Browsing by Author "Gumede, Nicksy"

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    Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021
    (Viruses, 2022) Morobe, John Mwita; Brigitte, Pool; Lina, Marie; Dwayne, Didon; Lambisia, Arnold W.; Makori, Timothy; Khadija, Said Mohammed; Zaydah, R. de Laurent; Ndwiga, Leonard; Mburu, Maureen W.; Moraa , Edidah; Murunga, Nickson; Musyoki , Jennifer; Mwacharo, Jedida; Lydia Nyamako; Debra, Riako; Pariken, Ephnatus; Gambo, Faith; Naimani, Josephine; Namulondo, Joyce; Tembo, Susan Zimba; Ogendi, Edwin; Thierno, Balde; Dratibi , Fred Athanasius; Yahaya, Ali Ahmed; Gumede, Nicksy; Achilla, Rachel A.; Peter, K. Borus; Dorcas, W. Wanjohi; Sofonias, K. Tessema; Mwangangi, Joseph; Bejon, Philip; David, J. Nokes; Ochola-Oyier, Lynette Isabella; Githinji, George; Leon, Biscornet; Agoti, Charles N.
    Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until January 2021, when a surge was observed. Here, we investigated the potential drivers of the surge by genomic analysis of 1056 SARS-CoV-2 positive samples collected in Seychelles between 14 March 2020 and 31 December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1042 of which fell within four variants of concern, i.e., Alpha, Beta, Delta and Omicron. Sporadic cases of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (lineage predominantly observed in Europe) but this lineage was rapidly replaced by Beta variant starting January 2021, and which was also subsequently replaced by the Delta variant in May 2021 that dominated till November 2021 when Omicron cases were identified. Using the ancestral state reconstruction approach, we estimated that at least 78 independent SARS-CoV-2 introduction events occurred in Seychelles during the study period. The majority of viral introductions into Seychelles occurred in 2021, despite substantial COVID-19 restrictions in place during this period. We conclude that the surge of SARS-CoV-2 cases in Seychelles in January 2021 was primarily due to the introduction of more transmissible SARS-CoV-2 variants into the islands.
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    Molecular characterization of non‐polio enteroviruses isolated from acute flaccid paralysis patients in Uganda
    (Journal of Medical Virology, 2021) Tushabe, Phionah; Howard, Wayne; Bwogi, Josephine; Birungi, Molly; Eliku, James P.; Kakooza, Proscovia; Bukenya, Henry; Namuwulya, Prossy; Gaizi, Joseph; Tibanagwa, Mayi; Kabaliisa, Theopista; Mulindwa, Julius; Muhanguzi, Dennis; Suchard, Melinda; Gumede, Nicksy; Bakamutumaho, Barnabas
    Enteroviruses (EVs) are RNA viruses that can cause many clinical syndromes including acute flaccid paralysis (AFP). Within the global polio laboratory network, EVs are categorized either as polioviruses or non‐polio enteroviruses (NPEVs). Specific NPEVs have been described in polio‐like residual paralytic events in AFP patients. Retrospective analysis of 112 NPEV isolates from AFP patients was performed and thirty one NPEV types were identified of which 91% were Enterovirus B and 9% were Enterovirus A species. The NPEVs were distributed across the country with most patients in the eastern region (41/89; 46.1%). The highest proportion of patients were children less than 5 years (77/89; 86.5%) and male patients were more common (54/89; 60.7%). Echovirus 11 (11/89; 12.4%) was frequently observed and phylogenetic analysis of these sequences revealed high diversity. Coxsackievirus B5 (CV‐B5), CV‐B6, E21, and EV‐B69 were only seen in patients with residual paralysis. Analyses of the EV‐A71 sequence indicated a unique genogroup.
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    SARS-CoV-2 Omicron variant of concern in the Seychelles: Introduction and spread
    (Wellcome Open Research, 2023) Morobe, John Mwita; Brigitte, Pool; Lina, Marie; Dwayne, Didon; Lambisia, Arnold W.; Makori, Timothy; Khadija, Said Mohammed; Ndwiga, Leonard; Mburu, Maureen W.; Moraa, Edidah; Murunga, Nickson; Mwanga, Mike; Musyoki, Jennifer; Moturi, Angela K.; Namulondo, Joyce; Tembo, Susan Zimba; Ogendi, Edwin; Thierno, Balde; Dratibi, Fred Athanasius; Yahaya, Ali Ahmed; Gumede, Nicksy; Achilla, Rachel A.; Peter, K. Borus; Wanjohi, Dorcas W.; Tessema, Sofonias K.; Mwangangi, Joseph; Bejon, Philip; Nokes, D. James; Ochola-Oyier, Lynette Isabella; Githinji, George; Leon, Biscornet; Charles, N. Agoti
    Background: The emergence of the Omicron variant of concern in late 2021 led to a resurgence of SARS-CoV-2 infections globally. By September 2022, Seychelles had experienced two major surges of SARS-CoV-2 infections driven by the Omicron variant. Here, we examine the genomic epidemiology of Omicron in the Seychelles between November 2021 and September 2022. Methods: We analysed 618 SARS-CoV-2 Omicron genomes identified in the Seychelles between November 2021 and September 2022 to infer virus introductions and local transmission patterns using phylogenetics and the ancestral state reconstruction approach. We then evaluated the impact of government coronavirus 2019 (COVID-19) countermeasures on the estimated number of viral introductions during the study period. Results: The genomes classified into 43 distinct Pango lineages. The first surge in Omicron cases (beginning November 2021 and peaking in January 2022) was predominated by the BA.1.1 lineage (59%) co-circulating with 11 other Omicron lineages. In the second surge (between April and June 2022), four lineages (BA.2, BA.2.10, BA.2.65 and BA.2.9) co-circulated and these were swiftly replaced by BA.5 subvariants in July 2022, which remained predominant through to September 2022. In the latter period, sporadic detections of BA.5 subvariants BQ.1, BE and BF were observed. We estimated 109 independent Omicron importations into Seychelles over the 11-month period, most of which occurred between December 2021 and March 2022 when strict government restrictions (SI>50%) were still in force. The districts Anse Royale, and Baie St. Anne Praslin appeared to be the major dispersal points fuelling local transmission. Conclusions: Our results suggest that the waves of Omicron infections in the Seychelles were driven by multiple lineages and multiple virus introductions. The introductions were followed by substantial local spread and successive lineage displacement that mirrored the global patterns.
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    The detection of 3 ambiguous type 2 vaccine-derived polioviruses (VDPV2s) in Uganda
    (Virology Journal, 2018) Nanteza, Mary Bridget; Bakamutumaho, Barnabas; Kisakye, Annet; Namuwulya, Prossy; Bukenya, Henry; Katushabe, Edson; Bwogi, Josephine; Byabamazima, Charles Rutebarika; Raffaella, Williams; Gumede, Nicksy
    Background The Oral Polio Vaccine (OPV or Sabin) is genetically unstable and may mutate to form vaccine-derived polioviruses (VDPVs). Methods In 2014, two VDPVs type 2 were identified during routine surveillance of acute flaccid paralysis (AFP) cases. Consequently, a retrospective VDPV survey was conducted to ensure that there was no circulating VDPV in the country. All Sabin poliovirus isolates identified in Uganda 6 months before and 6 months after were re-screened; Sabin 1 and 3 polioviruses were re-screened for Sabin 2 and Sabin 2 polioviruses were re-screened for VDPVs type 2. The Poliovirus rRT-PCR ITD/VDPV 4.0 assay and sequencing were used respectively. Results The first two VDPVs type2 were identified in Eastern Uganda and the third was identified during the survey from South-western Uganda. These regions had low OPV coverage and poor AFP surveillance indicators. Conclusion The retrospective VDPV survey was a useful strategy to screen for VDPVs more exhaustively. Supplementary surveillance methods need to be encouraged.
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    Vaccine Associated Paralytic Poliomyelitis Cases From Children Presenting With Acute Flaccid Paralysis in Uganda
    (Journal of medical virology, 2015) Nanteza, Mary B.; Kisakye, Annet; Ota, Martin O.; Gumede, Nicksy; Bwogi, Josephine
    Poliomyelitis is caused by Poliovirus 1, 2, and 3 which belong to the family Picornaviridae and the genus Enterovirus. Paralytic polio usually affects one lower limb and presents with hypotonia, reduced reflexes, wasting of muscles but with no loss of sensorium. Plans to eradicate poliomyelitis are intensively on-going and these are being achieved by the use of both oral polio vaccine (OPV) as well as the inactivated polio vaccine (IPV). The viral strains in OPV (Sabins) are unstable (Agol, 2006) for example Sabin poliovirus 1 harbors an attenuating mutation of A480G in the 50UTR whereas that of Sabin Poliovirus 2 and 3 are at the G481A and C472U sites respectively [Kew et al., 2004; Kew, 2009]. The mutations at these specific sites are not infrequent. They are associated rarely with increased neurovirulence and only infrequently cause AFP. This underrates their importance.