Establishment and evaluation of a loop-mediated isothermal assay (LAMP) for the semi-quantitative detection of HIV-1 group M virus in blood and plasma

The past decade has witnessed a dramatic increase of anti-retroviral treatment of Human Immunodeficiency Virus (HIV) infected patients in many African countries. Due to costs and sophistication of currently available commercial viral load assays, little attention has been paid to therapy monitoring through measurement of plasma viral load, a challenge that could reverse achievements already made against HIV/AIDS infection. Loop-mediated isothermal amplification (LAMP) has been shown to be simple, rapid and cost-effective, characteristics which make this assay ideal for viral load monitoring in resource limited settings. The aim of this study was to establish and evaluate LAMP for quantitative detection of HIV-1 group M virus in blood and plasma. Cell culture supernatants of HIV-1 subtype B (IIIB and MVP899-87) viruses were used to optimize reaction conditions and to test primer suitability. Together with HIV-1 M non-B subtypes, HIV-1 group O and HIV-2, the cell culture supernatants were used to evaluate the performance of LAMP, to generate a model for viral load estimation and to establish the limits of the assay. A panel of 467 clinical samples was analyzed (282 plasmas and 121 dry blood spots from Kenya and 112 plasmas from Germany) and the results obtained by LAMP were compared to those generated by the Abbott Real Time HIV-1 assay, an established commercial viral load quantification test. A linear regression equation was generated from time to detection values and used to estimate the viral loads of the samples by the LAMP assay. Kenyan samples were tested in Nairobi and Munich. LAMP primers targeting the integrase of the pol gene were found to be the most suitable compared to further 3 primer sets tested. Lower limit of detection (LLOD) of 1,200 copies/mL and lower limit of quantification (LLOQ) of 9,800 copies/mL were determined as suitable thresholds for quantitative estimations of the LAMP viral loads. Sensitivities of 82 and 86% (Kenyan samples) and 93% (German samples) and specificities of 99 and 100% were realized with plasma samples. The study also realized a sensitivity of 76% and specificity of 77% with dry blood spot samples from Kenya. In conclusion, LAMP assay shows obvious potential for diagnostic application in semi-quantification of HIV-1 group M viral load in resource limited countries. However there is a need for further improvement of primers in respect to detection of HIV-1 non-B viruses and evaluation of dry blood spot samples to ensure that more reliable results are obtained

Prevalence and Genetic Characterization of Rotavirus Infections Among Children Under Five Years in Mutaho Health District, Gitega Province and Bujumbura Municipality, Burundi

Rotavirus is the leading cause of severe diarrhea in children under five years worldwide. It is ranked as a priority for vaccine. In Burundi, vaccine against rotavirus was implemented in 2013. The impact of recent rotavirus vaccination on morbidities in Burundi is not well established. Moreover, no study has been carried out to document the genetic diversity of rotavirus strains circulating in Burundi. This cross-sectional health facility-based study aimed at determining the prevalence and molecular characteristics of rotavirus infections among children under five years of age in Mutaho Health District and the Municipality of Bujumbura, in Burundi. Stool specimens were collected from children presenting with acute diarrhea. These specimens were tested for rotavirus antigen using Diagnostar® rapid test kit.  Positive stool samples were confirmed at the Kenya Medical Research Institute (KEMRI) by ELISA. Positive confirmed samples underwent RT-PCR, G and P genotyping by multiplex semi-nested PCR using a cocktail of type specific primers or by sequencing. A total of 646 participants were enrolled in this study. The overall prevalence of rotavirus was 6.2% (40/646) with 4.0% (16/400) in Mutaho health district and 9.7% (24/246) in the Municipality of Bujumbura. Rotavirus detection rate tended to increase as the level of precipitation went down, showing a significant negative association between the two variables. (OR = 15.2; P = 0.0001). In addition, rotavirus detection rate was higher in Bujumbura Municipality than in Mutaho health district (OR = 2.6; P = 0.005). Two G genotypes were identified, G1 the predominating G genotype accounted for 53.8% (14/26) followed by G12 (46.2%, 12/26). The prevalence of the genotype G1 of Group A rotavirus was significantly higher in Bujumbura Municipality than in Mutaho health district while G12 predominated in Mutaho health district (OR = 7.33; P = 0.026). Rotavirus strains from pigs might have contributed to the high prevalence of human G12 rotavirus in that area. Three different P types were identified P[8] the most common, followed by P[6] and P[4]. The most common G/P combination genotype was G1P[8] which accounted for 45.5% of all rotavirus genotypes identified, followed by G12 P [8] (41.0%), G1P [6] (4.5%), G12 P [6] (4.5%) and G12 P [4] (4.5%). The emergence of G12 rotavirus strains which share neither G nor P genotypes with currently used rotavirus vaccines raises public health concerns as they have the potential to challenge their efficacy. Therefore, we recommend to initiate and maintain a continuous rotavirus strain surveillance in Burundi so as to monitor trends in the occurrence of these prevailing and potentially emerging new strains. Keywords: Rotavirus, diarrhea, genetic diversity, prevalence, Mutaho, Bujumbura, children DOI: 10.7176/JBAH/9-10-04 Publication date:May 31st 201

Utilization of Pre-travel Health Services Among Kenyan International Travelers in Jomo Kenyatta Airport Conducted From 2nd August to 30th September 2017

Introduction: The geographical movement of people from one area to another poses the threat of transmission of infectious diseases. Kenya is among the vulnerable countries when it comes to disease transmission, because it is a major transport hub in East Africa, yet data on the availability and uptake of pre-travel health services is limited. Methods: A cross-sectional descriptive study was conducted to determine the uptake of pre-travel health services. The systematic sampling method was used to obtain a sample size of 384 travelers among those in the waiting lounge prior to departure; four key informants were chosen purposively. A self-administered questionnaire was used for data collection. The results of data analysis are presented in the form of tables, graphs, charts, and text. Results: The majority of respondents (70.6%) knew of at least one health service offered to international travelers in Kenya. The most sought-after pre-travel health service was vaccination (70.97%), but very few (13.93%) travelers sought pre-travel health advice on how to stay healthy while abroad. The majority of travelers were positive about pre-travel health services. The Port Health Department focuses more on the health of international arrivals as opposed to departures; there are no functional travel health clinics. Conclusion: The results indicated that the government pays little attention to departing international travelers. Therefore, it is important for the government to develop policies, guidelines, and structures that will ensure that pre-travel health services are received by travelers prior to departure. Travel clinics need to be set up to increase the uptake of pre-travel health services. Moreover, further research should be conducted

Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection

Retraction.

This is a retraction of 'Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa' 10.1126/science.add873

Establishment and evaluation of a loop-mediated isothermal assay (LAMP) for the semi-quantitative detection of HIV-1 group M virus in blood and plasma

The past decade has witnessed a dramatic increase of anti-retroviral treatment of Human Immunodeficiency Virus (HIV) infected patients in many African countries. Due to costs and sophistication of currently available commercial viral load assays, little attention has been paid to therapy monitoring through measurement of plasma viral load, a challenge that could reverse achievements already made against HIV/AIDS infection. Loop-mediated isothermal amplification (LAMP) has been shown to be simple, rapid and cost-effective, characteristics which make this assay ideal for viral load monitoring in resource limited settings. The aim of this study was to establish and evaluate LAMP for quantitative detection of HIV-1 group M virus in blood and plasma. Cell culture supernatants of HIV-1 subtype B (IIIB and MVP899-87) viruses were used to optimize reaction conditions and to test primer suitability. Together with HIV-1 M non-B subtypes, HIV-1 group O and HIV-2, the cell culture supernatants were used to evaluate the performance of LAMP, to generate a model for viral load estimation and to establish the limits of the assay. A panel of 467 clinical samples was analyzed (282 plasmas and 121 dry blood spots from Kenya and 112 plasmas from Germany) and the results obtained by LAMP were compared to those generated by the Abbott Real Time HIV-1 assay, an established commercial viral load quantification test. A linear regression equation was generated from time to detection values and used to estimate the viral loads of the samples by the LAMP assay. Kenyan samples were tested in Nairobi and Munich. LAMP primers targeting the integrase of the pol gene were found to be the most suitable compared to further 3 primer sets tested. Lower limit of detection (LLOD) of 1,200 copies/mL and lower limit of quantification (LLOQ) of 9,800 copies/mL were determined as suitable thresholds for quantitative estimations of the LAMP viral loads. Sensitivities of 82 and 86% (Kenyan samples) and 93% (German samples) and specificities of 99 and 100% were realized with plasma samples. The study also realized a sensitivity of 76% and specificity of 77% with dry blood spot samples from Kenya. In conclusion, LAMP assay shows obvious potential for diagnostic application in semi-quantification of HIV-1 group M viral load in resource limited countries. However there is a need for further improvement of primers in respect to detection of HIV-1 non-B viruses and evaluation of dry blood spot samples to ensure that more reliable results are obtained

Increase in the Immune Response in Balb/c Mice after the Co-Administration of a Vector-Based COVID-19 Vaccine with Cytosine Phosphoguanine Oligodeoxynucleotide

The effects of cytosine phosphoguanine oligodeoxynucleotides (CPG ODNs) on immune response have been demonstrated for different vaccines; however, such information is limited for the vector-based Coronavirus disease 2019 (COVID-19). This paper aims to demonstrate the potential effect of CPG ODNs on immunological response against the vector-based COVID-19 vaccine on Balb/c mice using a JNJ-78436735 Ad26.COV2-S recombinant as a model vaccine. A total of 18 BALB/c mice clustered into six groups were used. All groups were observed for 14- and 28-days post immunization. Qualitative determination of IgG was performed using indirect Enzyme-Linked Immunosorbent Assay (ELISA) and qPCR for cytokine profiling. A significant (p ≤ 0.001) rise in antibody response was observed for groups 3 and 4, who also showed increased expression levels of Tumor Necrosis Factor (TNF) and Interferon Gamma (IFN-γ). Immunological parameters for toxicity were normal in all treatment groups. We conclude that supplementing vector-based COVID-19 vaccines with CpG ODNs has the potential to boost the body’s immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection