Biology subjects
Publications and source records attributed to Faleye, T. O. C..
In light of the ongoing cVDPV2 outbreak in Nigeria, we describe the draft genome of a CVA20 strain from a child with AFP. The non-structural region of this genome unambiguously unveiled the source of such regions in recombinant cVDPV2s (JX275140 and KX162716) found in Nigeria in 2008 and 2015, respectively.
We recently showed that Enteroviruses (EVs); majorly species Cs (EV-Cs) were present in about 46.7% of faecal samples from children <15 years old diagnosed with Acute Flaccid Paralysis (AFP) in Nigeria but declared to be EV free by the RD-L20B cell culture based algorithm. In this study, we investigated whether this observed preponderance of EVs (and EV-Cs) in such samples vary by geographical region.\n\nIn all, 108 samples (i.e. 54 paired stool suspensions from 54 AFP cases) previously confirmed negative for EVs by the WHO recommended RD-L20B cell culture based algorithm were analyzed in this study. The 108 samples were made into 54 pools (27 each from Northwest [NW] and Southsouth [SS] Nigeria). All samples were subjected to RNA extraction, cDNA synthesis and the WHO recommended seminestedPCR (snPCR) assay and its modifications. All amplicons were sequenced, and enteroviruses identified using the enterovirus genotyping tool and phylogenetic analysis.\n\nAltogether, EVs were detected in 16 (29.63%) of the 54 samples screened but successfully identified in 14 (25.93%): 10 from NW- and 4 from SS-Nigeria. Precisely, one (7.14%), two (14.29%) and 11 (78.57%) of the strains detected were EV-A, EV-B and EV-C respectively. The 10 strains from NW-Nigeria are 7 EV types and include CV-A10, E29, CV-A13, CV-A17, CV-A19, CV-A24 and EV-C99. The four EV types recovered from SS-Nigeria include E31, CV-A1, EV-C99 and EV-C116. EV-C99 is the only EV type that was detected in both NW- and SS-Nigeria.\n\nThe results of this study showed that the preponderance of EVs and consequently EV-Cs in AFP samples declared to be EV free by the RD-L20B cell culture based algorithm vary by geographical region in Nigeria. It further confirmed the EV-B bias of the RD-L20B cell culture based algorithm.
Echovirus 29 (E29) is a member of Species Enterovirus B (EV-B) in the genus Enterovirus, family Picornaviridae, order Picornavirinae. In Nigeria, molecular characterization of E29 was first described in 2002. In 2015, we found that a new clade of E29 had replaced that described in Nigeria in 2002-2003. To date, E29 isolates described from Nigeria were isolated in cultures of RD cell line. In 2016, we characterised an E29 strain that did not show cytopathology on RD cell line within the recommended 10 days of culture.\n\nHere we show that the E29 in question grows with evident CPE in RD cell culture like other members of the clade when allowed to stay in culture for 13 to 14 days. The findings of this study therefore suggest that some of the samples declared negative for enteroviruses by the current WHO cell culture based detection algorithm might be false negatives. It is therefore encouraged that those particularly interested in non-polio enteroviruses endeavour to maintain at least 14 days incubation in cell culture in a bid to accommodate NPEVs like E29 that might need longer time to develop CPE especially when present at low titre.
The CD4 T lymphocytes play a key role in achieving a regulated effective immune response to foreign antigens. It is also a valuable parameter for assessing HIV disease progression. However, variations in CD4 T lymphocyte values due to diverse factors have been reported. We evaluated CD4 T lymphocytes among healthy community dwellers who tested negative for hepatitis B, hepatitis C and hepatitis E viruses and compared the results with the National Reference Values (NRVs). Four hundred consenting participants who fulfilled the criteria for enrolment were evaluated for CD4 T lymphocyte counts. Estimated mean CD4 T lymphocyte count of 1,183 (CD4 Range: 328-2680) cells/l of blood was recorded for the participants. Four (1.0%), 151 (37.8%), 157 (39.2%), 74 (18.5), and 14 (3.5) of the participants had CD4 T lymphocyte count ranged 352-500, 501-1,000, 1,001-1500, 1501-2,000, and >2,000 cells/l of blood, respectively. Differences in the estimated mean CD4 count between different age groups varied significantly (P=0.010). In this study, significantly higher CD4 T lymphocyte values were observed among the study population in comparison to the NRVs, and consequently we advise careful interpretation and use of extrapolated CD4 T lymphocyte values in the management of persons with diverse geographical background or health conditions.
With poliovirus eradication within reach, the WHO has included in its recommendations a cell-culture independent algorithm for enterovirus surveillance. This study was designed to compare both the cell culture dependent and independent algorithms and assess how either might impact our perception of the diversity of enterovirus types present in a sample.\n\nSixteen paired samples (16 isolates from RD cell culture and their corresponding stool suspension. i.e. 32 samples) from AFP cases in Nigeria were analyzed in this study. One of these 16 sample pairs (the control) was previously identified and confirmed as poliovirus 2 (PV-2). All the samples were subjected to RNA extraction, cDNA synthesis, RT-snPCR (the WHO recommended cell-culture independent algorithm) and its modifications for co-infection detection and resolution. Amplicons were sequenced and strains identified using the enterovirus genotyping tool and phylogenetic analysis.\n\nThe enterovirus diversity was shown to be the same between RD cell culture isolates and fecal suspension for the control and five (7, 10, 11, 12 & 14) of the samples analyzed. It was however, different for the remaining 10 (62.5%) samples analyzed. Fourteen different enterovirus types were identified in this study. To be precise, 9 (CV-B4, E6, E7, E13, E14, E19, E29, EV-B75 and EV-B77) and 5 (CV-A1, CV-A11, CV-A13, EV-C99 and PV2) EV-B and EV-C types, respectively where detected in this study. It is crucial to mention that E19 and EV-B75were only recovered from RD cell culture isolates while E14, EV-B77, CV-A11 and CV-A13 were only recovered from fecal suspension.\n\nThe results of this study show that both the cell culture dependent and independent protocols recommended by the WHO for enterovirus detection unavoidably bias our perception of the diversity of enterovirus types present in a sample. Hence, rather than jettison one for the other, effort should be directed at harmonizing both for increased sensitivity.
Hepatitis E virus (HEV) remains a major public health concern in resource limited regions of the world. Yet data reporting is suboptimal and surveillance system inadequate. In Nigeria, there is dearth of information on prevalence of acute HEV infection. This study was therefore designed to describe acute HEV infection among antenatal clinic attendees and asymptomatic community dwellers from two geographical regions in Nigeria.\n\nIn this study 750 plasma samples were tested for HEV IgM by Enzyme Linked lmmunosorbent Assay (ELISA) technique. The tested samples were randomly selected from a pool of 1,115 samples previously collected from selected populations (pregnant women - 272, Oyo community dwellers - 438, Anambra community dwellers - 405) for viral hepatitis studies between September 2012 and August 2013.\n\nOne (0.4%) pregnant woman in her 3rd trimester had detectable HEV IgM, while community dwellers from the two study locations had zero prevalence rates of HEV IgM.\n\nDetection of HEV IgM in a pregnant woman, especially in her 3rd trimester is of clinical and epidemiological significance. The need therefore exists for establishment of a robust HEV surveillance system in Nigeria, and especially amidst the pregnant population in a bid to improve maternal and child health.
We describe the characterization of an enterovirus isolate recovered from untreated raw sewage in Ibadan, southwest Nigeria in 2010. The isolate was neutralized by specific antisera and consequently identified as Echovirus 7 (E7). Subsequent molecular characterization showed the isolate to be a mixture of E7 and Coxsackievirus A24 (CV-A24) thereby suggesting the CV-A24 strain to be non-cytopathology producing. Further molecular analysis suggested that the CV-A24 might have recombined with a Sabin poliovirus 2 (PV2) in its non-structural region. This is the first description of a Nigerian CV-A24 strain.
Samples showing cytopathology (CPE) on initial inoculation into L20B cell line but with no observed or reproducible CPE on passage in L20B or RD are considered negative for both poliovirus and nonpolio enteroviruses (NPEVs). The phenomenon is termed non-reproducible CPE. Its occurrence is usually ascribed to the likely presence of reoviruses, adenoviruses and other non-enteroviruses. This study aimed to investigate the likelihood that NPEVs are also present in cases with non-reproducible CPE.\n\nTwenty-six (26) cell culture suspensions were analyzed in this study. The suspensions were collected from the WHO National Polio Laboratory, Department of Virology, College of Medicine, University of Ibadan. The suspensions emanated from 13 L20B cell culture tubes that showed cytopathology within 5 days of inoculation with fecal suspension from AFP cases. However, on passage into one each of RD and L20B cell lines, the CPE was not reproducible. All samples were subjected to RNA extraction, cDNA synthesis, the WHO recommended VP1 RT-seminestedPCR assay, species resolution PCR assay, sequencing and phylogenetic analysis.\n\nSix (6) samples were positive for the VP1 RT-seminested PCR assay. Only four of which were positive by the species resolution PCR assay. The four amplicons were sequenced, however, only three (3) were successfully identified as Coxsackievirus A20 (2 isolates) and Echovirus 29 (1 isolate).\n\nThe results of this study unambiguously showed the presence of NPEVs (particularly CVA20 and E29) in cell culture supernatants of samples with CPE on initial inoculation into L20B cell line but with no observed or reproducible CPE on passage in RD cell line. Therefore, like reoviruses, adenoviruses and other non-enteroviruses, NPEVs can also be recovered in cases with non-reproducible CPE.
We recently detected EV-A119 and EV-B111 (previously shown to co-circulate between nonhuman primates (NHPs) and humans) in Nigerian children diagnosed with acute flaccid paralysis (AFP). This study was designed to investigate and catalogue EVs present in captive NHPs in Nigeria.\n\nTwenty-seven fecal samples collected from captive NHPs in a Wild Life Park and Zoological garden at Jos, Nigeria in April 2016 were analyzed in this study. Samples were resuspended in a phosphate buffered saline (PBS)/chloroform mixture, and the clarified supernatant was subjected to RNA extraction, cDNA synthesis, a Panenterovirus 5I-UTR assay, and three different enterovirus VP1 snPCR assays. All amplicons from the snPCR assays were sequenced, and enteroviruses identified using the enterovirus genotyping tool and phylogenetic analysis.\n\nEight (29.63%) (two each from Chimpanzees, Patas Monkey, Mona Monkey and Baboon) of the 27 samples were positive for the 5I-UTR assay. One (3.70%) of the 27 samples was positive for the enterovirus VP1 snPCR assays in addition to its positivity by 5I-UTR assay. The same sample happens to be one of the two samples from Chimpanzees that tested positive for the 5I-UTR assay, and it was subsequently identified as EV-A76 of South-East Asia ancestry.\n\nThis study documents the first recorded attempt to detect and identify enteroviruses in NHPs in Nigeria. It also reports the first detection and identification of EV-A76 in Nigeria and particularly in a NHP. It is of utmost importance that the enterovirus VP1 assays be improved to enable detection of EVs that have been detected in NHPs but yet to be described in humans.
AbstractsRecently, a reverse transcriptase seminested polymerase chain reaction (RT-snPCR) assay was recommended by the WHO for direct detection of enteroviruses from clinical specimen. In this study, we use the assay and its modification to screen acute flaccid paralysis (AFP) samples previously confirmed negative for enteroviruses by the RD-L20B algorithm.\n\nThirty paired stool suspensions collected in 2015 as part of the national AFP surveillance program in different states of Nigeria were analyzed in this study. The samples were previously confirmed negative for enteroviruses by the polio laboratory in accordance with the WHO recommended RD-L20B cell culture based algorithm. Two samples previously confirmed to contain enteroviruses were included as positive controls. All samples were subjected to RNA extraction, and the RT-snPCR assay and its modifications. All amplicons were sequenced and enteroviruses identified using the enterovirus genotyping tool.\n\nOverall, amplicons were recovered from the two controls and 50% (15/30) of samples screened. Fourteen were successfully typed of which, 7.1% (1/14), 21.4% (3/14), 64.3% (9/14) and 7.1% (1/14) were EV-A, EV-B, EV-C and a mixture of EV-B and C (EV-C99 and E25), respectively. The two controls were identified as EV-C99 and CV-A1, both EV-Cs. The PV-2 detected had VP1 ILE143. Hence, a vaccine strain.\n\nThe results of this study showed that about 50% of enterovirus infections (including some Sabin PV2s) are being missed by the RD-L20B cell culture based algorithm. This highlights the value of the RT-snPCR assay and its modifications. The circulation and preponderance of EV-Cs in Nigeria was also confirmed.
In a polio-free world there might be reduced funding for poliovirus surveillance. There is therefore the need to ensure that enterovirologist globally, especially those outside the global polio laboratory network (GPLN), can participate in poliovirus surveillance without neglecting their enterovirus type of interest. To accomplish this, assays are needed that allow such active participation.\n\nIn this light, we used 15 previously identified enterovirus isolates as reference samples for assay development. The first eight were enterovirus species B (EV-B). The remaining seven were EV-Cs; three of which were poliovirus (PV) 1, 2 and 3, respectively. A 16th sample was compounded; a mixture of two EV-Bs, three PVs and one nonPV EV-Cs (all part of the 15). In all, four samples contained PVs with the 16th consisting of mixture of the three PV types. All were subjected to the WHO recommended RT-snPCR assay, and five other modified (with substitution of the second round PCR forward primer) assays. The new primers included the previously described Species Resolution Primers (SRPs; 187and 189) and the Poliovirus Resolution Primers (PRPs: Sab 1, 2 and 3). All amplicons were sequenced and isolate identity confirmed using the Enterovirus Genotyping Tool.\n\nThe PRPs detected PV types in only the four samples that contained PVs. In addition, it was able to show that the sample 16 (mixture) contained all the three PV types. On the other hand, though the SRPs and the WHO assay also detected the three singleton PVs, in sample 16, they both detected only one of the three PV types present.\n\nThis study describes a sensitive and specific utility extension of the recently recommended WHO RT-snPCR assay that enables independent detection of the three poliovirus types especially in cases of co-infection. More importantly, it piggy-backs on the first round PCR product of the WHO recommended assay and consequently ensures that enterovirologists interested in nonpolio enteroviruses can continue their investigations, and contribute significantly and specifically to poliovirus surveillance, by using the excess of their first round PCR product.