Evaluating the performance of tools used to call minority variants from whole genome short-read data. by Said Mohammed, K, Kibinge, N, Prins, P, Agoti, CN, Cotten, M, Nokes, DJ, Brand, S, Githinji, G

Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant by Agoti, CN, Phan, MVT, Munywoki, PK, Githinji, G, Medley, GF, Cane, PA, Kellam, P, Cotten, M, Nokes, DJ

Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season by Nyasimi, FM, Owuor, DC, Ngoi, JM, Mwihuri, AG, Otieno, GP, Otieno, JR, Githinji, G, Nyiro, JU, Nokes, DJ, Agoti, CN

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis by Agoti, CN, Munywoki, PK, Phan, MVT, Otieno, JR, Kamau, E, Bett, A, Kombe, I, Githinji, G, Medley, GF, Cane, PA, Kellam, P, Cotten, M, Nokes, DJ

Spatio-temporal distribution of rhinovirus types in Kenya: a retrospective analysis, 2014 by Morobe, JM, Kamau, E, Luka, MM, Murunga, N, Lewa, C, Mutunga, M, Bigogo, G, Otieno, N, Nyawanda, B, Onyango, C, Nokes, DJ, Agoti, CN, Munywoki, PK

Optimization of the SARS-CoV-2 ARTIC network V4 primers and whole genome sequencing protocol by Lambisia, AW, Mohammed, KS, Makori, TO, Ndwiga, L, Mburu, MW, Morobe, JM, Moraa, EO, Musyoki, J, Murunga, N, Mwangi, JN, Nokes, DJ, Agoti, CN, Ochola-Oyier, LI, Githinji, G

Endemic chikungunya fever in Kenyan children: a prospective cohort study. by Nyamwaya, DK, Otiende, M, Omuoyo, DO, Githinji, G, Karanja, HK, Gitonga, JN, R de Laurent, Z, Otieno, JR, Sang, R, Kamau, E, Cheruiyot, S, Otieno, E, Agoti, CN, Bejon, P, Thumbi, SM, Warimwe, GM

Incidence of chikungunya virus infections among Kenyan children with neurological disease, 2014–2018: a cohort study by Nyamwaya, DK, Otiende, M, Mwango, L, Kariuki, SM, Otieno, B, Omuoyo, DO, Githinji, G, Kitsao, BS, Karanja, HK, Gitonga, JN, de Laurent, ZR, Davies, A, Mwarumba, S, Agoti, CN, Thumbi, SM, Hamaluba, MM, Newton, CR, Bejon, P, Warimwe, GM

Congenital microcephaly unrelated to flavivirus exposure in coastal Kenya by Barsosio, HC, Gitonga, JN, Karanja, HK, Nyamwaya, DK, Omuoyo, DO, Kamau, E, Hamaluba, MM, Nyiro, JU, Kitsao, BS, Nyaguara, A, Mwakio, S, Newton, CR, Sang, R, Wright, D, Sanders, EJ, Seale, AC, Agoti, CN, Berkley, JA, Bejon, P, Warimwe, GM

Evaluation of population immunity against SARS-CoV-2 variants, EG.5.1, FY.4, BA.2.86, JN.1, JN.1.4, and KP.3.1.1 using samples from two health demographic surveillance systems in K... by Lugano, D, Kutima, B, Kimani, M, Sigilai, A, Gitonga, J, Karani, A, Akech, D, Karia, B, Ziraba, AK, Maina, A, Lambisia, A, Omuoyo, D, Mugo, D, Lucinde, R, Owuor, S, Konyino, G, Newman, J, Bailey, D, Nduati, E, Githinji, G, Agoti, CN, Bejon, P, Scott, JAG, Agweyu, A, Warimwe, GM

Epidemiology of COVID-19 infections on routine polymerase chain reaction (PCR) and serology testing in Coastal Kenya by Nyagwange, J, Ndwiga, L, Muteru, K, Wamae, K, Tuju, J, Testing Team, C, Kutima, B, Gitonga, J, Karanja, H, Mugo, D, Kasera, K, Amoth, P, Murunga, N, Babu, L, Otieno, E, Githinji, G, Nokes, DJ, Tsofa, B, Orindi, B, Barasa, E, Warimwe, G, Agoti, CN, Bejon, P, Ochola-Oyier, LI

Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya. by Orangi, S, Ojal, J, Brand, SP, Orlendo, C, Kairu, A, Aziza, R, Ogero, M, Agweyu, A, Warimwe, GM, Uyoga, S, Otieno, E, Ochola-Oyier, LI, Agoti, CN, Kasera, K, Amoth, P, Mwangangi, M, Aman, R, Ng'ang'a, W, Adetifa, IM, Scott, JAG, Bejon, P, Keeling, MJ, Flasche, S, Nokes, DJ, Barasa, E

Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data by Ojal, J, Brand, SP, Were, V, Okiro, EA, Kombe, IK, Mburu, C, Aziza, R, Ogero, M, Agweyu, A, Warimwe, GM, Uyoga, S, Adetifa, IMO, Scott, JAG, Otieno, E, Ochola-Oyier, LI, Agoti, CN, Kasera, K, Amoth, P, Mwangangi, M, Aman, R, Ng’ang’a, W, Tsofa, B, Bejon, P, Barasa, E, Keeling, MJ, Nokes, DJ

Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data by Ojal, J, Brand, SPC, Were, V, Okiro, EA, Kombe, IK, Mburu, C, Aziza, R, Ogero, M, Agweyu, A, Warimwe, GM, Uyoga, S, Adetifa, IMO, Scott, JAG, Otieno, E, Ochola-Oyier, LI, Agoti, CN, Kasera, K, Amoth, P, Mwangangi, M, Aman, R, Ng'ang'a, W, Tsofa, B, Bejon, P, Barasa, E, Keeling, MJ, Nokes, DJ

COVID-19 transmission dynamics underlying epidemic waves in Kenya by Brand, SPC, Ojal, J, Aziza, R, Were, V, Okiro, EA, Kombe, IK, Mburu, C, Ogero, M, Agweyu, A, Warimwe, GM, Nyagwange, J, Karanja, H, Gitonga, JN, Mugo, D, Uyoga, S, Adetifa, IMO, Scott, JAG, Otieno, E, Murunga, N, Otiende, M, Ochola-Oyier, LI, Agoti, CN, Githinji, G, Kasera, K, Amoth, P, Mwangangi, M, Aman, R, Ng'ang'a, W, Tsofa, B, Bejon, P, Keeling, MJ, Nokes, DJ, Barasa, E

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: a retrospective genomic study by Agoti, CN, Ochola-Oyier, LI, Dellicour, S, Mohammed, KS, Lambisia, AW, de Laurent, ZR, Morobe, JM, Mburu, MW, Omuoyo, DO, Ongera, EM, Ndwiga, L, Maitha, E, Kitole, B, Suleiman, T, Mwakinangu, M, Nyambu, JK, Otieno, J, Salim, B, Musyoki, J, Murunga, N, Otieno, E, Kiiru, JN, Kasera, K, Amoth, P, Mwangangi, M, Aman, R, Kinyanjui, S, Warimwe, G, Phan, M, Agweyu, A, Cotten, M, Barasa, E, Tsofa, B, Nokes, DJ, Bejon, P, Githinji, G

Genomic epidemiology of SARS-CoV-2 in Seychelles, 2020–2021 by Morobe, JM, Pool, B, Marie, L, Didon, D, Lambisia, AW, Makori, T, Mohammed, KS, de Laurent, ZR, Ndwiga, L, Mburu, MW, Moraa, E, Murunga, N, Musyoki, J, Mwacharo, J, Nyamako, L, Riako, D, Ephnatus, P, Gambo, F, Naimani, J, Namulondo, J, Tembo, SZ, Ogendi, E, Balde, T, Dratibi, FA, Yahaya, AA, Gumede, N, Achilla, RA, Borus, PK, Wanjohi, DW, Tessema, SK, Mwangangi, J, Bejon, P, Nokes, DJ, Ochola-Oyier, LI, Githinji, G, Biscornet, L, Agoti, CN

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors by Uyoga, S, Adetifa, IMO, Karanja, H, Nyagwange, J, Tuju, J, Wanjiku, P, Aman, R, Mwangangi, M, Amoth, P, Kasera, K, Ng’ang’a, W, Rombo, C, Yegon, C, Kithi, K, Odhiambo, E, Rotich, T, Orgut, I, Kihara, S, Otiende, M, Bottomley, C, Mupe, ZN, Kagucia, EW, Gallagher, KE, Etyang, A, Voller, S, Gitonga, JN, Mugo, D, Agoti, CN, Otieno, E, Ndwiga, L, Lambe, T, Wright, D, Barasa, E, Tsofa, B, Bejon, P, Ochola-Oyier, LI, Agweyu, A, Scott, A, Warimwe, G

Anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin g antibody seroprevalence among truck drivers and assistants in Kenya by Kagucia, EW, Gitonga, JN, Kalu, C, Ochomo, E, Ochieng, B, Kuya, N, Karani, A, Nyagwange, J, Karia, B, Mugo, D, Karanja, HK, Tuju, J, Mutiso, A, Maroko, H, Okubi, L, Maitha, E, Ajuck, H, Mukabi, D, Moracha, W, Bulimu, D, Andanje, N, Aman, R, Mwangangi, M, Amoth, P, Kasera, K, Ng'ang'a, W, Nyaguara, A, Voller, S, Otiende, M, Bottomley, C, Agoti, CN, Adetifa, IMO, Etyang, AO, Gallagher, KE, Uyoga, S, Barasa, E, Ochola-Oyier, LI, Bejon, P, Tsofa, B, Agweyu, A, Warimwe, GM, Scott, JAG

SARS-CoV-2 seroprevalence in three Kenyan health and demographic surveillance sites, December 2020-May 2021 by Etyang, AO, Adetifa, I, Omore, R, Misore, T, Ziraba, AK, Ng'oda, MA, Gitau, E, Gitonga, J, Mugo, D, Kutima, B, Karanja, H, Toroitich, M, Nyagwange, J, Tuju, J, Wanjiku, P, Aman, R, Amoth, P, Mwangangi, M, Kasera, K, Ng'ang'a, W, Akech, D, Sigilai, A, Karia, B, Karani, A, Voller, S, Agoti, CN, Ochola-Oyier, LI, Otiende, M, Bottomley, C, Nyaguara, A, Uyoga, S, Gallagher, K, Kagucia, EW, Onyango, D, Tsofa, B, Mwangangi, J, Maitha, E, Barasa, E, Bejon, P, Warimwe, GM, Scott, JAG, Agweyu, A