Whole-Genome Characterization of SARS-CoV-2 Reveals Simultaneous Circulation of Three Variants and a Putative Recombination (20B/20H) in Pets, Brazzaville, Republic of the Congo.

Following the emergence of SARS-CoV-2, cases of pets infected with variants circulating among humans were reported. In order to evaluate the occurrence of SARS-CoV-2 circulation among pets in the Republic of the Congo, we conducted a ten-month study of dogs and cats living in COVID-19-positive households in Brazzaville and neighboring localities. Real-time PCR and the Luminex platform were used to detect SARS-CoV-2 RNA and antibodies to SARS-CoV-2 RBD and S proteins, respectively. Our results show for the first time the simultaneous circulation of several variants of SARS-CoV-2, including viruses from clades 20A and 20H and a putative recombinant variant between viruses from clades 20B and 20H. We found a high seroprevalence of 38.6%, with 14% of tested pets positive for SARS-CoV-2 RNA. Thirty-four percent of infected pets developed mild clinical signs, including respiratory and digestive signs, and shed the virus for about one day to two weeks. These results highlight the potential risk of SARS-CoV-2 interspecies transmission and the benefits of a "One Health" approach that includes SARS-CoV-2 diagnosis and surveillance of viral diversity in pets. This approach aims to prevent transmission to surrounding wildlife as well as spillback to humans.

Zaire ebolavirus surveillance near the Bikoro region of the Democratic Republic of the Congo during the 2018 outbreak reveals presence of seropositive bats.

On the 8th of May, 2018, an outbreak of Ebola virus disease (EVD) was declared, originating in the Bikoro region of the Democratic Republic of the Congo (DRC) near the border with neighboring Republic of the Congo (ROC). Frequent trade and migration occur between DRC and ROC-based communities residing along the Congo River. In June 2018, a field team was deployed to determine whether Zaire ebolavirus (Ebola virus (EBOV)) was contemporaneously circulating in local bats at the human-animal interface in ROC near the Bikoro EVD outbreak. Samples were collected from bats in the Cuvette and Likouala departments, ROC, bordering the Équateur Province in DRC where the Bikoro EVD outbreak was first detected. EBOV genomic material was not detected in bat-derived samples by targeted quantitative reverse transcription-polymerase chain reaction or by family-level consensus polymerase chain reaction; however, serological data suggests recent exposure to EBOV in bats in the region. We collected serum from 144 bats in the Cuvette department with 6.9% seropositivity against the EBOV glycoprotein and 14.3% seropositivity for serum collected from 27 fruit bats and one Molossinae in the Likouala department. We conclude that proactive investment in longitudinal sampling for filoviruses at the human-animal interface, coupled with ecological investigations are needed to identify EBOV wildlife reservoirs.

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats.

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development's (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security.

HIV-1 genetic diversity and primary drug resistance mutations before large-scale access to antiretroviral therapy, Republic of Congo.

BACKGROUND: In this work, we investigated the genetic diversity of HIV-1 and the presence of mutations conferring antiretroviral drug resistance in 50 drug-naïve infected persons in the Republic of Congo (RoC). Samples were obtained before large-scale access to HAART in 2002 and 2004. METHODS: To assess the HIV-1 genetic recombination, the sequencing of the pol gene encoding a protease and partial reverse transcriptase was performed and analyzed with updated references, including newly characterized CRFs. The assessment of drug resistance was conducted according to the WHO protocol. RESULTS: Among the 50 samples analyzed for the pol gene, 50% were classified as intersubtype recombinants, charring complex structures inside the pol fragment. Five samples could not be classified (noted U). The most prevalent subtypes were G with 10 isolates and D with 11 isolates. One isolate of A, J, H, CRF05, CRF18 and CRF37 were also found. Two samples (4%) harboring the mutations M230L and Y181C associated with the TAMs M41L and T215Y, respectively, were found. CONCLUSION: This first study in the RoC, based on WHO classification, shows that the threshold of transmitted drug resistance before large-scale access to antiretroviral therapy is 4%.

A study on HIV, Syphilis, and Hepatitis B and C virus infections among female sex workers in the Republic of Congo.

BACKGROUND: Female Sex Workers (FSWs) are considered to be at high risk for transmission of Sexually Transmitted Infections (STIs) and are defined as a priority of the national HIV/AIDS response in the Republic of Congo (RoC). However, no data are available regarding STIs in this group. This study aimed to determine the prevalences of HIV, syphilis and hepatitis B and C among FSWs in five cities in the country. METHODS: A cross-sectional study was conducted from November 2nd 2011 to May 15th 2012. Participants were recruited in Brazzaville, Pointe-Noire, Dolisie, Nkayi and Pokola using a respondent-driven sampling method. RESULTS: A total of 805 FSWs were recruited with an average age of 28.31 ± 9.15 years. The overall prevalences of HIV, syphilis, HBV and HCV were 7.50%, 2.20%, 4.20% and 0.70%, respectively. The age groups 35-39 (20.51% [0%-36.93%], p = 0.0057) and greater than 40 years (16.67% [0%-34.93%], P = 0.016) were positively associated with behaviors at high risk of HIV infection. For syphilis, the most infected age group was the one greater than 40 years, at 6.25% ([1.06% -72.37%] p = 0.04). Pointe-Noire was the most infected city for syphilis and HBV, with 5.15% (p = 0.0061) and 4.22% (p˂0.001), respectively. No risk factors were associated with HCV infection. FSWs practicing in mobile prostitution sites had a significantly higher infection rate (2.1% [0%-11.09%] p = 0.04). CONCLUSION: This study shows that the prevalence of HIV and other STIs in FSWs is high. Therefore, a combination of individual and structural interventions could reduce the risk of an STI "reservoir" among this population.

Surprisingly high prevalence of subtype C and specific HIV-1 subtype/CRF distribution in men having sex with men in Senegal.

BACKGROUND: Recent reports showed the high vulnerability for HIV infection of men who have sex with men (MSM) in Africa. Here, we report the HIV-1 variants that circulate among MSM in Senegal. METHODS: HIV-1 subtype/circulating recombinant form (CRF) was determined in an 1800-base pair fragment of pol for 70 HIV-1-positive samples from MSM. Phylogenetic trees were constructed using the neighbor-joining method with CLUSTALX. Similarity and bootstrap plots were then done for recombination analysis. The maximum likelihood approach was used for the identification of transmission clusters. RESULTS: Sixty-seven samples (95%) were from Senegalese MSM, 90% unmarried with a median age of 30 years. Fifty-five MSM had regular male partners, but 39 of 70 had also a regular female partner. The overall subtype/CRF distribution was as follows: 28 C (40%), 17 CRF02_AG (24.3%), 13 B (18.6%), 6 G (8.6%), 3 CRF09_cpx (4.3%), and 3 (4.3%) unique recombinants. In addition, 47 sequences (67.15%) were segregated into 15 transmission clusters. CONCLUSIONS: These variants circulate also among the general population or female sex workers, but the proportions are significantly different. Despite the massive stigma, the majority (80%) of MSM recognized having sex with women and could serve as a bridge for intermixing of HIV-1 variants between high-risk men and low-risk women.

HIV-1 subtypes and recombinants in the Republic of Congo.

To document the actual genetic diversity of HIV-1 strains in the Republic of Congo, 114 HIV-1 positives persons were sampled in 2003 and 2004 after their informed consent. They were attending the teaching hospital, the reference health center in Makelekele, Brazzaville and the regional hospital centers in Pointe-Noire, Gamboma and Ouesso. A total of 104 samples were genetically characterized by direct sequencing of the p24 gag region and 80 were also subtyped in the V3-V5 env region. The genetic subtype distribution of the Congolese strains showed the predominance of subtype A (36.5% and 32.5% in gag and env, respectively) and G (30.8% and 21.25%), whereas subtype D strains represented 12.5% and 15%. Subtypes C, F, H, J, K and the CRFs-01, -02, -05 -06, and also the recently characterized CRF18 were seen at lower rates. Finally, 4.8% (gag) and 6.25% (env) of the strains could not be classified. Moreover, a high intra-subtype diversity was observed in our study. Among 70 strains which have been characterized in the two genomic regions, 14 (20%) appeared to be unique recombinants. These data show a high genetic variability in the Republic of Congo, where all the subtypes have been documented together with certain subsubtypes and several CRFs.