Wildlife in Cameroon harbor diverse coronaviruses including many isolates closely related to human coronavirus 229E

Abstract

Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. SARS-CoV-2 highlights the global impact emergence events can have. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n=8) and beta (n=9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human derived HCoV-229E isolates closest to those from camels in terms of the S and N genes, but closest to isolates from bats for the E, M, and RdRp genes. The CoV RNA positivity rate in bats varied significantly (p<0.001) between the wet (8.2%) and dry season (4.5%). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.

Virome characterization of game animals in China reveals a spectrum of emerging pathogens

“…Collectively, we suggest that cross-species transmission from bats to game animals may represent a possible pathway for the virus to move from bats to humans. Indeed, bat-associated alpha-and beta-coronaviruses are the ancestors for those viruses that cause disease outbreaks in humans, including SARS-CoV (Rota et al, 2003;Ksiazek et al, 2003), SARS-CoV-2 (Zhou et al, 2020), MERS-CoV (Assiri et al, 2013;Zaki et al, 2012), HCoV-229E (Fau and Procknow, 1966;Ntumvi et al, 2021), andHCoV-NL63 (van der Hoek et al, 2006), although they commonly pass through the so-called ''intermediate'' hosts such as civets and raccoon dogs for SARS-CoVs (Guan et al, 2003), camels for MERS-CoVs (Dudas et al, 2018), and alpacas for HCoV-229E (Crossley et al, 2012).…”

Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats

“…These swabs had been collected as part of the PREDICT project, a large-scale United States Agency for International Development (USAID) Emerging Pandemic Threats initiative that has collected over 20,000 animal specimens from 20 CoV hotspot countries [ e.g. Anthony 2017, Lacroix 2017, Nziza 2020, Valitutto 2020, Ntumvi 2022]. Most libraries (n=19) were prepared from archived RNA that had been previously extracted from these specimens, although some libraries (n=6) were prepared from RNA that was freshly extracted from archived primary specimens (Table 1).…”

“…The vastness of CoV diversity that remains to be characterized is evident by the continuing high rate of novel CoV discovery by research studies and surveillance programs, this current work included [ e.g. Tao 2017, Wang 2017, Markotter 2019, Wang 2019, Nziza 2020, Valitutto 2020, Kumakamba 2021, Shapiro 2021, Tan 2021, Wang 2021, Zhou 2021, Alkhovsky 2022, Ntumvi 2022].…”

Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens

“…Collectively, we suggest that the crossspecies transmission from bats or avian hosts to game animals may represent a possible pathway for the virus to move from bats to humans. Indeed, bat-associated alpha-and beta-coronaviruses are notorious for being the ancestors for those viruses that cause disease outbreaks in humans, including SARS-CoV 43,44 , SARS-CoV-2 34 , MERS-CoV 45,46 , HCoV-229E 47,48 and HCoV-NL63 49 , although they commonly pass through so-called "intermediate" hosts such as civets and raccoon dogs for SARS-CoVs 10 , camels for MERS-CoVs 50 , and alpacas for HCoV-229E 51 . As such, our study underlines the fact that coronaviruses are subject to relatively frequent host shifts from reservoir hosts to terrestrial mammals and therefore pose a direct threat to wildlife animal handlers or during food consumption.…”