improvement of clinical features, the gut mucosa remains compromised.

Corrigendum: Decreased influenza activity during the COVID-19 pandemic in Ghana, 2020.

[This corrects the article DOI: 10.3389/fpubh.2023.1290553.].

Influenza surveillance in 15 countries in Africa, 2006-2010.

BACKGROUND: In response to the potential threat of an influenza pandemic, several international institutions and governments, in partnership with African countries, invested in the development of epidemiologic and laboratory influenza surveillance capacity in Africa and the African Network of Influenza Surveillance and Epidemiology (ANISE) was formed. METHODS: We used a standardized form to collect information on influenza surveillance system characteristics, the number and percent of influenza-positive patients with influenza-like illness (ILI), or severe acute respiratory infection (SARI) and virologic data from countries participating in ANISE. RESULTS: Between 2006 and 2010, the number of ILI and SARI sites in 15 African countries increased from 21 to 127 and from 2 to 98, respectively. Children 0-4 years accounted for 48% of all ILI and SARI cases of which 22% and 10%, respectively, were positive for influenza. Influenza peaks were generally discernible in North and South Africa. Substantial cocirculation of influenza A and B occurred most years. CONCLUSIONS: Influenza is a major cause of respiratory illness in Africa, especially in children. Further strengthening influenza surveillance, along with conducting special studies on influenza burden, cost of illness, and role of other respiratory pathogens will help detect novel influenza viruses and inform and develop targeted influenza prevention policy decisions in the region.

Effect of antipyretics on performance of influenza surveillance in Ghana.

BACKGROUND: The World Health Organization's case definition for influenza-like illness (ILI) includes a measured temperature of ≥38°C. We conducted this study to assess the effect of antipyretics on performance of ILI surveillance in Ghana. METHODS: A cross-sectional study was conducted in two districts of Ghana from September 2013 to May 2014. We collected epidemiological data and respiratory specimens from an expanded ILI case definition, which included patients presenting to health facilities with measured temperature ≥38°C or reported fever (but afebrile at the time of evaluation), and cough, with onset in the last 10 days. Specimens were tested for influenza viruses by real time reverse-transcription polymerase chain reaction. RESULTS: Of 321 participants who met our expanded ILI case definition, 236 presented with temperature of <38°C but reported subjective fever. Of these, 17% (39/236) were positive for influenza virus; Of those with fever ≤38°C who took antipyretics, 21%(16/77) were positive for influenza, compared with 14%(23/159) of those who did not take antipyretics. The addition of subjective fever to the standard ILI case definition captured approximately an additional 57% influenza cases but also required testing of approximately four times as many patients. However, including those without fever on presentation that had taken antipyretics found an additional 23% of Influenza cases and only two times as much testing. CONCLUSION: Depending on the goals of surveillance (monitoring virus circulation or determining disease burden) and available resources, a more sensitive case definition including subjective fever and history of use of antipyretics may be warranted.

Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis.

BACKGROUND: Genomic surveillance of SARS-CoV-2 is crucial for monitoring the spread of COVID-19 and guiding public health decisions, but the capacity for SARS-CoV-2 testing and sequencing in Africa is low. We integrated SARS-CoV-2 surveillance into an existing influenza surveillance network with the aim of providing insights into SARS-CoV-2 transmission and genomics in Ghana. METHODS: In this molecular epidemiological analysis, which is part of a wider multifaceted prospective observational study, we collected national SARS-CoV-2 test data from 35 sites across 16 regions in Ghana from Sept 1, 2020, to Nov 30, 2021, via the Ghanaian integrated influenza and SARS-CoV-2 surveillance network. SARS-CoV-2-positive samples collected through this integrated national influenza surveillance network and from international travellers arriving in Accra were sequenced with Oxford Nanopore Technology sequencing and the ARTIC tiled amplicon method. The sequence lineages were typed with pangolin and the phylogenetic analysis was conducted with IQ-Tree2 and TreeTime. FINDINGS: During the study period, 5495 samples were submitted for diagnostic testing through the national influenza surveillance network (2121 [46·1%] of 4021 samples with complete demographic data were from female individuals and 2479 [53·9%] of 4021 samples were from male individuals). We also obtained 2289 samples from travellers who arrived in Accra and had a positive lateral flow test, of whom 1626 (71·0%, 95% CI 69·1-72·9) were confirmed to be SARS-CoV-2 positive. Co-circulation of influenza and SARS-CoV-2 in Ghana was detected, with increased cases of influenza in November, 2020, November, 2021, and January and June, 2021. In 4124 samples from individuals with influenza-like illness, SARS-CoV-2 was identified in 583 (14·1%, 95% CI 13·1-15·2) samples and influenza in 356 (8·6%, 7·8-9·5). Conversely, in 476 samples from individuals with of severe acute respiratory illness, SARS-CoV-2 was detected in 58 (12·2%, 9·5-15·5) samples and influenza in 95 (19·9%, 16·5-23·9). We detected four waves of SARS-CoV-2 infections in Ghana; each wave was driven by a different variant: B.1 and B.1.1 were the most prevalent lineages in wave 1, alpha (B.1.1.7) was responsible for wave 2, delta (B.1.617.2) and its sublineages (closely related to delta genomes from India) were responsible for wave 3, and omicron variants were responsible for wave 4. We detected omicron variants among 47 (32%) of 145 samples from travellers during the start of the omicron spread in Ghana (wave 4). INTERPRETATION: This study shows the value of repurposing existing influenza surveillance platforms to monitor SARS-CoV-2. Influenza continued to circulate in Ghana in 2020 and 2021, and remained a major cause of severe acute respiratory illness. We detected importations of SARS-CoV-2 variants into Ghana, including those that did or did not lead to onward community transmission. Investment in strengthening national influenza surveillance platforms in low-income and middle-income countries has potential for ongoing monitoring of SARS-CoV-2 and future pandemics. FUNDING: The EDCTP2 programme supported by the EU.

Decreased influenza activity during the COVID-19 pandemic in Ghana, 2020.

Introduction: The COVID-19 pandemic had a significant effect on influenza activity globally. In this study, we analyzed trends of influenza activity in 2020 during the COVID-19 pandemic in Ghana. Methods: This was a cross-sectional study using active prospective influenza surveillance data from 29 sentinel sites. At the sentinel sites, we enrolled patients presenting with symptoms based on the WHO case definition for influenza-like illness (ILI) and severe acute respiratory illness (SARI). Oro and nasopharyngeal swabs were collected from patients and tested for the presence of influenza viruses using specific primers and probes described by the US-CDC. The percentage of positivity for influenza between 2017-2019 and 2021 was compared to 2020. Using the test for proportions in STATA 17.0 we estimated the difference in influenza activities between two periods. Results and discussion: Influenza activity occurred in a single wave during the 2020 surveillance season into 2021, September 28 2020-March 7 2021 (week 40, 2020-week 9, 2021). Influenza activity in 2020 was significantly lower compared to previous years (2017- 2019, 2021). Influenza A (H3) was more commonly detected during the early part of the year (December 30, 2019-March 8, 2020), while influenza B Victoria was more commonly detected toward the end of the year (September 28-December 28). In Ghana, adherence to the community mitigation strategies introduced to reduce transmission of SARS-CoV-2, which affected the transmission of other infectious diseases, may have also impacted the transmission of influenza. To the best of our knowledge, this is the first study in Ghana to describe the effect of the COVID-19 pandemic on influenza activity. The continuation and strict adherence to the non-pharmaceutical interventions at the community level can help reduce influenza transmission in subsequent seasons.

Surveillance for potentially zoonotic viruses in rodent and bat populations and behavioral risk in an agricultural settlement in Ghana.

BACKGROUND: In Ghana, the conversion of land to agriculture, especially across the vegetative belt has resulted in fragmented forest landscapes with increased interactions among humans, domestic animals, and wildlife. METHODS: We investigated viruses in bats and rodents, key reservoir hosts for zoonotic viral pathogens, in a small agricultural community in the vegetation belt of Ghana. We also administered questionnaires among the local community members to learn more about people's awareness and perceptions of zoonotic disease risks and the environmental factors and types of activities in which they engage that might influence pathogen transmission from wildlife. RESULTS: Our study detected the RNA from paramyxoviruses and coronaviruses in rodents and bats, including sequences from novel viruses with unknown zoonotic potential. Samples collected from Epomophorus gambianus bats were significantly more likely to be positive for coronavirus RNA during the rainy season, when higher numbers of young susceptible individuals are present in the population. Almost all community members who responded to the questionnaire reported contact with wildlife, especially bats, rodents, and non-human primates in and around their homes and in the agricultural fields. Over half of the respondents were not aware or did not perceive any zoonotic disease risks associated with close contact with animals, such as harvesting and processing animals for food. To address gaps in awareness and mitigation strategies for pathogen transmission risks, we organized community education campaigns using risk reduction and outreach tools focused around living safely with bats and rodents. CONCLUSIONS: These findings expand our knowledge of the viruses circulating in bats and rodents in Ghana and of the beliefs, perceptions, and practices that put community members at risk of zoonotic virus spillover through direct and indirect contact with bats and rodents. This study also highlights the importance of community engagement in research and interventions focused on mitigating risk and living safely with wildlife.

Assessment of the Proportion of Recent HIV-1 Infections in Newly-Diagnosed Cases in Ghana.

Accurate monitoring of epidemics is a key strategy for controlling human immunodeficiency virus type-1 (HIV-1) infection. To delineate the characteristics of newly diagnosed cases of HIV-1 infection, we assessed the proportion of recent HIV-1 infections using a recent infection-testing algorithm (RITA). In 2015, 248 cases were newly diagnosed with HIV infection at the Regional Hospital Koforidua, Ghana. Of these, 234 cases (94.4%) were infected with HIV-1 only, four (1.6%) were infected with HIV-2 only, and 10 (4.0%) were co-infected with HIV-1 and HIV-2. All HIV-1 single-seropositive samples were used in the HIV-1 LAg avidity assay for RITA. Our analysis revealed that 18 cases (7.7%) were recently infected, indicating that early diagnosis was not achieved in Ghana. This is the first report to assess the proportion of recent infections in Ghana using a biomarker approach. The accumulation of these data will contribute to the accurate estimation of HIV-1 incidence and prevalence in Ghana.

Strengthening surveillance in Ghana against public health emergencies of international concern.

Among western African countries, the Republic of Ghana has maintained an economic growth rate of 5% since the 1980s and is now categorized as a middle-income country. However, as with other developing countries, Ghana still has challenges in the effective implementation of surveillance for infectious diseases. Facing public health emergencies of international concern (PHEIC), it is crucial to establish a reliable sample transportation system to the referral laboratory. Previously, surveillance capacity in Ghana was limited based on Integrated Disease Surveillance and Response, and therefore the "Surveillance and Laboratory Support for Emerging Pathogens of Public Health Importance in Ghana (SLEP)" was introduced to strengthen diarrhea surveillance. The SLEP project started with a sentinel diarrhea survey supported by SATREPS/JICA in collaboration with National Public Health Reference Laboratory (NHPRL) and Noguchi Memorial Institute of Medicine (NMIMR). The base-line survey revealed the limited capacity to detect diarrhea pathogens and to transfer samples from health centers to NHPRL. The involvement of private clinic/hospital facilities into the surveillance network is also crucial to strengthen surveillance in Ghana. The strong and interactive relationship between the two top referral laboratories, NHPRL under the Ministry of Health NMIMR and under the Ministry of Education, enables Ghana Health Services and is critical for the rapid response against PHEIC. In future, we hope that the outcome of the SLEP surveillance project could contribute to building a surveillance network with more timely investigation and transfer of samples to referral labs.

High-level resistance to non-nucleos(t)ide reverse transcriptase inhibitor based first-line antiretroviral therapy in Ghana; A 2017 study.

Expanding access to effective antiretroviral therapy (ART) is a major tool for management of Human Immunodeficiency Virus (HIV) infection. However, rising levels of HIV drug-resistance have significantly hampered the anticipated success of ART in persons living with HIV (PLWH), particularly those from Africa. Though great strides have been made in Ghana toward achieving the UNAIDS "95-95-95" target, a substantial number of PLWH receiving ART have not attained viral suppression. This study investigated patterns of drug resistance mutations in ART naïve as well as ART-experienced PLWH receiving first-line regimen drugs from Ghana. In a cross-sectional study, blood samples were collected from HIV-1 infected adults (≥18 years) attending HIV/AIDS clinic at the Eastern Regional Hospital, Koforidua, Ghana from September to October 2017. Viral RNA isolated from plasma were subjected to genotypic drug resistance testing for Protease Inhibitors (PI), Reverse Transcriptase Inhibitors (RTI), and Integrase Strand Transfer Inhibitors (INSTI). A total of 95 (84 ART experienced, 11 ART naïve) HIV-1 infected participants were sampled in this study. Sixty percent (50/84) of the ART-experienced participants were controlling viremia (viral load < 1,000 copies/ml). Of the 95 patient samples, 32, 34, and 33 were successfully sequenced for protease, reverse-transcriptase, and integrase regions, respectively. The dominant HIV-1 subtypes detected were CRF02_AG (70%), and A3 (10%). Major drug resistance associated mutations were only detected for reverse transcriptase inhibitors. The predominant drug resistance mutations were against nucleos(t)ide reverse transcriptase inhibitors (NRTI)-M184V/I and non-nucleos(t)ide reverse transcriptase inhibitors (NNRTI)-K103N. In the ART-experienced group, M184V/I and K103N were detected in 54% (15/28) and 46% (13/28) of individuals, respectively. Both mutations were each detected in 33% (2/6) of ART naïve individuals. Multiclass resistance to NRTI and NNRTI was detected in 57% of ART-experienced individuals and two ART naïve individuals. This study reports high-level resistance to NNRTI-based antiretroviral therapy in PLWH in Ghana. However, the absence of major PI and INSTI associated-mutations is a good signal that the current WHO recommendation of Dolutegravir in combination with an NRTI backbone will yield maximum benefits as first-line regimen for PLWH in Ghana.

Phylogenetic and genetic characterization of influenza A H9N2 viruses isolated from backyard poultry in selected farms in Ghana.

INTRODUCTION: Avian influenza viruses (AIV) cause significant economic losses to poultry farmers worldwide. These viruses have the ability to spread rapidly, infect entire poultry flocks, and can pose a threat to human health. The National Influenza Centre (NIC) at the Noguchi Memorial Institute for Medical Research in collaboration with the Ghana Armed forces (GAF) and the U.S. Naval Medical Research Unit No. 3, Ghana Detachment (NAMRU-3) performs biannual surveillance for influenza viruses among poultry at military barracks throughout Ghana. This study presents poultry surveillance data from the years 2017 to 2019. METHODOLOGY: Tracheal and cloacal swabs from sick and healthy poultry were collected from the backyards of GAF personnel living quarters and transported at 4°C to the NIC. Viral ribonucleic acid (RNA) was isolated and analyzed for the presence of influenza viruses using real-time polymerase chain reaction (PCR) assays. Viral nucleic acids extracted from influenza A-positive specimens were sequenced using universal influenza A-specific primers. RESULTS: Influenza A H9N2 virus was detected in 11 avian species out of 2000 samples tested. Phylogenetic analysis of viral haemagglutinin (HA) protein confirms the possibility of importation of viruses from North Africa and Burkina Faso. Although the detected viruses possess molecular markers of virulence and mammalian host adaptation, the HA cleavage site anlaysis confirmed low pathogenicity of the viruses. CONCLUSIONS: These findings confirm the ongoing spread of H9 viruses among poultry in Ghana. Poultry farmers need to be vigilant for sick birds and take the appropriate public health steps to limit the spread to other animals and spillover to humans.

Epidemiology of influenza in Ghana, 2011 to 2019.

Influenza virus is an important contributor to acute respiratory illnesses and is estimated to cause up to 650,000 respiratory deaths each year. Ghana recorded influenza viruses as far back as 1918 when the Spanish influenza pandemic led to the death of >100,000 people in a population of 4 million at the time. An outbreak of highly pathogenic avian influenza A(H5N1) among poultry in Ghana in 2007, led to the establishment of virological surveillance for influenza-like illness (ILI) by the Noguchi Memorial Institute for Medical Research (NMIMR). This surveillance system, supported by the U.S. Naval Medical Research Unit-No. 3 (NAMRU-3) and the Ghana Health Service (GHS), monitors circulating influenza strains and activity to better understand the epidemiology of influenza in Ghana. We present here the results of this surveillance system from 2011 to 2019. As part of the Integrated Disease Surveillance and Response (IDSR) system of the GHS under the Ministry of Health (MOH), oropharyngeal and nasopharyngeal swabs were collected from patients who met a modified World Health Organization (WHO) case definition for ILI or severe acute respiratory illness (SARI) through a sentinel surveillance system in the country. Samples were transported to the National Influenza Centre (NIC) at the NMIMR and tested for influenza virus using protocols defined by the United States Centers for Disease Control and Prevention (CDC). Selected isolates were sent to the WHO collaborating centre in the United Kingdom for further antigenic characterization. From 2011 to 2019, the NIC tested a total of 21,747 ILI samples and 3,429 SARI samples. Influenza positivity rates were highest in the 5-14 year old group for both ILI (20.8%) and SARI (23.8%). Compared to females, more males were seen at the health facilities for ILI and SARI symptoms with a statistically significant difference in influenza positive ILI (15% vs 13.2%, p <0.001). In terms of absolute numbers, more cases were seen at the health centres during the wet seasons (April to October) compared to the dry seasons (November to March) in Ghana. This study presents 9 years of surveillance data from outpatient and inpatient setting on influenza activity as well as the influenza A subtypes and B lineages that drive the activity. This presents useful information for influenza vaccine selection and administration. Ghana's unique influenza activity patterns also present a challenge in predicting when an outbreak could occur.

Molecular characterization of haemagglutinin genes of influenza B viruses circulating in Ghana during 2016 and 2017.

Recent reports of haemagglutinin antigen (HA) mismatch between vaccine composition strains and circulating strains, have led to renewed interest in influenza B viruses. Additionally, there are concerns about resistance to neuraminidase inhibitors in new influenza B isolates. To assess the potential impact in Ghana, we characterized the lineages of influenza B viruses that circulated in Ghana between 2016 and 2017 from different regions of the country: Southern, Northern and Central Ghana. Eight representative specimens from the three regions that were positive for influenza B virus by real-time RT-PCR were sequenced and compared to reference genomes from each lineage. A total of eleven amino acids substitutions were detected in the B/Victoria lineage and six in the B/Yamagata lineage. The strains of influenza B viruses were closely related to influenza B/Brisbane/60/2008 and influenza B/Phuket/3073/2013 for the Victoria and Yamagata lineages, respectively. Three main amino acid substitutions (P31S, I117V and R151K) were found in B/Victoria lineages circulating between 2016 and 2017, while one strain of B/Victoria possessed a unique glycosylation site at amino acid position 51 in the HA2 subunit. Two main substitutions (L172Q and M251V) were detected in the HA gene of the B/Yamagata lineage. The U.S. CDC recently reported a deletion sub-group in influenza B virus, but this was not identified among the Ghanaian specimens. Close monitoring of the patterns of influenza B evolution is necessary for the efficient selection of representative viruses for the design and formulation of effective influenza vaccines.