Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022.
Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022.
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DOI：
10.1128/spectrum.01328-23
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发表时间：
2023-12-12
影响因子：
3.7
通讯作者：
Realegeno, Susan
中科院分区：
文献类型：
--
作者：
Kayiwa, John T.;Nassuna, Charity;Mulei, Sophia;Kiggundu, Gladys;Nakaseegu, Joweria;Nabbuto, Maria;Amwine, Esther;Nakamoga, Bridget;Nankinga, Sarah;Atuhaire, Phiona;Nabiryo, Pheobe;Alunzi, Pixy;Mbaziira, Tony;Isabirye, Paul;Ayuro, Noel;Owor, Nicholas;Kiconco, Jocelyn;Bakamutumaho, Barnabas;Middlebrook, Earl Austin;Kaleebu, Pontiano;Lutwama, Julius J.;Bartlow, Andrew William;Realegeno, Susan
乌干达病毒研究所国家流感中心实验室将SARS-CoV-2聚合酶链式反应检测和基因组测序纳入2007年建立的流感监测项目。2022年1月至12月，从全国各地的ILI/SARI哨所采集和分析了7698份鼻咽/口咽(NP/OP)拭子样本。所有样本都进行了流感和SARS-CoV-2检测。其中甲型流感阳性252例(3.3%)，乙型流感162例(2.1%)，SARS-CoV-2阳性589例(7.7%)。在414份流感阳性样本中，122份(29.5%)为AH1pdm09,130份(31.4%)为AH3,162份(39.1%)为B-Victoria。所有SARS-CoV-2测序样本都是Omicron变种，存在已知的逃避免疫系统的令人担忧的亚变异体，如BQ.1和XBB.2。从监测点以外的社区其他卫生中心收集的其他SARS-CoV-2阳性样本被纳入SARS-CoV-2基因组测序，其变异体的模式相似。总而言之，ILI/SARI监测系统已被证明是一个有效、成本效益高和可持续的计划，提供了一个现成的平台，在国家一级监测社区中SARS-CoV-2的传播，同时保持对持续的流感威胁的警惕。将SARS-CoV-2检测和基因组监测整合到流感监测计划中，将加强实验室的反应能力，并有助于及时发布SARS-CoV-2基因组信息，用于补充新冠肺炎大流行的多重应对战略。呼吸道病原体在全球造成高发病率和高死亡率，并具有很高的大流行潜力。在SARS-CoV-2大流行期间，由于资源被转用于SARS-CoV-2检测和测序，流感监测严重中断。根据世界卫生组织的建议，乌干达病毒研究所、国家流感中心实验室将SARS-CoV-2检测和基因组测序纳入流感监测计划。我们描述了从乌干达各地16个哨所监测点采集的样本的流感和SARS-CoV-2检测结果，以及其他卫生中心的SARS-CoV-2检测和测序结果。监测系统显示，SARS-CoV-2和流感都可以在国家一级的社区进行监测。将SARS-CoV-2检测和基因组监测整合到流感监测计划中，将有助于及时发布用于缓解新冠肺炎大流行的SARS-CoV-2信息，并提供有关流感持续威胁的重要信息。
The Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 polymerase chain reaction testing and genomic sequencing into the influenza surveillance program that was established in 2007. A total of 7,698 nasopharyngeal/oropharyngeal (NP/OP) swab samples were collected and analyzed from ILI/SARI sentinel sites across the country from January to December 2022. All samples were tested for influenza and SARS-CoV-2. Of these, 252 (3.3%), 162 (2.1%), and 589 (7.7%) were positive for influenza A, influenza B, and SARS-CoV-2, respectively. Out of 414 influenza-positive samples, 122 (29.5%) were AH1pdm09, 130 (31.4%) were AH3, and 162 (39.1%) were B-Victoria. All SARS-CoV-2 sequenced samples were of the Omicron variant, with subvariants of concern known to evade the immune system being detected, such as BQ.1 and XBB.2. Other SARS-CoV-2 positive samples collected from other health centers in the community outside the surveillance sites were included into SARS-CoV-2 genomic sequencing with similar patterns with respect to variants. In all, the ILI/SARI surveillance system has shown to be an efficient, cost-effective, and sustainable program, providing a ready platform to monitor the circulation of SARS-CoV-2 in communities at the national level while remaining vigilant for the persistent threat of influenza. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will strengthen the laboratory response capacity, as well as facilitate the timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation. Respiratory pathogens cause high rates of morbidity and mortality globally and have high pandemic potential. During the SARS-CoV-2 pandemic, influenza surveillance was significantly interrupted because of resources being diverted to SARS-CoV-2 testing and sequencing. Based on recommendations from the World Health Organization, the Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 testing and genomic sequencing into the influenza surveillance program. We describe the results of influenza and SARS-CoV-2 testing of samples collected from 16 sentinel surveillance sites located throughout Uganda as well as SARS-CoV-2 testing and sequencing in other health centers. The surveillance system showed that both SARS-CoV-2 and influenza can be monitored in communities at the national level. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will help facilitate the timely release of SARS-CoV-2 information for COVID-19 pandemic mitigation and provide important information regarding the persistent threat of influenza.
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DOI：
10.1371/journal.pgph.0000811
发表时间：
2022
期刊：
PLOS global public health
影响因子：
--
作者：
通讯作者：
--
影响因子：
11.8
作者：
Shu B;Kirby MK;Davis WG;Warnes C;Liddell J;Liu J;Wu KH;Hassell N;Benitez AJ;Wilson MM;Keller MW;Rambo-Martin BL;Camara Y;Winter J;Kondor RJ;Zhou B;Spies S;Rose LE;Winchell JM;Limbago BM;Wentworth DE;Barnes JR
通讯作者：
Barnes JR
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
4.1
作者：
Shrestha, Lasata;Lin, Michelle J.;Xie, Hong;Mills, Margaret G.;Bakhash, Shah A. Mohamed;Gaur, Vinod P.;Livingston, Robert J.;Castor, Jared;Bruce, Emily A.;Botten, Jason W.;Huang, Meei-Li;Jerome, Keith R.;Greninger, Alexander L.;Roychoudhury, Pavitra
通讯作者：
Roychoudhury, Pavitra
DOI：
10.1093/infdis/jiy517
发表时间：
2019-01-09
期刊：
The Journal of infectious diseases
影响因子：
--
作者：
Caballero MT;Bianchi AM;Nuño A;Ferretti AJP;Polack LM;Remondino I;Rodriguez MG;Orizzonte L;Vallone F;Bergel E;Polack FP
通讯作者：
Polack FP