HIV-1 Coreceptor Tropism among Kenyans Under Highly Active Antiretroviral Therapy.

Despite the scale up of the use of combined highly active antiretroviral (ARV) therapy, many HIV-1 infected patients are still failing treatment in Kenya. In 2007, the Food Drug and Administration (FDA) approved the use of CCR5 antagonists in treatment experienced patients. CCR5 antagonists work by inhibiting the entry of HIV-1 that uses CCR5 as a coreceptor to gain entry into cells. CCR5 59029 A/G (promoter region—rs1799987) is a polymorphism that leads to the upregulation of the expression of the CCR5 protein thereby affecting the rate of HIV-1 infection. The use of these CCR5 antagonists in Kenya is limited partly because of minimal data on host genetics and coreceptor tropism among HIV-1 infected patients. In this study, we aimed at determining the prevalence of CCR5 tropic variants and CCR5 59029AG promoter polymorphism known to influence HIV-1 infection. We sequenced the V3 region of the env gene and inferred the HIV-1 tropism using clonal model of Geno2Pheno algorithm (FPR= 5%).   Also, we assessed the frequency of the CCR5 promoter polymorphisms among the patients by sequencing the polymorphic region of the CCR5 promoter. Majority of the patients (77.27%) had R5 tropic viruses whereas 22.73% of the study subjects had detectable CCR4 using viruses. The frequencies of the CCR5 59029 AA, AG, and GG genotypes were 14 (31.82%), 9 (20.45%) and 21(47.73%), respectively. Taken together, these results indicate that CCR5 antagonists could have potential therapeutic effects in the clinical management of HIV-1 among the infected patients in Kenya. Key words: CCR5 antagonists, CCR5 59029AG, HAART, HIV-1, Polymorphism, Tropis

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

Expression of odorant co-receptor Orco in tissues and development stages of Glossina morsitans morsitans, Glossina fuscipies fuscipies and Glossina pallidipies

Tsetse flies (Glossina) depend on their olfactory system to identify host, larviposition sites and mates. Previous studies have characterized olfactory organs and evaluated the odorant receptor (OR) expression to host-derived chemicals. However, no studies thus far have investigated the odorant co-receptor (Orco) associated with these olfaction processes in tissues and developmental stages in tsetse flies. In this study, quantitative polymerase chain reaction was done with Glossina morsitans morsitans, Glossina pallidipies and Glossina fuscipes fuscipes tissues (antennae and legs) and developmental stage (larvae and pupae) to quantify Orco expression levels and G. m. morsitans OR genes in G. m. morsitans larvae and pupae. Our findings indicate that expression of Orco were elevated in G. f. fuscipes male antennae and legs relative to G. f. fuscipes female antennae and relative to male antennae in G. m. morsitans and G. pallidipies. However, in female G. m. morsitans antennae, expression of Orco was higher than in female G. pallidipies and G. f. fuscipes. Orco levels were also significantly higher in pupal stages of G. f. fuscipes and G. pallidipies relative to the three larval stages and G. m. morsitans pupae. Two G. m. morsitans OR genes (GmmOR20 and GmmOR28) were highly expressed in G. m. morsitans larvae and pupae respectively. This study demonstrate that the Orco gene was significantly expressed in adult male and female tissues as well as in the developmental stages of Glossina species. The G. m. morsitans OR genes reported in larvae and pupae could mean co-expression of Orco and ORs in developmental stages. These findings pinpointed the olfactory differences that exists amongst G. m. morsitans, G. pallidipies and G. f. fuscipes, and provide valuable information to the probable role of olfactory genes in Glossina contributing further to the understanding of olfactory processes and the evolution of olfactory genes in tsetse flies. Keywords: Glossina, Olfaction, Orco, Odorant receptors, RNA expressio

Phylogenetic Variants of <i>Rickettsia africae</i>, and Incidental Identification of "<i>Candidatus</i> Rickettsia Moyalensis" in Kenya

<div><p>Background</p><p><i>Rickettsia africae</i>, the etiological agent of African tick bite fever, is widely distributed in sub-Saharan Africa. Contrary to reports of its homogeneity, a localized study in Asembo, Kenya recently reported high genetic diversity. The present study aims to elucidate the extent of this heterogeneity by examining archived <i>Rickettsia africae</i> DNA samples collected from different eco-regions of Kenya.</p><p>Methods</p><p>To evaluate their phylogenetic relationships, archived genomic DNA obtained from 57 ticks <i>a priori</i> identified to contain <i>R</i>. <i>africae</i> by comparison to <i>ompA</i>, <i>ompB</i> and <i>gltA</i> genes was used to amplify five rickettsial genes i.e. <i>gltA</i>, <i>ompA</i>, <i>ompB</i>, 17kDa and <i>sca4</i>. The resulting amplicons were sequenced. Translated amino acid alignments were used to guide the nucleotide alignments. Single gene and concatenated alignments were used to infer phylogenetic relationships.</p><p>Results</p><p>Out of the 57 DNA samples, three were determined to be <i>R</i>. <i>aeschlimanii</i> and not <i>R</i>. <i>africae</i>. One sample turned out to be a novel rickettsiae and an interim name of “<i>Candidatus</i> Rickettsia moyalensis” is proposed. The bonafide <i>R</i>. <i>africae</i> formed two distinct clades. Clade I contained 9% of the samples and branched with the validated <i>R</i>. <i>africae str ESF-5</i>, while clade II (two samples) formed a distinct sub-lineage.</p><p>Conclusions</p><p>This data supports the use of multiple genes for phylogenetic inferences. It is determined that, despite its recent emergence, the <i>R</i>. <i>africae</i> lineage is diverse. This data also provides evidence of a novel Rickettsia species, <i>Candidatus</i> Rickettsia moyalensis.</p></div

Phylogeny of Rickettsia study samples isolated from diverse eco-regions of Kenya.

<p>Maximum Likelihood trees were obtained from (A) <i>gltA</i>, (B) <i>ompA</i>, (C) <i>ompB</i>, (D) 17kDa and (E) <i>sca4</i> partial nucleotide sequences. Members of clade I, II and III are shown beside the bolded red, blue and green lines respectively. Numbers at the nodes are bootstrap proportions with 1000 replicates. Only bootstrap values >50% are shown. The scale bar indicates the number of substitutions per nucleotide position.</p

Epidemiological Trends of Five Common Diarrhea-Associated Enteric Viruses Pre- and Post-Rotavirus Vaccine Introduction in Coastal Kenya

Using real-time RT-PCR, we screened stool samples from children aged &lt;5 years presenting with diarrhea and admitted to Kilifi County Hospital, coastal Kenya, pre- (2003 and 2013) and post-rotavirus vaccine introduction (2016 and 2019) for five viruses, namely rotavirus group A (RVA), norovirus GII, adenovirus, astrovirus and sapovirus. Of the 984 samples analyzed, at least one virus was detected in 401 (40.8%) patients. Post rotavirus vaccine introduction, the prevalence of RVA decreased (23.3% vs. 13.8%, p &lt; 0.001) while that of norovirus GII increased (6.6% vs. 10.9%, p = 0.023). The prevalence of adenovirus, astrovirus and sapovirus remained statistically unchanged between the two periods: 9.9% vs. 14.2%, 2.4% vs. 3.2 %, 4.6% vs. 2.6%, (p = 0.053, 0.585 and 0.133), respectively. The median age of diarrhea cases was higher post vaccine introduction (12.5 months, interquartile range (IQR): 7.9&ndash;21 vs. 11.2 months pre-introduction, IQR: 6.8&ndash;16.5, p &lt; 0.001). In this setting, RVA and adenovirus cases peaked in the dry months while norovirus GII and sapovirus peaked in the rainy season. Astrovirus did not display clear seasonality. In conclusion, following rotavirus vaccine introduction, we found a significant reduction in the prevalence of RVA in coastal Kenya but an increase in norovirus GII prevalence in hospitalized children

Phylogeny of Rickettsia sequences from this study and those collected previously in Kenya [23, 31].

<p><i>ompA</i> nucleotide sequences of study isolates and other <i>R</i>. <i>africae</i> reported from previous studies [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004788#pntd.0004788.ref023" target="_blank">23</a>,<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004788#pntd.0004788.ref031" target="_blank">31</a>] were analysed by Maximum Likelihood method using MEGA v7 based on the Hasegawa-Kishino-Yano (HKY) model of substitution. The tree has a log likelihood ratio of -1049 and involved all codon positions. Members of clade I, II and III are shown beside the bolded red, blue and green lines respectively. Sequences from Parola et al 2001 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004788#pntd.0004788.ref023" target="_blank">23</a>] are shown as black triangles and those from Macaluso et al 2003 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004788#pntd.0004788.ref031" target="_blank">31</a>] by black circles. Numbers at the nodes are bootstrap proportions with 1000 replicates. Only bootstrap values >50% are shown. The scale bar indicates the number of substitutions per nucleotide position. Clearly, five of our sequences (044, 045 and 164 from Wajir, 176 Moyale and 195 Machakos) are distinct from those described previously.</p

Primers used for PCR and sequencing.

<p>Primers used for PCR and sequencing.</p

Bayesian probability tree of study samples with validated <i>Rickettsia</i> species.

<p>The tree is based on partitioned concatenated datasets of <i>gltA</i>, <i>ompA</i>, <i>ompB</i>, 17kDa and <i>sca4</i> partial nucleotide sequences. Amino acid alignments were used to guide the nucleotide alignments. The tree is estimated using a GTR+G substitution model as implemented in MrBayes v3.2. The tree is a consensus of 15,002 trees (post burn-in) pooled from two independent Markov Chain run in parallel. Thin lines indicate posterior probability values of < 1. Lineage diversity within the <i>R</i>. <i>africae</i> study samples is highlighted in red and blue to indicate clades i and ii respectively. Samples previously misclassified as <i>R</i>. <i>africae</i> are now classified as <i>R</i>. <i>aeschlimanii</i> (black diamond). Study sample 176_Moyale branches distinctly from other rickettsiae and is considered a novel rickettsia species and a provisional name "<i>Candidatus</i> rickettsia moyalensis" (black circle) is proposed. NB: Although 293_Migori (open circle) branched as a lone taxon, it clustered with <i>R</i>. <i>aeschlimanii</i> by Maximum Likelihood method. Non-spotted fever group lineages are highlighted orange for transition group and grey for typhus group. The status of <i>R</i>. <i>helvetica</i> (shown in black cross), originally in spotted fever group is now uncertain [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004788#pntd.0004788.ref020" target="_blank">20</a>].</p