Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009-2012.

BACKGROUND: Human Coronaviruses (HCoV) are a common cause of respiratory illnesses and are responsible for considerable morbidity and hospitalization across all age groups especially in individuals with compromised immunity. There are six known species of HCoV: HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV and SARS-HCoV. Although studies have shown evidence of global distribution of HCoVs, there is limited information on their presence and distribution in Kenya. METHODS: HCoV strains that circulated in Kenya were retrospectively diagnosed and molecularly characterized. A total of 417 nasopharyngeal specimens obtained between January 2009 and December 2012 from around Kenya were analyzed by a real time RT-PCR using HCoV-specific primers. HCoV-positive specimens were subsequently inoculated onto monolayers of LL-CMK2 cells. The isolated viruses were characterized by RT-PCR amplification and sequencing of the partial polymerase (pol) gene. RESULTS: The prevalence of HCoV infection was as follows: out of the 417 specimens, 35 (8.4 %) were positive for HCoV, comprising 10 (2.4 %) HCoV-NL63, 12 (2.9 %) HCoV-OC43, 9 (2.1 %) HCoV-HKU1, and 4 (1 %) HCoV-229E. The Kenyan HCoV strains displayed high sequence homology to the prototypes and contemporaneous strains. Evolution analysis showed that the Kenyan HCoV-OC43 and HCoV-NL63 isolates were under purifying selection. Phylogenetic evolutionary analyses confirmed the identities of three HCoV-HKU1, five HCoV-NL63, eight HCoV-OC43 and three HCoV-229E. CONCLUSIONS: There were yearly variations in the prevalence and circulation patterns of individual HCoVs in Kenya. This paper reports on the first molecular characterization of human Coronaviruses in Kenya, which play an important role in causing acute respiratory infections among children.

Detection of dengue virus serotypes 1, 2 and 3 in selected regions of Kenya: 2011-2014.

BACKGROUND: Dengue fever, a mosquito-borne disease, is associated with illness of varying severity in countries in the tropics and sub tropics. Dengue cases continue to be detected more frequently and its geographic range continues to expand. We report the largest documented laboratory confirmed circulation of dengue virus in parts of Kenya since 1982. METHODS: From September 2011 to December 2014, 868 samples from febrile patients were received from hospitals in Nairobi, northern and coastal Kenya. The immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against dengue, yellow fever, West Nile and Zika. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus family, yellow fever, West Nile, consensus and sero type dengue primers were used to detect acute arbovirus infections and determine the infecting serotypes. Representative samples of PCR positive samples for each of the three dengue serotypes detected were sequenced to confirm circulation of the various dengue serotypes. RESULTS: Forty percent (345/868) of the samples tested positive for dengue by either IgM ELISA (14.6 %) or by RT-PCR (25.1 %). Three dengue serotypes 1-3 (DENV1-3) were detected by serotype specific RT-PCR and sequencing with their numbers varying from year to year and by region. The overall predominant serotype detected from 2011-2014 was DENV1 accounting for 44 % (96/218) of all the serotypes detected, followed by DENV2 accounting for 38.5 % (84/218) and then DENV3 which accounted for 17.4 % (38/218). Yellow fever, West Nile and Zika was not detected in any of the samples tested. CONCLUSION: From 2011-2014 serotypes 1, 2 and 3 were detected in the Northern and Coastal parts of Kenya. This confirmed the occurrence of cases and active circulation of dengue in parts of Kenya. These results have documented three circulating serotypes and highlight the need for the establishment of active dengue surveillance to continuously detect cases, circulating serotypes, and determine dengue fever disease burden in the country and region.

Antibiotics for leptospirosis.

BACKGROUND: Leptospirosis has a wide-ranging clinical and public health impact. Leptospira are globally distributed. Case attack rates are as high as 1:4 to 2:5 persons in exposed populations. In some settings mortality has exceeded 10% of infected people. The benefit of antibiotic therapy in the disease has been unclear. OBJECTIVES: We sought to characterise the risks and benefits associated with use of antibiotic therapy in the management of leptospirosis. SEARCH METHODS: We searched the The Cochrane Hepato-Biliary Group Controlled Trials Register, the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library, MEDLINE, EMBASE, and Science Citation Index Expanded regardless of study language. This was augmented by a manual search. The last date of search was November, 2011. SELECTION CRITERIA: To be included in assessment of benefits, trials had to specifically assess the use of antibiotics in a randomised clinical trial. A broad range of study types were incorporated to seek potential harms. DATA COLLECTION AND ANALYSIS: Included trials were systematically abstracted, as were excluded studies for the purposes of assessing harms. Analyses were conducted in accordance with The Cochrane Handbook and practices of The Cochrane Hepato-Biliary Group. MAIN RESULTS: Seven randomised trials were included.  Four trials with 403 patients compared an antibiotic with placebo or no intervention. Three trials compared at least one antibiotic regimen with another antibiotic regimen. The trials all had high risk of bias. The trials varied in the severity of leptospirosis among trial patients. The ability to group data for meta-analysis was limited. While all four trials that compared antibiotics with placebo reported mortality and used parenteral penicillin, there were no deaths in two of them. Since odds ratio calculations cannot employ zero-event trials, only two trials contributed to this estimate. The number of deaths were 16/200 (8.0%) in the antibiotic arm versus 11/203 (5.4%) in the placebo arm giving a fixed-effect OR 1.56 (95% CI 0.70 to 3.46). The random-effects OR is 1.16 (95% CI 0.23 to 5.95). The heterogeneity among these four trials for the mortality outcome was moderate (I(2)= 50%). Only one trial (253 patients) reported days of hospitalisation. It compared parenteral penicillin to placebo without significant effect of therapy (8.9 versus 8.8 days; mean difference (MD) 0.10 days, 95% CI -0.83 to 1.03). The difference in days of clinical illness was reported in two of these trials (71 patients). While parenteral penicillin therapy conferred 4.7 to 5.6 days of clinical illness in contrast to 7.7 to 11.6 days in the placebo arm, the size of the estimate of effect increased but statistical significance was lost under the random-effect model (fixed-effect: MD -2.13 days, 95% CI -2.46 to -1.80; random-effects: MD -4.04, 95% CI -8.66 to 0.58). I(2) for this outcome was high (81%). When duration of fever alone was assessed between antibiotics and placebo in a single trial (79 patients), no significant difference existed (6.9 versus 6.6 days; MD 0.30, 95% CI -1.26 to 1.86). Two trials with 332 patients in relatively severe and possibly late leptospirosis, resulted in trends towards increased dialysis when penicillin was used rather than placebo, but the estimate of effect was small and did not reach statistical significance (42/163 (25.8%) versus 31/169 (18.4%); OR 1.54, 95% CI 0.91 to 2.60). When one antibiotic was assessed against another antibiotic, there were no statistically significant results. For mortality in particular, these comparisons included cephalosporin versus penicillin (2 trials, 6/176 (3.4%) versus 9/175 (5.2%); fixed-effect: OR 0.65, 95% CI 0.23 to 1.87, I(2)= 16%), doxycycline versus penicillin (1 trial, 2/81 (2.5%) versus 4/89 (4.5); OR 0.54, 95% CI 0.10 to 3.02), cephalosporin versus doxycycline (1 trial, 1/88 (1.1%) versus 2/81 (2.5%); OR 0.45, 95% CI 0.04 to 5.10). There were no adverse events of therapy which reached statistical significance. AUTHORS' CONCLUSIONS: Insufficient evidence is available to advocate for or against the use of antibiotics in the therapy for leptospirosis. Among survivors who were hospitalised for leptospirosis, use of antibiotics for leptospirosis may have decreased the duration of clinical illness by two to four days, though this result was not statistically significant. When electing to treat with an antibiotic, selection of penicillin, doxycycline, or cephalosporin does not seem to impact mortality nor duration of fever. The benefit of antibiotic therapy in the treatment of leptospirosis remains unclear, particularly for severe disease. Further clinical research is needed to include broader panels of therapy tested against placebo.

No effect of mild nonconcussive injury on neurocognitive functioning in U.S. Army soldiers deployed to Iraq.

UNLABELLED: With neurocognitive testing being heavily relied on for concussion assessments in the U.S. Warfighter, there is a need to investigate the impact of nonconcussive injury on neurocognitive functioning. OBJECTIVES: To determine if a nonconcussive injury may have a negative effect on neurocognitive functioning in a deployment setting. METHODS: The current study compared scores on computerized and traditional neurocognitive tests of 166 Soldiers deployed to Iraq. Performance on a battery of tests was compared between a group of healthy deployed Soldiers (n = 102) versus a group of deployed Soldiers seeking outpatient care for mild injuries not involving the head or blast exposure (n = 62). RESULTS: The injured group's performance was not significantly lower on any of the measures administered compared to healthy Soldiers. CONCLUSIONS: The results suggest that there was no significant effect of nonconcussive injury on neurocognitive functioning. Findings lend support to feasibility of using neurocognitive tests to evaluate the effects of concussion in theater.

The ANAM lacks utility as a diagnostic or screening tool for concussion more than 10 days following injury.

Congress has mandated that the Department of Defense perform screening for concussion, or mild traumatic brain injury, on all service members redeploying from Iraq and Afghanistan. However, the retrospective diagnosis of concussion is complicated by the subjective nature of the complaints, overlap of symptoms with other conditions, and the normally rapid recovery of neurocognitive function following a concussive event. One diagnostic and screening test in current use by the Department of Defense is the Automated Neuropsychological Assessment Metrics (ANAM). A team of researchers deployed to Iraq between January and April 2009 to test the validity of the ANAM for the diagnosis of concussion in the combat environment. Performance by concussed participants on all six ANAM subtests was compared with that of controls. The ANAM appears to have no utility as an individual diagnostic or population screening tool for the detection of neurocognitive dysfunction from a single, uncomplicated concussion when administered 10 or more days following injury. Further studies are required to determine the modalities providing optimal sensitivity and specificity for use as diagnostic or screening tests beyond the first 72-hour acute postinjury period.

Perceptions of Seasonal Influenza Vaccine Among U.S. Army Civilians and Dependents in the Kaiserslautern Military Community: A Mixed-Methods Survey.

INTRODUCTION: Influenza is a globally occurring viral respiratory infection that can lead to hospitalizations and death. An influenza outbreak can interfere with combat readiness in a military setting, as the infection can incapacitate soldiers. Vaccination remains the most effective tool to prevent and mitigate seasonal influenza. Although influenza vaccinations for U.S. Army soldiers can be monitored through military health systems, those systems cannot capture DoD civilians and Army dependents who may not use military health services. This study aims to gauge flu vaccine uptake and perceptions in U.S. Army civilians and dependents. MATERIALS AND METHODS: An online survey was e-mailed to civilian and dependent enrollees of Landstuhl Regional Medical Center. The survey contained 24 questions pertaining to demographics, vaccine history, history of the flu, and beliefs toward vaccines. Chi-square tests, t-tests, and logistic regressions were performed to investigate the association between demographic, behavior, and belief factors with vaccine uptake. Free-text answers were coded and categorized by themes. RESULTS: Over 70% of respondents were vaccinated for the flu. There were differences between vaccinated and unvaccinated respondents regarding their perceptions of barriers to vaccination, benefits of the flu vaccine, severity of flu symptoms, and personal risk of getting ill with the flu. After controlling for confounders, flu vaccination in the previous season and healthcare worker status were associated with increased vaccine uptake, while perceived barriers to influenza vaccination were associated with decreased vaccine uptake. CONCLUSIONS: Flu vaccine uptake may be increased by increasing access to vaccination, promoting vaccination and addressing concerns at the provider level, and engaging positively framed public messaging. Increasing flu vaccine uptake is of particular importance as the flu season approaches during the COVID-19 (Coronavirus disease 2019) pandemic.

Seroprevalence and distribution of arboviral infections among rural Kenyan adults: a cross-sectional study.

BACKGROUND: Arthorpod-borne viruses (arboviruses) cause wide-spread morbidity in sub-Saharan Africa, but little research has documented the burden and distribution of these pathogens. METHODS: Using a population-based, cross-sectional study design, we administered a detailed questionnaire and used ELISA to test the blood of 1,141 healthy Kenyan adults from three districts for the presence of anti-viral Immunoglobulin G (IgG) antibodies to the following viruses: dengue (DENV), West Nile (WNV), yellow fever (YFV), Chikungunya (CHIKV), and Rift Valley fever (RVFV). RESULTS: Of these, 14.4% were positive for DENV, 9.5% were WNV positive, 9.2% were YFV positive, 34.0% were positive for CHIKV and 0.7% were RVFV positive. In total, 46.6% had antibodies to at least one of these arboviruses. CONCLUSIONS: For all arboviruses, district of residence was strongly associated with seropositivity. Seroprevalence to YFV, DENV and WNV increased with age, while there was no correlation between age and seropositivity for CHIKV, suggesting that much of the seropositivity to CHIKV is due to sporadic epidemics. Paradoxically, literacy was associated with increased seropositivity of CHIKV and DENV.

A growing global network's role in outbreak response: AFHSC-GEIS 2008-2009.

A cornerstone of effective disease surveillance programs comprises the early identification of infectious threats and the subsequent rapid response to prevent further spread. Effectively identifying, tracking and responding to these threats is often difficult and requires international cooperation due to the rapidity with which diseases cross national borders and spread throughout the global community as a result of travel and migration by humans and animals. From Oct.1, 2008 to Sept. 30, 2009, the United States Department of Defense's (DoD) Armed Forces Health Surveillance Center Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) identified 76 outbreaks in 53 countries. Emerging infectious disease outbreaks were identified by the global network and included a wide spectrum of support activities in collaboration with host country partners, several of which were in direct support of the World Health Organization's (WHO) International Health Regulations (IHR) (2005). The network also supported military forces around the world affected by the novel influenza A/H1N1 pandemic of 2009. With IHR (2005) as the guiding framework for action, the AFHSC-GEIS network of international partners and overseas research laboratories continues to develop into a far-reaching system for identifying, analyzing and responding to emerging disease threats.

Training initiatives within the AFHSC-Global Emerging Infections Surveillance and Response System: support for IHR (2005).

Training is a key component of building capacity for public health surveillance and response, but has often been difficult to quantify. During fiscal 2009, the Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) supported 18 partner organizations in conducting 123 training initiatives in 40 countries for 3,130 U.S. military, civilian and host-country personnel. The training assisted with supporting compliance with International Health Regulations, IHR (2005). Training activities in pandemic preparedness, outbreak investigation and response, emerging infectious disease (EID) surveillance and pathogen diagnostic techniques were expanded significantly. By engaging local health and other government officials and civilian institutions, the U.S. military's role as a key stakeholder in global public health has been strengthened and has contributed to EID-related surveillance, research and capacity-building initiatives specified elsewhere in this issue. Public health and emerging infections surveillance training accomplished by AFHSC-GEIS and its Department of Defense (DoD) partners during fiscal 2009 will be tabulated and described.

Health care workers and researchers traveling to developing-world clinical settings: disease transmission risk and mitigation.

With the recent emphasis on funding and training opportunities for global health and humanitarian aid and the increased interest in the field, many health care workers and medical researchers are traveling from resource-replete to resource-limited settings. This type of travel brings unique disease risks not routinely considered for the business or vacationing traveler. This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation.

Increased prevalence of the pfdhfr/phdhps quintuple mutant and rapid emergence of pfdhps resistance mutations at codons 581 and 613 in Kisumu, Kenya.

BACKGROUND: Anti-malarial drug resistance in Kenya prompted two drug policy changes within a decade: sulphadoxine-pyrimethamine (SP) replaced chloroquine (CQ) as the first-line anti-malarial in 1998 and artemether-lumefantrine (AL) replaced SP in 2004. Two cross-sectional studies were conducted to monitor changes in the prevalence of molecular markers of drug resistance over the period in which SP was used as the first-line anti-malarial. The baseline study was carried out from 1999-2000, shortly after implementation of SP, and the follow-up study occurred from 2003-2005, during the transition to AL. MATERIALS AND METHODS: Blood was collected from malaria smear-positive, symptomatic patients presenting to outpatient centers in Kisumu, Kenya, during the baseline and follow-up studies. Isolates were genotyped at codons associated with SP and CQ resistance. In vitro IC50 values for antifolates and quinolones were determined for isolates from the follow-up study. RESULTS: The prevalence of isolates containing the pfdhfr N51I/C59R/S108N/pfdhps A437G/K540E quintuple mutant associated with SP-resistance rose from 21% in the baseline study to 53% in the follow-up study (p < 0.001). Isolates containing the pfdhfr I164L mutation were absent from both studies. The pfdhps mutations A581G and A613S/T were absent from the baseline study but were present in 85% and 61%, respectively, of isolates from the follow-up study. At follow-up, parasites with mutations at five pfdhps codons, 436, 437, 540, 581, and 613, accounted for 39% of isolates. The CQ resistance-associated mutations pfcrt K76T and pfmdr1 N86Y rose from 82% to 97% (p = 0.001) and 44% to 76% (p < 0.001), respectively, from baseline to follow-up. CONCLUSIONS: During the period in which SP was the first-line anti-malarial in Kenya, highly SP-resistant parasites emerged, including isolates harboring pfdhps mutations not previously observed there. SP continues to be widely used in Kenya; however, given the highly resistant genotypes observed in this study, its use as a first-line anti-malarial should be discouraged, particularly for populations without acquired immunity to malaria. The increase in the pfcrt K76T prevalence, despite efforts to reduce CQ use, suggests that either these efforts are not adequate to alleviate CQ pressure in Kisumu, or that drug pressure is derived from another source, such as the second-line anti-malarial amodiaquine.

Evaluation of the Military Acute Concussion Evaluation for use in combat operations more than 12 hours after injury.

The diagnosis and management of concussion can be difficult in a combat environment, especially in the absence of loss of consciousness or post-traumatic amnesia. As no validated test exists to diagnose or grade neurocognitive impairment from a concussion, the military currently employs the Military Acute Concussion Evaluation (MACE) in Iraq. This is a two-part test, which incorporates the standardized assessment of concussion (SAC) as its objective score, although it has not been shown to be valid unless administered shortly after injury. A research team deployed to Iraq between January and April 2009 to examine the validity of several tests of neurocognitive function following a concussion, including the MACE. When administered more than 12 hours after the concussive injury, the MACE lacked sufficient sensitivity and specificity to be clinically useful.

The importance of militaries from developing countries in global infectious disease surveillance.

Military forces from developing countries have become increasingly important as facilitators of their government's foreign policy, taking part in peacekeeping operations, military exercises and humanitarian relief missions. Deployment of these forces presents both challenges and opportunities for infectious disease surveillance and control. Troop movements may cause or extend epidemics by introducing novel agents to susceptible populations. Conversely, military units with disease surveillance and response capabilities can extend those capabilities to civilian populations not served by civilian public health programmes, such as those in remote or post-disaster settings. In Peru and Thailand, military health organizations in partnership with the military of the United States use their laboratory, epidemiological, communications and logistical resources to support civilian ministry of health efforts. As their role in international affairs expands, surveillance capabilities of militaries from developing countries should be enhanced, perhaps through partnerships with militaries from high-income countries. Military-to-military and military-to-civilian partnerships, with the support of national and international civilian health organizations, could also greatly strengthen global infectious disease surveillance, particularly in remote and post-disaster areas where military forces are present.

Outcomes From U.S. Military-Supported Overseas Training Rotations in Tropical Medicine and Global Health, 2006-2015.

BACKGROUND: Since 2006, the Division of Tropical Public Health at the Uniformed Services University (USU) has sponsored the Tropical Medicine Training Program (TMTP). Despite practice guidelines stating that global health education should include the collection and evaluation of data on the impact of the training experiences, no quantitative evaluation of program outcomes had previously occurred. The objective of this report was to evaluate TMTP outcomes to guide program improvement. METHODS: We developed an anonymous, web-based survey to assess program outcomes as part of routine program evaluation. The survey addressed four main areas of potential TMTP impact: (1) career engagement, (2) military service contributions, (3) scholarly activity, and (4) acquisition of knowledge and skills. In February 2016, we sent the survey electronically to 222 program participants between Fiscal Years 2006 and 2015 who had e-mails available in DoD administrative systems. FINDINGS: Ninety-eight (44%) of these responded to the survey. TMTP demonstrated impact in several areas. Increased knowledge and skills were reported by 81% of trainees, and 70% reported increased interest in serving at military overseas medical research laboratories. Subsequent career engagement by trainees included seven assignments to overseas research laboratories, 71 military deployments, and 193 short-term military missions. The ability to achieve many of the desired outcomes was associated with time elapsed since completion of formal medical education, including 24% who were still enrolled in graduate medical education. DISCUSSION/IMPACT/RECOMMENDATIONS: The TMTP has improved the U.S. military's ability to perform surveillance for emerging tropical and infectious diseases and has contributed to force health protection and readiness. Although many of the outcomes, such as service in the overseas research laboratories and military deployments, are dependent on military service requirements, these results remain perhaps the most relevant ways that the TMTP meets global health requirements of the US military and the nation. Additional outcomes from this training are expected to accrue as these participants complete their medical postgraduate training programs.

DoD-Supported Overseas Training Rotations in Tropical Medicine and Global Health, 2000-2015.

In 1999, the Department of Defense developed a tropical medicine training program (TMTP) to train military physicians, medical students, and scientists in performing surveillance activities in an overseas environment. This review describes the competencies, educational approach, program participants, institutional collaborations, and process outcomes of the TMTP from 2000 to 2015. TMTP-sponsored rotations addressed a wide variety of interdisciplinary competencies, many of which have military-unique applications. Rotations consisted of both didactic and experiential (overseas) components. The program provided 282 rotations for 260 trainees between 2006 and 2015, the years for which data were available. The Department of Defense accrues benefits from this training program in three main ways: (1) building a cadre of health care professionals who will go on to work at the overseas research laboratories, (2) supporting force health protection and readiness through experiential tropical medicine training, and (3) engaging in global health collaborations and partnerships. The primary challenges include funding, health and security, trainee and site heterogeneity, supervision, trainee engagement, and burden on the host institution. The program will continue to focus on improvement in these areas, with special attention to trainee preparation, communication with both trainees and host sites, and increasing reciprocity with host sites and their faculty.

Literacy and recent history of diarrhoea are predictive of Plasmodium falciparum parasitaemia in Kenyan adults.

BACKGROUND: Malaria is one of the most serious health problems in Kenya. In 2004, the Kenya Medical Research Institute and the US Army Medical Research Unit--Kenya surveyed adults in Samburu, Malindi, and Busia districts to determine socioeconomic risk factors for infection. METHODS: Sociodemographic, health, and antimalarial data were collected along with blood for malaria testing. A smear was considered negative only if no Plasmodium falciparum parasites were observed in 100 high-powered fields. Univariate analysis was performed with Pearson's Chi-square test and univariate logistic regression. A multivariate logistic regression model was then created which included only variables found to be at least marginally significant in univariate analysis. RESULTS: A total of 1,141 subjects were recruited: 238 from Samburu, 442 from Malindi, and 461 from Busia. Smear positivities for P. falciparum were 1.7% in Samburu, 7.2% in Malindi and 22.3% in Busia. Interdistrict differences were statistically significant (p < 0.001) in univariate analysis and in a multivariate logistic regression model which included district, literacy, occupation, and recent illness as independent variables. In the model, literacy and recent diarrhoeal illness were positively and at least marginally significantly associated with parasitaemia (p = 0.023 and p = 0.067, respectively). Neither age, sex, occupation, history of malaria in the previous three months, nor use of antimalarials in the previous four weeks were significantly associated with parasitaemia. CONCLUSION: While district of residence was the variable most highly predictive for parasitaemia among Kenyan adults surveyed, both a recent history of diarrhoeal illness and literacy were at least marginally statistically significant predictors.

Department of Defense Global Emerging Infections Surveillance and Response System Indian Ocean tsunami response.

The Department of Defense (DoD) Global Emerging Infections Surveillance and Response System (DoD-GEIS) identifies and addresses DoD vulnerabilities to emerging infections through a global network of partners. Following the Indian Ocean tsunami of December 26, 2004, DoD-GEIS facilitated the DoD medical response and coordination with the Centers for Disease Control and Prevention and the World Health Organization. DoD-GEIS partners in Southeast Asia (U.S. Naval Medical Research Unit 2, Jakarta, Indonesia; and Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand) rapidly conducted health assessments and established surveillance for communicable diseases that threatened survivors. Preexisting collaboration with the Centers for Disease Control and Prevention, the World Health Organization, and host countries was critical for the DoD-GEIS tsunami response.

Genotyping of enteroviruses isolated in Kenya from pediatric patients using partial VP1 region.

Enteroviruses (EV) are responsible for a wide range of clinical diseases in humans. Though studied broadly in several regions of the world, the genetic diversity of human enteroviruses (HEV) circulating in the sub-Saharan Africa remains under-documented. In the current study, we molecularly typed 61 HEV strains isolated in Kenya between 2008 and 2011 targeting the 3'-end of the VP1 gene. Viral RNA was extracted from the archived isolates and part of the VP1 gene amplified by RT-PCR, followed by sequence analysis. Twenty-two different EV types were detected. Majority (72.0 %) of these belonged to Enterovirus B species followed by Enterovirus D (21.3 %) and Enterovirus A (6.5 %). The most frequently detected types were Enterovirus-D68 (EV-D68), followed by Coxsackievirus B2 (CV-B2), CV-B1, CV-B4 and CV-B3. Phylogenetic analyses of these viruses revealed that Kenyan CV-B1 isolates were segregated among sequences of global CV-B1 strains. Conversely, the Kenyan CV-B2, CV-B3, CV-B4 and EV-D68 strains generally grouped together with those detected from other countries. Notably, the Kenyan EV-D68 strains largely clustered with sequences of global strains obtained between 2008 and 2010 than those circulating in recent years. Overall, our results indicate that HEV strains belonging to Enterovirus D and Enterovirus B species pre-dominantly circulated and played a significant role in pediatric respiratory infection in Kenya, during the study period. The Kenyan CV-B1 strains were genetically divergent from those circulating in other countries. Phylogenetic clustering of Kenyan EV-D68 strains with sequences of global strains circulating between 2008 and 2010 than those obtained in recent years suggests a high genomic variability associated with the surface protein encoding VP1 gene in these enteroviruses.